From vwong at umn.edu  Tue Jul  2 10:38:26 2013
From: vwong at umn.edu (V Wong)
Date: Tue, 2 Jul 2013 10:38:26 -0500
Subject: [maker-devel] maker2jbrowse implementation
Message-ID: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
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From carsonhh at gmail.com  Tue Jul  2 11:27:19 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 12:27:19 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>
Message-ID: <CDF873FE.65B7%carsonhh@gmail.com>

The Jbrowse codebase tends to undergo very rapid alteration (much of which
is not backwards compatible with other Jbrowse versions), as a result the
script maker2jbrowse has had to evolve with Jbrowse (and will not work with
all versions).  I'm not sure if the script is currently behind or ahead of
Jbrowse version 1.9.3 (I'm guessing behind). I can have it working with
whatever the most current repository is if you were to give me a week, or
you can try loading the GFF3's using Jbrowse's own loader (tutorial here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012).  Of course this tutorial is
also likely to be somewhat out of date :-( But the 2013 version is supposed
to be up and running as part of this years GMOD summer school in ~3 weeks.
They use MAKER generated data for the tutorial, so it should be relevant to
what you are doing.

Thanks,
Carson



From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Tuesday, July 2, 2013 11:38 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker2jbrowse implementation

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From rbuels at gmail.com  Tue Jul  2 12:32:40 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 02 Jul 2013 13:32:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D30EB8.5090002@gmail.com>

One of my objectives has been maintaining complete backward 
compatibility with data formatted from JBrowse 1.2.1 onward.  I add 
capabilities, and the look and feel of the browser improves, but you can 
still view data in it that was formatted with JBrowse 1.2.1 (released 
March 17, 2011).

I would try to have a look at the maker2jbrowse implementation to 
troubleshoot further, but your source code doesn't seem to be public. 
Or at least the link to the source browser on the GMOD wiki page 
(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't 
find any kind of source code links under 
http://www.yandell-lab.org/software/maker.html.  Is the MAKER source 
code actually open?

Regarding the 2012 tutorial, the directions in the 2012 tutorial should 
still work, since I have been keeping backward compatibility with the 
scripts also.

Val, Carson, could you elaborate with details on the backward 
compatibility problems you're seeing?  Or could you give me access to 
the maker2jbrowse source code?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Tue Jul  2 14:19:40 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 15:19:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D30EB8.5090002@gmail.com>
Message-ID: <CDF89913.661B%carsonhh@gmail.com>

Good to know the tutorial is up to date.  I had to make several
consecutive updates to my script about a year ago with Jbrowse updates, so
I'm glad to know I can likely just fix whatever is wrong now and that will
be good for most previous and upcoming Jbrowse version :-)

It has more to do with converting data from GFF3.  maker2jbrowse is just a
script that wraps the flatfile-to-json.pl calls together with some css
files (all included in maker tar ball - it's open source).  So if anything
changes in flatfile-to-json.pl or the expected tags in css files then
maker2jbrowse won't work (the css files are where I usually get into
trouble). I just have to figure out what the changes are and then fix
them.  I know I had to do some updates for colors in Web Apollo recently
and I imagine I can just use that as a template.

Thanks,
Carson




On 7/2/13 1:32 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>One of my objectives has been maintaining complete backward
>compatibility with data formatted from JBrowse 1.2.1 onward.  I add
>capabilities, and the look and feel of the browser improves, but you can
>still view data in it that was formatted with JBrowse 1.2.1 (released
>March 17, 2011).
>
>I would try to have a look at the maker2jbrowse implementation to
>troubleshoot further, but your source code doesn't seem to be public.
>Or at least the link to the source browser on the GMOD wiki page
>(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't
>find any kind of source code links under
>http://www.yandell-lab.org/software/maker.html.  Is the MAKER source
>code actually open?
>
>Regarding the 2012 tutorial, the directions in the 2012 tutorial should
>still work, since I have been keeping backward compatibility with the
>scripts also.
>
>Val, Carson, could you elaborate with details on the backward
>compatibility problems you're seeing?  Or could you give me access to
>the maker2jbrowse source code?
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Jul  2 14:24:43 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 2 Jul 2013 13:24:43 -0600
Subject: [maker-devel] maker2jbrowse
References: <mailman.69.1372786364.6126.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <E031B282-253C-4DFE-9D08-ECC02501CCAD@genetics.utah.edu>

Hi Robert,

Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use.  You can download the code here:

http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.

Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)

B

> From: Robert Buels <rbuels at gmail.com>
> Subject: Re: [maker-devel] maker2jbrowse implementation
> Date: July 2, 2013 11:32:40 AM MDT
> To: <maker-devel at yandell-lab.org>
> 
> 
> One of my objectives has been maintaining complete backward compatibility with data formatted from JBrowse 1.2.1 onward.  I add capabilities, and the look and feel of the browser improves, but you can still view data in it that was formatted with JBrowse 1.2.1 (released March 17, 2011).
> 
> I would try to have a look at the maker2jbrowse implementation to troubleshoot further, but your source code doesn't seem to be public. Or at least the link to the source browser on the GMOD wiki page (http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't find any kind of source code links under http://www.yandell-lab.org/software/maker.html.  Is the MAKER source code actually open?
> 
> Regarding the 2012 tutorial, the directions in the 2012 tutorial should still work, since I have been keeping backward compatibility with the scripts also.
> 
> Val, Carson, could you elaborate with details on the backward compatibility problems you're seeing?  Or could you give me access to the maker2jbrowse source code?
> 
> 
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
> 
> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>  Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>> 
>> Hi Maker team,
>> 
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>> 
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> 
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>> 
>> Any advice for getting past this will be most appreciated.  Thank you!
>> 
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 
> 
> 
> From: <maker-devel-request at yandell-lab.org>
> Subject: confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc
> Date: July 2, 2013 11:32:44 AM MDT
> 
> 
> If you reply to this message, keeping the Subject: header intact,
> Mailman will discard the held message.  Do this if the message is
> spam.  If you reply to this message and include an Approved: header
> with the list password in it, the message will be approved for posting
> to the list.  The Approved: header can also appear in the first line
> of the body of the reply.
> 
> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From rbuels at gmail.com  Wed Jul  3 10:45:53 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 11:45:53 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D44731.6060308@gmail.com>

After looking at the maker2jbrowse source (thanks for giving me access), 
there seems to be some kind of problem with the way maker2jbrowse is 
parsing the MAKER datastore index, leading to the script complaining of 
'no track information'.

This would probably be easier for a MAKER developer to look into.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Wed Jul  3 11:02:23 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 12:02:23 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D44731.6060308@gmail.com>
Message-ID: <CDF9C28B.66AF%carsonhh@gmail.com>

I think you may not have it set up right.  If you run the example data,
you can then use that.  For me it populates the JSON data tracks
information, but nothing displays.  I think the problem is with the maker
genome.css.  It is very out of date.  I'll do some work on it and then get
your feedback.

Thanks,
Carson



On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:

>After looking at the maker2jbrowse source (thanks for giving me access),
>there seems to be some kind of problem with the way maker2jbrowse is
>parsing the MAKER datastore index, leading to the script complaining of
>'no track information'.
>
>This would probably be easier for a MAKER developer to look into.
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>





From rbuels at gmail.com  Wed Jul  3 11:14:49 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:14:49 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D44DF9.9050908@gmail.com>

How does this have anything to do with CSS?  The errors Val is talking 
about are coming from the maker2jbrowse script:

ERROR: No track information for source
 >>> 'AK_assembly_datastore/22/D4/AK_contig_1/'


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From vwong at umn.edu  Wed Jul  3 11:15:38 2013
From: vwong at umn.edu (V Wong)
Date: Wed, 3 Jul 2013 11:15:38 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <51D44731.6060308@gmail.com>
	<CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <CAEi2voZNLhwS=u2FvTukC6HoxMuF7_3p8K2y1VCy7RAFsw_xgw@mail.gmail.com>

Hi Carson and Robert,

Thank you for your feedback on this!  Carson, could you describe the set up
a little more?  For instance, are you running the script in a specific
location in the JBrowse directory?  I seem to be running into the same
problem as Robert.

Best,
Val


On Wed, Jul 3, 2013 at 11:02 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
> >After looking at the maker2jbrowse source (thanks for giving me access),
> >there seems to be some kind of problem with the way maker2jbrowse is
> >parsing the MAKER datastore index, leading to the script complaining of
> >'no track information'.
> >
> >This would probably be easier for a MAKER developer to look into.
> >
> >
> >Robert Buels
> >Lead Developer
> >JBrowse - http://jbrowse.org
> >
> >On 07/02/2013 12:27 PM, Carson Holt wrote:
> >> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >> which is not backwards compatible with other Jbrowse versions), as a
> >> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> >> not work with all versions).  I'm not sure if the script is currently
> >> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >> have it working with whatever the most current repository is if you were
> >> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> >> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>   Of course this tutorial is also likely to be somewhat out of date
> >> :-( But the 2013 version is supposed to be up and running as part of
> >> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >> data for the tutorial, so it should be relevant to what you are doing.
> >>
> >> Thanks,
> >> Carson
> >>
> >>
> >>
> >> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Date: Tuesday, July 2, 2013 11:38 AM
> >> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> >> Subject: [maker-devel] maker2jbrowse implementation
> >>
> >> Hi Maker team,
> >>
> >> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >> server, using the -d option for the index.log file.  However, I am
> >> getting this error for each contig:
> >>
> >> ERROR: No track information for source
> >> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>
> >> Looking at the perl script, the file locations are getting read, but
> >> then the tracks aren't getting found in the hash of commands.
> >>
> >> Any advice for getting past this will be most appreciated.  Thank you!
> >>
> >> Best,
> >> Val
> >> _______________________________________________ maker-devel mailing list
> >> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com
> >
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >>
> >> _______________________________________________
> >> maker-devel mailing list
> >> maker-devel at box290.bluehost.com
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
>
>
>
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From rbuels at gmail.com  Wed Jul  3 11:39:51 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:39:51 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D453D7.4070801@gmail.com>

Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what 
you're doing with that, but it appears to be a fork of a very old 
JBrowse main css file.  If that's overriding or being copied over the 
JBrowse released CSS, it will break pretty much everything.  It would be 
like me randomly replacing one of MAKER's Perl modules with my own old 
forked copy.

If what you're trying to accomplish is to add some custom styles, the 
best way to do that would be to do one of:

* add just your custom feature styles on the flatfile-to-json.pl command 
line
* add a "css": { "url": "http://url/of/your/custom.css" } to the
   JBrowse trackList.json someplace in the workflow (easy to add
   things to JSON files with JSON.pm) that loads your custom CSS
   (containing only your custom feature styles!)
* add all of the custom styles to the trackList.json as a
   string: "css": "string { of: lots and lots of; css: properties; }"


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From carsonhh at gmail.com  Wed Jul  3 14:26:32 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 15:26:32 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D453D7.4070801@gmail.com>
Message-ID: <CDF9E0AE.6703%carsonhh@gmail.com>

Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
documentation had you modify the genome.css file to create your own
tracks.  Version 1.2.1 looks like it is the last version where the
genome.css file that maker provided works. I can still get simple test
GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
But I need to fix some things, because they are all indistinguishable from
each other (so it is not the desired behavior).

Indepent of that issue though, to regenerate the original error, I do the
following -->
    maker2jbrowse  
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 
    ERROR: No track information for source
'dpp_contig_datastore/05/1F/contig-dpp-500-500/'

Basically you are missing the '-d' flag (whiteout that the script is
expecting a list of GFF3 files).

So this works -->
    maker2jbrowse -d
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 


Of course all tracks look the same though per the original issue I
mentioned.

Thanks,
Carson



Some versions of Jbrowse still load fine with the script as is Jbrowse
1.3, 

On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>you're doing with that, but it appears to be a fork of a very old
>JBrowse main css file.  If that's overriding or being copied over the
>JBrowse released CSS, it will break pretty much everything.  It would be
>like me randomly replacing one of MAKER's Perl modules with my own old
>forked copy.
>
>If what you're trying to accomplish is to add some custom styles, the
>best way to do that would be to do one of:
>
>* add just your custom feature styles on the flatfile-to-json.pl command
>line
>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>   JBrowse trackList.json someplace in the workflow (easy to add
>   things to JSON files with JSON.pm) that loads your custom CSS
>   (containing only your custom feature styles!)
>* add all of the custom styles to the trackList.json as a
>   string: "css": "string { of: lots and lots of; css: properties; }"
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> I think you may not have it set up right.  If you run the example data,
>> you can then use that.  For me it populates the JSON data tracks
>> information, but nothing displays.  I think the problem is with the
>>maker
>> genome.css.  It is very out of date.  I'll do some work on it and then
>>get
>> your feedback.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>
>>> After looking at the maker2jbrowse source (thanks for giving me
>>>access),
>>> there seems to be some kind of problem with the way maker2jbrowse is
>>> parsing the MAKER datastore index, leading to the script complaining of
>>> 'no track information'.
>>>
>>> This would probably be easier for a MAKER developer to look into.
>>>
>>>
>>> Robert Buels
>>> Lead Developer
>>> JBrowse - http://jbrowse.org
>>>
>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>will
>>>> not work with all versions).  I'm not sure if the script is currently
>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>> have it working with whatever the most current repository is if you
>>>>were
>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>own
>>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>> data for the tutorial, so it should be relevant to what you are doing.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>
>>>> Hi Maker team,
>>>>
>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>> server, using the -d option for the index.log file.  However, I am
>>>> getting this error for each contig:
>>>>
>>>> ERROR: No track information for source
>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>
>>>> Looking at the perl script, the file locations are getting read, but
>>>> then the tracks aren't getting found in the hash of commands.
>>>>
>>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>>
>>>> Best,
>>>> Val
>>>> _______________________________________________ maker-devel mailing
>>>>list
>>>> maker-devel at box290.bluehost.com
>>>><mailto:maker-devel at box290.bluehost.com>
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>
>>
>>





From benayoun at stanford.edu  Fri Jul  5 16:35:44 2013
From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:35:44 -0700
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
References: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
Message-ID: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
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From carsonhh at gmail.com  Mon Jul  8 09:20:53 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 10:20:53 -0400
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>
Message-ID: <CE00422F.6A5C%carsonhh@gmail.com>

In your MAKER STDERR (printed to screen or captured as part of run), search
for the word ERROR.  That will give a more specific explanation as to why it
is failing.  If you did not capture this on your first run, you may need to
redirect it to a file on a retry.

Example --> maker 2> error.log

Thanks,
Carson

From:  B?r?nice Benayoun <benayoun at stanford.edu>
Date:  Friday, July 5, 2013 5:35 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] FAILED contigs

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From berenice.benayoun at gmail.com  Fri Jul  5 16:33:35 2013
From: berenice.benayoun at gmail.com (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:33:35 -0700
Subject: [maker-devel] FAILED contigs
Message-ID: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice

-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/
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From onson001 at umn.edu  Mon Jul  8 17:12:06 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Mon, 8 Jul 2013 17:12:06 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
Message-ID: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>

Maker Developers,

I am testing Maker on a well annotated contig from the encode project and
in one of the genes, maker does not output an exon despite HSPs supporting
it. I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question.

I even set the parameters est2genome and protein2genome to 1 but still
Maker did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks,
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From carsonhh at gmail.com  Mon Jul  8 20:55:15 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 21:55:15 -0400
Subject: [maker-devel] Maker not outputting exons with EST and Protein
 Evidence
In-Reply-To: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
Message-ID: <CE00DF97.6C2A%carsonhh@gmail.com>

This is because augustus never calls it either without hints or after being
given hints by MAKER.  This may be because even though the exon has support
from ESTs and protein alignments, it breaks the open reading frame (you can
check using apollo ? just click and drag them into the annotation tier).  I
did this individually for each of the polished proteins and ESTs, and none
have proper open reading frame.

Perhaps the official annotation contains a frame shift or something to make
it work (augustus can't do that).  Such a thing is not all that uncommon.
There are many instances of RefSeq annotations for example where if you cut
out the exons and try and translate them, they won't translate.  This can
happen because the reference sequence changed or is incorrect, and if the
annotation was generated from a different assembly, then it just gets mapped
as best as possible to the current assembly and the correct protein
translation is saved elsewhere in the database (even though manual
translation won't directly reproduce it).  Genes where this happens make up
just under 1% of the human genome (but they can drive you nuts especially if
your analysis expects protein sequence to match the nucleotide sequence
translation).  It's really just an artifacts of the process used to move
annotations forward on the humans genome every time they update the
assembly.

Thanks,
Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Monday, July 8, 2013 6:12 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker not outputting exons with EST and Protein
Evidence

Maker Developers, 

I am testing Maker on a well annotated contig from the encode project and in
one of the genes, maker does not output an exon despite HSPs supporting it.
I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question. 

I even set the parameters est2genome and protein2genome to 1 but still Maker
did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks, 
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Tue Jul  9 10:57:09 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 09 Jul 2013 11:57:09 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9E0AE.6703%carsonhh@gmail.com>
Message-ID: <CE01A884.6C92%carsonhh@gmail.com>

Hi Val,

I've attached new files for you to test.  These will be bundled in the
next maker release pending successful tests (~ 1 week).

Instructions:
1. Place maker2jbrowse in your .../maker/bin/ directory and
.../maker/src/bin/ directory (this is just to ensure you don't
accidentally overwrite it if you reinstall at any time).
2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
3. You must be in the jbrowse installation directory when running
maker2jbrowse.  Run the script with the -d flag and the datastore index
file.

This new version will assign colors by copying maker.css to the jbrowse
installation as apposed to replacing the genome.css file, and it will also
edit the genome.css file to add the import call for maker.css.  In
addition I have updated command line flags in the wrapper to do what is
currently expected by flatfile-to-json.pl.

Could you test it out and let me know how it goes.

Thanks,
Carson



On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:

>Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>documentation had you modify the genome.css file to create your own
>tracks.  Version 1.2.1 looks like it is the last version where the
>genome.css file that maker provided works. I can still get simple test
>GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>But I need to fix some things, because they are all indistinguishable from
>each other (so it is not the desired behavior).
>
>Indepent of that issue though, to regenerate the original error, I do the
>following -->
>    maker2jbrowse 
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>    ERROR: No track information for source
>'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>
>Basically you are missing the '-d' flag (whiteout that the script is
>expecting a list of GFF3 files).
>
>So this works -->
>    maker2jbrowse -d
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>
>
>Of course all tracks look the same though per the original issue I
>mentioned.
>
>Thanks,
>Carson
>
>
>
>Some versions of Jbrowse still load fine with the script as is Jbrowse
>1.3, 
>
>On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>you're doing with that, but it appears to be a fork of a very old
>>JBrowse main css file.  If that's overriding or being copied over the
>>JBrowse released CSS, it will break pretty much everything.  It would be
>>like me randomly replacing one of MAKER's Perl modules with my own old
>>forked copy.
>>
>>If what you're trying to accomplish is to add some custom styles, the
>>best way to do that would be to do one of:
>>
>>* add just your custom feature styles on the flatfile-to-json.pl command
>>line
>>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>   JBrowse trackList.json someplace in the workflow (easy to add
>>   things to JSON files with JSON.pm) that loads your custom CSS
>>   (containing only your custom feature styles!)
>>* add all of the custom styles to the trackList.json as a
>>   string: "css": "string { of: lots and lots of; css: properties; }"
>>
>>
>>Robert Buels
>>Lead Developer
>>JBrowse - http://jbrowse.org
>>
>>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>> I think you may not have it set up right.  If you run the example data,
>>> you can then use that.  For me it populates the JSON data tracks
>>> information, but nothing displays.  I think the problem is with the
>>>maker
>>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>get
>>> your feedback.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>
>>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>access),
>>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>> parsing the MAKER datastore index, leading to the script complaining
>>>>of
>>>> 'no track information'.
>>>>
>>>> This would probably be easier for a MAKER developer to look into.
>>>>
>>>>
>>>> Robert Buels
>>>> Lead Developer
>>>> JBrowse - http://jbrowse.org
>>>>
>>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>will
>>>>> not work with all versions).  I'm not sure if the script is currently
>>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>>> have it working with whatever the most current repository is if you
>>>>>were
>>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>>own
>>>>> loader (tutorial here -->
>>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>>> data for the tutorial, so it should be relevant to what you are
>>>>>doing.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>> To: <maker-devel at yandell-lab.org
>>>>><mailto:maker-devel at yandell-lab.org>>
>>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>
>>>>> Hi Maker team,
>>>>>
>>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>> server, using the -d option for the index.log file.  However, I am
>>>>> getting this error for each contig:
>>>>>
>>>>> ERROR: No track information for source
>>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>
>>>>> Looking at the perl script, the file locations are getting read, but
>>>>> then the tracks aren't getting found in the hash of commands.
>>>>>
>>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>you!
>>>>>
>>>>> Best,
>>>>> Val
>>>>> _______________________________________________ maker-devel mailing
>>>>>list
>>>>> maker-devel at box290.bluehost.com
>>>>><mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>
>>>
>>>
>
>

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From Carson.Holt at oicr.on.ca  Tue Jul  9 14:19:14 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 9 Jul 2013 19:19:14 +0000
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE01D9F3.6CF4%carson.holt@oicr.on.ca>

It's perfectly safe to kill.

If you are constantly getting FAIL in the datastore index, then something
is wrong.  If you are capturing the jobs STDERR, try looking for the term
ERROR or FATAL for a better explanation as to why it's failing and send
the error to me.

Thanks,
Carson


On 7/9/13 2:47 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hello Maker Developers!
>
>I have a quick question... I've been using MAKER to annotate a genome (it
>has been running for about 6 days with 48 cpus).  Many of my contigs have
>failed, surely because most of them are smaller than the 10 kb limit I
>set, which is fine.  My concern is that although I've set tries = 2, the
>index log seems to indicate that MAKER is on its fourth try for some of
>the contigs (see attached).  Is is safe to shut MAKER down, or are there
>clean-up steps at the end of the annotation process that need to be
>allowed to occur?  Oh, and I'm using MAKER 2.28.
>
>Best, Jacqueline
>
>




From onson001 at umn.edu  Tue Jul  9 16:29:21 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Tue, 9 Jul 2013 16:29:21 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
In-Reply-To: <CE00DF97.6C2A%carsonhh@gmail.com>
References: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
	<CE00DF97.6C2A%carsonhh@gmail.com>
Message-ID: <CACFwDdLkUR3A-j8dzFj=GujNz6oKmL0RpXjpH6bZhr53Tr1rcg@mail.gmail.com>

Thanks for the insight.


On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> This is because augustus never calls it either without hints or after
> being given hints by MAKER.  This may be because even though the exon has
> support from ESTs and protein alignments, it breaks the open reading frame
> (you can check using apollo ? just click and drag them into the annotation
> tier).  I did this individually for each of the polished proteins and ESTs,
> and none have proper open reading frame.
>
> Perhaps the official annotation contains a frame shift or something to
> make it work (augustus can't do that).  Such a thing is not all that
> uncommon.  There are many instances of RefSeq annotations for example where
> if you cut out the exons and try and translate them, they won't translate.
>  This can happen because the reference sequence changed or is incorrect,
> and if the annotation was generated from a different assembly, then it just
> gets mapped as best as possible to the current assembly and the correct
> protein translation is saved elsewhere in the database (even though manual
> translation won't directly reproduce it).  Genes where this happens make up
> just under 1% of the human genome (but they can drive you nuts especially
> if your analysis expects protein sequence to match the nucleotide sequence
> translation).  It's really just an artifacts of the process used to move
> annotations forward on the humans genome every time they update the
> assembly.
>
> Thanks,
> Carson
>
>
> From: Innocent Onsongo <onson001 at umn.edu>
> Date: Monday, July 8, 2013 6:12 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker not outputting exons with EST and Protein
> Evidence
>
> Maker Developers,
>
> I am testing Maker on a well annotated contig from the encode project and
> in one of the genes, maker does not output an exon despite HSPs supporting
> it. I have attached a compressed folder with
>
> ENr122_genes.gff: The validated genes as per encode
> ENr122.gff: Makers output
> maker_opts.ctl: The control file I used
> ENr122_98669-134249.pptx: A power point visually illustrated the exon in
> question.
>
> I even set the parameters est2genome and protein2genome to 1 but still
> Maker did not output this exon.
>
> Is there a good reason Maker does no have this exon in its final model
> despite the HSPs supporting it?
>
> Thanks,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From jmdoyle at purdue.edu  Tue Jul  9 13:47:46 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Tue, 9 Jul 2013 14:47:46 -0400 (EDT)
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <53458481.77205.1373395049899.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>

Hello Maker Developers!

I have a quick question... I've been using MAKER to annotate a genome (it has been running for about 6 days with 48 cpus).  Many of my contigs have failed, surely because most of them are smaller than the 10 kb limit I set, which is fine.  My concern is that although I've set tries = 2, the index log seems to indicate that MAKER is on its fourth try for some of the contigs (see attached).  Is is safe to shut MAKER down, or are there clean-up steps at the end of the annotation process that need to be allowed to occur?  Oh, and I'm using MAKER 2.28.

Best, Jacqueline


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From yuharas at takara-bio.co.jp  Wed Jul 10 21:27:12 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 11:27:12 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>

Dear developers

I'm considering using MAKER2 to annotate plant genome (~1Gb) I've assembled using illumina HiSeq data.
And I'm planning to obtain mRNA-seq data by using HiSeq.
Do you have any recommendation of sequencing depth of RNA-seq data for using MAKER2 annotation pipeline?

Thanks,
Satoshi




From carsonhh at gmail.com  Wed Jul 10 21:40:52 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 10 Jul 2013 22:40:52 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
Message-ID: <CE039117.6E22%carsonhh@gmail.com>

As far as total depth I don't know, but I'd recommend using something like
trinity to assemble the reads and supply them to the est= option in fasta
format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From yuharas at takara-bio.co.jp  Wed Jul 10 23:47:10 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 13:47:10 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE039117.6E22%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
	<CE039117.6E22%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>

Dear Carson

Thank you for your quick reply.
Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
although the tutorial contains information about Tophat and Cufflinks?

Satoshi


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 11:41 AM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

As far as total depth I don't know, but I'd recommend using something like trinity to assemble the reads and supply them to the est= option in fasta format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for 
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From vwong at umn.edu  Thu Jul 11 00:10:52 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 00:10:52 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE01A884.6C92%carsonhh@gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
Message-ID: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser,
but that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Val,
>
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
>
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
>
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl.
>
> Could you test it out and let me know how it goes.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
> >documentation had you modify the genome.css file to create your own
> >tracks.  Version 1.2.1 looks like it is the last version where the
> >genome.css file that maker provided works. I can still get simple test
> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
> >But I need to fix some things, because they are all indistinguishable from
> >each other (so it is not the desired behavior).
> >
> >Indepent of that issue though, to regenerate the original error, I do the
> >following -->
> >    maker2jbrowse
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >    ERROR: No track information for source
> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
> >
> >Basically you are missing the '-d' flag (whiteout that the script is
> >expecting a list of GFF3 files).
> >
> >So this works -->
> >    maker2jbrowse -d
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >
> >
> >Of course all tracks look the same though per the original issue I
> >mentioned.
> >
> >Thanks,
> >Carson
> >
> >
> >
> >Some versions of Jbrowse still load fine with the script as is Jbrowse
> >1.3,
> >
> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
> >
> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
> >>you're doing with that, but it appears to be a fork of a very old
> >>JBrowse main css file.  If that's overriding or being copied over the
> >>JBrowse released CSS, it will break pretty much everything.  It would be
> >>like me randomly replacing one of MAKER's Perl modules with my own old
> >>forked copy.
> >>
> >>If what you're trying to accomplish is to add some custom styles, the
> >>best way to do that would be to do one of:
> >>
> >>* add just your custom feature styles on the flatfile-to-json.pl command
> >>line
> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
> >>   JBrowse trackList.json someplace in the workflow (easy to add
> >>   things to JSON files with JSON.pm) that loads your custom CSS
> >>   (containing only your custom feature styles!)
> >>* add all of the custom styles to the trackList.json as a
> >>   string: "css": "string { of: lots and lots of; css: properties; }"
> >>
> >>
> >>Robert Buels
> >>Lead Developer
> >>JBrowse - http://jbrowse.org
> >>
> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
> >>> I think you may not have it set up right.  If you run the example data,
> >>> you can then use that.  For me it populates the JSON data tracks
> >>> information, but nothing displays.  I think the problem is with the
> >>>maker
> >>> genome.css.  It is very out of date.  I'll do some work on it and then
> >>>get
> >>> your feedback.
> >>>
> >>> Thanks,
> >>> Carson
> >>>
> >>>
> >>>
> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
> >>>
> >>>> After looking at the maker2jbrowse source (thanks for giving me
> >>>>access),
> >>>> there seems to be some kind of problem with the way maker2jbrowse is
> >>>> parsing the MAKER datastore index, leading to the script complaining
> >>>>of
> >>>> 'no track information'.
> >>>>
> >>>> This would probably be easier for a MAKER developer to look into.
> >>>>
> >>>>
> >>>> Robert Buels
> >>>> Lead Developer
> >>>> JBrowse - http://jbrowse.org
> >>>>
> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >>>>> which is not backwards compatible with other Jbrowse versions), as a
> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
> >>>>>will
> >>>>> not work with all versions).  I'm not sure if the script is currently
> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >>>>> have it working with whatever the most current repository is if you
> >>>>>were
> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
> >>>>>own
> >>>>> loader (tutorial here -->
> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>>>>    Of course this tutorial is also likely to be somewhat out of date
> >>>>> :-( But the 2013 version is supposed to be up and running as part of
> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >>>>> data for the tutorial, so it should be relevant to what you are
> >>>>>doing.
> >>>>>
> >>>>> Thanks,
> >>>>> Carson
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
> >>>>> To: <maker-devel at yandell-lab.org
> >>>>><mailto:maker-devel at yandell-lab.org>>
> >>>>> Subject: [maker-devel] maker2jbrowse implementation
> >>>>>
> >>>>> Hi Maker team,
> >>>>>
> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >>>>> server, using the -d option for the index.log file.  However, I am
> >>>>> getting this error for each contig:
> >>>>>
> >>>>> ERROR: No track information for source
> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>>>>
> >>>>> Looking at the perl script, the file locations are getting read, but
> >>>>> then the tracks aren't getting found in the hash of commands.
> >>>>>
> >>>>> Any advice for getting past this will be most appreciated.  Thank
> >>>>>you!
> >>>>>
> >>>>> Best,
> >>>>> Val
> >>>>> _______________________________________________ maker-devel mailing
> >>>>>list
> >>>>> maker-devel at box290.bluehost.com
> >>>>><mailto:maker-devel at box290.bluehost.com>
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> maker-devel mailing list
> >>>>> maker-devel at box290.bluehost.com
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>
> >>>
> >>>
> >
> >
>
>
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From carsonhh at gmail.com  Thu Jul 11 06:37:13 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:37:13 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
Message-ID: <CE0410D8.6E4A%carsonhh@gmail.com>

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to
cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks,
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something
>like trinity to assemble the reads and supply them to the est= option in
>fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>





From carsonhh at gmail.com  Thu Jul 11 06:44:07 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:44:07 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <CE04120C.6E55%carsonhh@gmail.com>

You next put the entire JBrowse directory into the /var/www/html/ directory
or wherever you have apache set up to load from (if it's not already there).
Then it will be accessible as a webpage (browser is inside the JBrowse
directory).

Example /var/www/html/Jbrowse/
Webpage --> http://localhost/Jbrowse/

--Carson

From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:10 AM
To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser, but
that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Hi Val,
> 
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
> 
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
> 
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
> 
> Could you test it out and let me know how it goes.
> 
> Thanks,
> Carson
> 
> 
> 
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>> >>you're doing with that, but it appears to be a fork of a very old
>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>> >>forked copy.
>>> >>
>>> >>If what you're trying to accomplish is to add some custom styles, the
>>> >>best way to do that would be to do one of:
>>> >>
>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>> <http://flatfile-to-json.pl>  command
>>> >>line
>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>> >>   (containing only your custom feature styles!)
>>> >>* add all of the custom styles to the trackList.json as a
>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>> >>
>>> >>
>>> >>Robert Buels
>>> >>Lead Developer
>>> >>JBrowse - http://jbrowse.org
>>> >>
>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>> >>> I think you may not have it set up right.  If you run the example data,
>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>> >>> information, but nothing displays.  I think the problem is with the
>>>> >>>maker
>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>> >>>get
>>>> >>> your feedback.
>>>> >>>
>>>> >>> Thanks,
>>>> >>> Carson
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>> >>>
>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>> >>>>access),
>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>> >>>>of
>>>>> >>>> 'no track information'.
>>>>> >>>>
>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>> >>>>
>>>>> >>>>
>>>>> >>>> Robert Buels
>>>>> >>>> Lead Developer
>>>>> >>>> JBrowse - http://jbrowse.org
>>>>> >>>>
>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>> >>>>>will
>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>> currently
>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>> >>>>> have it working with whatever the most current repository is if you
>>>>>> >>>>>were
>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>> Jbrowse's
>>>>>> >>>>>own
>>>>>> >>>>> loader (tutorial here -->
>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>> generated
>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>> >>>>>doing.
>>>>>> >>>>>
>>>>>> >>>>> Thanks,
>>>>>> >>>>> Carson
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>> >>>>>
>>>>>> >>>>> Hi Maker team,
>>>>>> >>>>>
>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>> >>>>> getting this error for each contig:
>>>>>> >>>>>
>>>>>> >>>>> ERROR: No track information for source
>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>> >>>>>
>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>> >>>>>
>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>> >>>>>you!
>>>>>> >>>>>
>>>>>> >>>>> Best,
>>>>>> >>>>> Val
>>>>>> >>>>> _______________________________________________ maker-devel mailing
>>>>>> >>>>>list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> maker-devel mailing list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>> >
>> >
> 



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From vwong at umn.edu  Thu Jul 11 12:58:42 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 12:58:42 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE04120C.6E55%carsonhh@gmail.com>
References: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
	<CE04120C.6E55%carsonhh@gmail.com>
Message-ID: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl is doing the job.  Is it possible to merge these tracks
into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You next put the entire JBrowse directory into the /var/www/html/
> directory or wherever you have apache set up to load from (if it's not
> already there).  Then it will be accessible as a webpage (browser is inside
> the JBrowse directory).
>
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
>
> --Carson
>
> From: V Wong <vwong at umn.edu>
> Reply-To: <vwong at umn.edu>
> Date: Thursday, July 11, 2013 1:10 AM
> To: Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc: <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Thanks!  I followed your instructions, and maker2jbrowse, and it
> successfully populated the ../JBrowse/data/tracks directory with
> RepeatMasker, Augustus, and GeneMark predictions.
>
> I'm not entirely sure how to get these numerous tracks into the browser,
> but that may be something to work out with JBrowse rather than Maker.
>
> Best,
> Val
>
>
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Hi Val,
>>
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>>
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>>
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl.
>>
>> Could you test it out and let me know how it goes.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>>
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable
>> from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>> >>you're doing with that, but it appears to be a fork of a very old
>> >>JBrowse main css file.  If that's overriding or being copied over the
>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>> >>forked copy.
>> >>
>> >>If what you're trying to accomplish is to add some custom styles, the
>> >>best way to do that would be to do one of:
>> >>
>> >>* add just your custom feature styles on the flatfile-to-json.plcommand
>> >>line
>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>> >>   (containing only your custom feature styles!)
>> >>* add all of the custom styles to the trackList.json as a
>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>> >>
>> >>
>> >>Robert Buels
>> >>Lead Developer
>> >>JBrowse - http://jbrowse.org
>> >>
>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> >>> I think you may not have it set up right.  If you run the example
>> data,
>> >>> you can then use that.  For me it populates the JSON data tracks
>> >>> information, but nothing displays.  I think the problem is with the
>> >>>maker
>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>> >>>get
>> >>> your feedback.
>> >>>
>> >>> Thanks,
>> >>> Carson
>> >>>
>> >>>
>> >>>
>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >>>
>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>> >>>>access),
>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>> >>>> parsing the MAKER datastore index, leading to the script complaining
>> >>>>of
>> >>>> 'no track information'.
>> >>>>
>> >>>> This would probably be easier for a MAKER developer to look into.
>> >>>>
>> >>>>
>> >>>> Robert Buels
>> >>>> Lead Developer
>> >>>> JBrowse - http://jbrowse.org
>> >>>>
>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> >>>>> which is not backwards compatible with other Jbrowse versions), as a
>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>> >>>>>will
>> >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
>> can
>> >>>>> have it working with whatever the most current repository is if you
>> >>>>>were
>> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>> >>>>>own
>> >>>>> loader (tutorial here -->
>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>> >>>>>    Of course this tutorial is also likely to be somewhat out of date
>> >>>>> :-( But the 2013 version is supposed to be up and running as part of
>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> >>>>> data for the tutorial, so it should be relevant to what you are
>> >>>>>doing.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Carson
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>> >>>>> To: <maker-devel at yandell-lab.org
>> >>>>><mailto:maker-devel at yandell-lab.org>>
>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>> >>>>>
>> >>>>> Hi Maker team,
>> >>>>>
>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> >>>>> server, using the -d option for the index.log file.  However, I am
>> >>>>> getting this error for each contig:
>> >>>>>
>> >>>>> ERROR: No track information for source
>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> >>>>>
>> >>>>> Looking at the perl script, the file locations are getting read, but
>> >>>>> then the tracks aren't getting found in the hash of commands.
>> >>>>>
>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>> >>>>>you!
>> >>>>>
>> >>>>> Best,
>> >>>>> Val
>> >>>>> _______________________________________________ maker-devel mailing
>> >>>>>list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>><mailto:maker-devel at box290.bluehost.com>
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> maker-devel mailing list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>
>> >>>
>> >>>
>> >
>> >
>>
>>
>
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From carsonhh at gmail.com  Thu Jul 11 13:23:04 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 14:23:04 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>
Message-ID: <CE046E99.6E7F%carsonhh@gmail.com>

If you have a previous Jbrowse with already populated tracks you can just,
run maker2jbrowse in that directory instead of the new Jbrowse directory,
then the maker features will be added there.  Make a backup copy of the
directory before you do this of course incase you need to roll back the
changes.

Alternatively you will have to add those to the new Jbrowse directory using
bin/bam-to-json.pl and following the instructions here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data

I guess Robert can chime in here as well, since we have now moved outside of
MAKER scripts and fully into JBrowse.

--Carson


From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:58 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Ignazio Carbone <icarbon at ncsu.edu>, <maker-devel at yandell-lab.org>,
Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl <http://add-track-json.pl>  is doing the job.  Is it
possible to merge these tracks into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:
> You next put the entire JBrowse directory into the /var/www/html/ directory or
> wherever you have apache set up to load from (if it's not already there).
> Then it will be accessible as a webpage (browser is inside the JBrowse
> directory).
> 
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
> 
> --Carson
> 
> From:  V Wong <vwong at umn.edu>
> Reply-To:  <vwong at umn.edu>
> Date:  Thursday, July 11, 2013 1:10 AM
> To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
> 
> Subject:  Re: [maker-devel] maker2jbrowse implementation
> 
> Hi Carson,
> 
> Thanks!  I followed your instructions, and maker2jbrowse, and it successfully
> populated the ../JBrowse/data/tracks directory with RepeatMasker, Augustus,
> and GeneMark predictions.
> 
> I'm not entirely sure how to get these numerous tracks into the browser, but
> that may be something to work out with JBrowse rather than Maker.
> 
> Best,
> Val
> 
> 
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> Hi Val,
>> 
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>> 
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>> 
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
>> 
>> Could you test it out and let me know how it goes.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>>> >documentation had you modify the genome.css file to create your own
>>> >tracks.  Version 1.2.1 looks like it is the last version where the
>>> >genome.css file that maker provided works. I can still get simple test
>>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>>> >But I need to fix some things, because they are all indistinguishable from
>>> >each other (so it is not the desired behavior).
>>> >
>>> >Indepent of that issue though, to regenerate the original error, I do the
>>> >following -->
>>> >    maker2jbrowse
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >    ERROR: No track information for source
>>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>>> >
>>> >Basically you are missing the '-d' flag (whiteout that the script is
>>> >expecting a list of GFF3 files).
>>> >
>>> >So this works -->
>>> >    maker2jbrowse -d
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >
>>> >
>>> >Of course all tracks look the same though per the original issue I
>>> >mentioned.
>>> >
>>> >Thanks,
>>> >Carson
>>> >
>>> >
>>> >
>>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>>> >1.3,
>>> >
>>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>>> >
>>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>>> >>you're doing with that, but it appears to be a fork of a very old
>>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>>> >>forked copy.
>>>> >>
>>>> >>If what you're trying to accomplish is to add some custom styles, the
>>>> >>best way to do that would be to do one of:
>>>> >>
>>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>>> <http://flatfile-to-json.pl>  command
>>>> >>line
>>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>>> >>   (containing only your custom feature styles!)
>>>> >>* add all of the custom styles to the trackList.json as a
>>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>>> >>
>>>> >>
>>>> >>Robert Buels
>>>> >>Lead Developer
>>>> >>JBrowse - http://jbrowse.org
>>>> >>
>>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>>> >>> I think you may not have it set up right.  If you run the example
>>>>> data,
>>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>>> >>> information, but nothing displays.  I think the problem is with the
>>>>> >>>maker
>>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>>> >>>get
>>>>> >>> your feedback.
>>>>> >>>
>>>>> >>> Thanks,
>>>>> >>> Carson
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>>> >>>
>>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>>> >>>>access),
>>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>>> >>>>of
>>>>>> >>>> 'no track information'.
>>>>>> >>>>
>>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>> Robert Buels
>>>>>> >>>> Lead Developer
>>>>>> >>>> JBrowse - http://jbrowse.org
>>>>>> >>>>
>>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse
(and
>>>>>>> >>>>>will
>>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>>> currently
>>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>>> >>>>> have it working with whatever the most current repository is if
you
>>>>>>> >>>>>were
>>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>>> Jbrowse's
>>>>>>> >>>>>own
>>>>>>> >>>>> loader (tutorial here -->
>>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>>> generated
>>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>>> >>>>>doing.
>>>>>>> >>>>>
>>>>>>> >>>>> Thanks,
>>>>>>> >>>>> Carson
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>>> >>>>>
>>>>>>> >>>>> Hi Maker team,
>>>>>>> >>>>>
>>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>>> >>>>> getting this error for each contig:
>>>>>>> >>>>>
>>>>>>> >>>>> ERROR: No track information for source
>>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>>> >>>>>
>>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>>> >>>>>
>>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>>> >>>>>you!
>>>>>>> >>>>>
>>>>>>> >>>>> Best,
>>>>>>> >>>>> Val
>>>>>>> >>>>> _______________________________________________ maker-devel
>>>>>>> mailing
>>>>>>> >>>>>list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> _______________________________________________
>>>>>>> >>>>> maker-devel mailing list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>> >
>>> >
>> 
> 



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From rbuels at gmail.com  Thu Jul 11 13:27:10 2013
From: rbuels at gmail.com (Robert Buels)
Date: Thu, 11 Jul 2013 14:27:10 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE046E99.6E7F%carsonhh@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
Message-ID: <51DEF8FE.2000907@gmail.com>

These days, it's better to use direct BAM access.  bam-to-json.pl still 
works, but the direct BAM access is much better.

See 
http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/11/2013 02:23 PM, Carson Holt wrote:
> If you have a previous Jbrowse with already populated tracks you can
> just, run maker2jbrowse in that directory instead of the new Jbrowse
> directory, then the maker features will be added there.  Make a backup
> copy of the directory before you do this of course incase you need to
> roll back the changes.
>
> Alternatively you will have to add those to the new Jbrowse directory
> using bin/bam-to-json.pl and following the instructions here -->
> http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data
>
> I guess Robert can chime in here as well, since we have now moved
> outside of MAKER scripts and fully into JBrowse.
>
> --Carson
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Thursday, July 11, 2013 1:58 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>,
> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
> directory, the Maker tracks are now on view.
>
> However, I'm having some trouble getting our older tracks (bam
> alignments and coverage tracks) into the same browser.  Neither 1.
> copying and pasting the tracks from the previous trackList.json to the
> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
> doing the job.  Is it possible to merge these tracks into one browser?
>
> Best,
> Val
>
>
> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
> <mailto:carsonhh at gmail.com>> wrote:
>
>     You next put the entire JBrowse directory into the /var/www/html/
>     directory or wherever you have apache set up to load from (if it's
>     not already there).  Then it will be accessible as a webpage
>     (browser is inside the JBrowse directory).
>
>     Example /var/www/html/Jbrowse/
>     Webpage --> http://localhost/Jbrowse/
>
>     --Carson
>
>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Date: Thursday, July 11, 2013 1:10 AM
>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>     Cc: <maker-devel at yandell-lab.org
>     <mailto:maker-devel at yandell-lab.org>>, Robert Buels
>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>
>     Subject: Re: [maker-devel] maker2jbrowse implementation
>
>     Hi Carson,
>
>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>     successfully populated the ../JBrowse/data/tracks directory with
>     RepeatMasker, Augustus, and GeneMark predictions.
>
>     I'm not entirely sure how to get these numerous tracks into the
>     browser, but that may be something to work out with JBrowse rather
>     than Maker.
>
>     Best,
>     Val
>
>
>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>     <mailto:carsonhh at gmail.com>> wrote:
>
>         Hi Val,
>
>         I've attached new files for you to test.  These will be bundled
>         in the
>         next maker release pending successful tests (~ 1 week).
>
>         Instructions:
>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>         .../maker/src/bin/ directory (this is just to ensure you don't
>         accidentally overwrite it if you reinstall at any time).
>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>         3. You must be in the jbrowse installation directory when running
>         maker2jbrowse.  Run the script with the -d flag and the
>         datastore index
>         file.
>
>         This new version will assign colors by copying maker.css to the
>         jbrowse
>         installation as apposed to replacing the genome.css file, and it
>         will also
>         edit the genome.css file to add the import call for maker.css.  In
>         addition I have updated command line flags in the wrapper to do
>         what is
>         currently expected by flatfile-to-json.pl
>         <http://flatfile-to-json.pl>.
>
>         Could you test it out and let me know how it goes.
>
>         Thanks,
>         Carson
>
>
>
>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>         <mailto:carsonhh at gmail.com>> wrote:
>
>         >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>         >documentation had you modify the genome.css file to create your own
>         >tracks.  Version 1.2.1 looks like it is the last version where the
>         >genome.css file that maker provided works. I can still get simple test
>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>         >But I need to fix some things, because they are all indistinguishable from
>         >each other (so it is not the desired behavior).
>         >
>         >Indepent of that issue though, to regenerate the original error, I do the
>         >following -->
>         >    maker2jbrowse
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >    ERROR: No track information for source
>         >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>         >
>         >Basically you are missing the '-d' flag (whiteout that the script is
>         >expecting a list of GFF3 files).
>         >
>         >So this works -->
>         >    maker2jbrowse -d
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >
>         >
>         >Of course all tracks look the same though per the original issue I
>         >mentioned.
>         >
>         >Thanks,
>         >Carson
>         >
>         >
>         >
>         >Some versions of Jbrowse still load fine with the script as is Jbrowse
>         >1.3,
>         >
>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >
>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>         >>you're doing with that, but it appears to be a fork of a very old
>         >>JBrowse main css file.  If that's overriding or being copied over the
>         >>JBrowse released CSS, it will break pretty much everything.  It would be
>         >>like me randomly replacing one of MAKER's Perl modules with my own old
>         >>forked copy.
>         >>
>         >>If what you're trying to accomplish is to add some custom styles, the
>         >>best way to do that would be to do one of:
>         >>
>         >>* add just your custom feature styles on theflatfile-to-json.pl <http://flatfile-to-json.pl> command
>         >>line
>         >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>         >>   (containing only your custom feature styles!)
>         >>* add all of the custom styles to the trackList.json as a
>         >>   string: "css": "string { of: lots and lots of; css: properties; }"
>         >>
>         >>
>         >>Robert Buels
>         >>Lead Developer
>         >>JBrowse -http://jbrowse.org
>         >>
>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>         >>> I think you may not have it set up right.  If you run the example data,
>         >>> you can then use that.  For me it populates the JSON data tracks
>         >>> information, but nothing displays.  I think the problem is with the
>         >>>maker
>         >>> genome.css.  It is very out of date.  I'll do some work on it and then
>         >>>get
>         >>> your feedback.
>         >>>
>         >>> Thanks,
>         >>> Carson
>         >>>
>         >>>
>         >>>
>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >>>
>         >>>> After looking at the maker2jbrowse source (thanks for giving me
>         >>>>access),
>         >>>> there seems to be some kind of problem with the way maker2jbrowse is
>         >>>> parsing the MAKER datastore index, leading to the script complaining
>         >>>>of
>         >>>> 'no track information'.
>         >>>>
>         >>>> This would probably be easier for a MAKER developer to look into.
>         >>>>
>         >>>>
>         >>>> Robert Buels
>         >>>> Lead Developer
>         >>>> JBrowse -http://jbrowse.org
>         >>>>
>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>         >>>>> which is not backwards compatible with other Jbrowse versions), as a
>         >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>         >>>>>will
>         >>>>> not work with all versions).  I'm not sure if the script is currently
>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>         >>>>> have it working with whatever the most current repository is if you
>         >>>>>were
>         >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>         >>>>>own
>         >>>>> loader (tutorial here -->
>         >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>         >>>>>    Of course this tutorial is also likely to be somewhat out of date
>         >>>>> :-( But the 2013 version is supposed to be up and running as part of
>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>         >>>>> data for the tutorial, so it should be relevant to what you are
>         >>>>>doing.
>         >>>>>
>         >>>>> Thanks,
>         >>>>> Carson
>         >>>>>
>         >>>>>
>         >>>>>
>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>         >>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>         >>>>><mailto:maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>>
>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>         >>>>>
>         >>>>> Hi Maker team,
>         >>>>>
>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>         >>>>> server, using the -d option for the index.log file.  However, I am
>         >>>>> getting this error for each contig:
>         >>>>>
>         >>>>> ERROR: No track information for source
>         >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>         >>>>>
>         >>>>> Looking at the perl script, the file locations are getting read, but
>         >>>>> then the tracks aren't getting found in the hash of commands.
>         >>>>>
>         >>>>> Any advice for getting past this will be most appreciated.  Thank
>         >>>>>you!
>         >>>>>
>         >>>>> Best,
>         >>>>> Val
>         >>>>> _______________________________________________ maker-devel mailing
>         >>>>>list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>><mailto:maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>>>
>         >>>>> _______________________________________________
>         >>>>> maker-devel mailing list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>
>         >>>
>         >>>
>         >
>         >
>
>
>



From yuharas at takara-bio.co.jp  Fri Jul 12 01:19:39 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Fri, 12 Jul 2013 15:19:39 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE0410D8.6E4A%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
	<CE0410D8.6E4A%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3F37@TKREXMB3.central.takara.co.jp>

I understand?
Thank you for your useful information.

Satoshi

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 8:37 PM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something 
>like trinity to assemble the reads and supply them to the est= option 
>in fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" 
><yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for 
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>





From Carson.Holt at oicr.on.ca  Fri Jul 12 08:34:06 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Fri, 12 Jul 2013 13:34:06 +0000
Subject: [maker-devel] failed contigs error report
In-Reply-To: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>
Message-ID: <CE05726A.6EBE%carson.holt@oicr.on.ca>

Could you pack up and send me this directory (use dropbox if they are too
big) -->
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.m
aker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_co
ntig_12295/

And this file -->
AG1-IA_China_Prot.fasta

--Carson


On 7/12/13 6:47 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have collected my failed contigs and I have rerun them in Maker v. 2.28
>but they have failed again. I don't know what the error codes mean but I
>have attached the run log for your review. Any help would be appreciated.
>
>Cheers
>Ian
>
>
>




From ianmisner at my.uri.edu  Fri Jul 12 05:47:39 2013
From: ianmisner at my.uri.edu (Ian Misner)
Date: Fri, 12 Jul 2013 06:47:39 -0400
Subject: [maker-devel] failed contigs error report
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
	<CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>

Hello,

I have collected my failed contigs and I have rerun them in Maker v. 2.28 but they have failed again. I don't know what the error codes mean but I have attached the run log for your review. Any help would be appreciated. 

Cheers
Ian

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From vwong at umn.edu  Mon Jul 15 12:57:30 2013
From: vwong at umn.edu (V Wong)
Date: Mon, 15 Jul 2013 12:57:30 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51DEF8FE.2000907@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
	<51DEF8FE.2000907@gmail.com>
Message-ID: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>

Hi Carson,

I tried running maker2jbrowse in the browser directory with existing
tracks, but the script expects to be run in the JBrowse directory and
printed this error:

FATAL: Can not find ./bin/flatfile-to-json.pl

Make sure you are running inside the JBrowse directory


Hi Robert,

I tried adding an Alignment2 track in the format of the example to the
browser with Maker tracks (those get viewed fine), but I am getting the
error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
though the specified file is in that location.


Thank you both for your continued aid.

Since this is departing Maker for strictly JBrowse territory, would it be
more appropriate to move to the JBrowse list?

Best,

Val


On Thu, Jul 11, 2013 at 1:27 PM, Robert Buels <rbuels at gmail.com> wrote:

> These days, it's better to use direct BAM access.  bam-to-json.pl still
> works, but the direct BAM access is much better.
>
> See http://gmod.org/wiki/JBrowse_**Configuration_Guide#Alignment_**
> Tracks_.28BAM.29<http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29>
>
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 07/11/2013 02:23 PM, Carson Holt wrote:
>
>> If you have a previous Jbrowse with already populated tracks you can
>> just, run maker2jbrowse in that directory instead of the new Jbrowse
>> directory, then the maker features will be added there.  Make a backup
>> copy of the directory before you do this of course incase you need to
>> roll back the changes.
>>
>> Alternatively you will have to add those to the new Jbrowse directory
>> using bin/bam-to-json.pl and following the instructions here -->
>> http://gmod.org/wiki/JBrowse_**Tutorial_2012#BAM_data<http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data>
>>
>> I guess Robert can chime in here as well, since we have now moved
>> outside of MAKER scripts and fully into JBrowse.
>>
>> --Carson
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Thursday, July 11, 2013 1:58 PM
>> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
>> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-**lab.org<maker-devel at yandell-lab.org>
>> >>,
>> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>> Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>> Hi Carson,
>>
>> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
>> directory, the Maker tracks are now on view.
>>
>> However, I'm having some trouble getting our older tracks (bam
>> alignments and coverage tracks) into the same browser.  Neither 1.
>> copying and pasting the tracks from the previous trackList.json to the
>> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
>>
>> doing the job.  Is it possible to merge these tracks into one browser?
>>
>> Best,
>> Val
>>
>>
>> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
>> <mailto:carsonhh at gmail.com>> wrote:
>>
>>     You next put the entire JBrowse directory into the /var/www/html/
>>     directory or wherever you have apache set up to load from (if it's
>>     not already there).  Then it will be accessible as a webpage
>>     (browser is inside the JBrowse directory).
>>
>>     Example /var/www/html/Jbrowse/
>>     Webpage --> http://localhost/Jbrowse/
>>
>>     --Carson
>>
>>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Date: Thursday, July 11, 2013 1:10 AM
>>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>>     Cc: <maker-devel at yandell-lab.org
>>     <mailto:maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>,
>> Robert Buels
>>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>>
>>     Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>>     Hi Carson,
>>
>>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>>     successfully populated the ../JBrowse/data/tracks directory with
>>     RepeatMasker, Augustus, and GeneMark predictions.
>>
>>     I'm not entirely sure how to get these numerous tracks into the
>>     browser, but that may be something to work out with JBrowse rather
>>     than Maker.
>>
>>     Best,
>>     Val
>>
>>
>>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>>     <mailto:carsonhh at gmail.com>> wrote:
>>
>>         Hi Val,
>>
>>         I've attached new files for you to test.  These will be bundled
>>         in the
>>         next maker release pending successful tests (~ 1 week).
>>
>>         Instructions:
>>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>>         .../maker/src/bin/ directory (this is just to ensure you don't
>>         accidentally overwrite it if you reinstall at any time).
>>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>>         3. You must be in the jbrowse installation directory when running
>>         maker2jbrowse.  Run the script with the -d flag and the
>>         datastore index
>>         file.
>>
>>         This new version will assign colors by copying maker.css to the
>>         jbrowse
>>         installation as apposed to replacing the genome.css file, and it
>>         will also
>>         edit the genome.css file to add the import call for maker.css.  In
>>         addition I have updated command line flags in the wrapper to do
>>         what is
>>         currently expected by flatfile-to-json.pl
>>         <http://flatfile-to-json.pl>.
>>
>>
>>         Could you test it out and let me know how it goes.
>>
>>         Thanks,
>>         Carson
>>
>>
>>
>>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>>         <mailto:carsonhh at gmail.com>> wrote:
>>
>>         >Like I said that css file is ~1 year old.  Once upon a time the
>> Jbrowse
>>         >documentation had you modify the genome.css file to create your
>> own
>>         >tracks.  Version 1.2.1 looks like it is the last version where
>> the
>>         >genome.css file that maker provided works. I can still get
>> simple test
>>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse
>> script.
>>         >But I need to fix some things, because they are all
>> indistinguishable from
>>         >each other (so it is not the desired behavior).
>>         >
>>         >Indepent of that issue though, to regenerate the original error,
>> I do the
>>         >following -->
>>         >    maker2jbrowse
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >    ERROR: No track information for source
>>         >'dpp_contig_datastore/05/1F/**contig-dpp-500-500/'
>>         >
>>         >Basically you are missing the '-d' flag (whiteout that the
>> script is
>>         >expecting a list of GFF3 files).
>>         >
>>         >So this works -->
>>         >    maker2jbrowse -d
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >
>>         >
>>         >Of course all tracks look the same though per the original issue
>> I
>>         >mentioned.
>>         >
>>         >Thanks,
>>         >Carson
>>         >
>>         >
>>         >
>>         >Some versions of Jbrowse still load fine with the script as is
>> Jbrowse
>>         >1.3,
>>         >
>>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >
>>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not
>> sure what
>>         >>you're doing with that, but it appears to be a fork of a very
>> old
>>         >>JBrowse main css file.  If that's overriding or being copied
>> over the
>>         >>JBrowse released CSS, it will break pretty much everything.  It
>> would be
>>         >>like me randomly replacing one of MAKER's Perl modules with my
>> own old
>>         >>forked copy.
>>         >>
>>         >>If what you're trying to accomplish is to add some custom
>> styles, the
>>         >>best way to do that would be to do one of:
>>         >>
>>         >>* add just your custom feature styles on theflatfile-to-json.pl<
>> http://flatfile-to-json.pl> command
>>
>>         >>line
>>         >>* add a "css": { "url": "http://url/of/your/custom.css**" } to
>> the
>>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>>         >>   (containing only your custom feature styles!)
>>         >>* add all of the custom styles to the trackList.json as a
>>         >>   string: "css": "string { of: lots and lots of; css:
>> properties; }"
>>         >>
>>         >>
>>         >>Robert Buels
>>         >>Lead Developer
>>         >>JBrowse -http://jbrowse.org
>>
>>         >>
>>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>         >>> I think you may not have it set up right.  If you run the
>> example data,
>>         >>> you can then use that.  For me it populates the JSON data
>> tracks
>>         >>> information, but nothing displays.  I think the problem is
>> with the
>>         >>>maker
>>         >>> genome.css.  It is very out of date.  I'll do some work on it
>> and then
>>         >>>get
>>         >>> your feedback.
>>         >>>
>>         >>> Thanks,
>>         >>> Carson
>>         >>>
>>         >>>
>>         >>>
>>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >>>
>>         >>>> After looking at the maker2jbrowse source (thanks for giving
>> me
>>         >>>>access),
>>         >>>> there seems to be some kind of problem with the way
>> maker2jbrowse is
>>         >>>> parsing the MAKER datastore index, leading to the script
>> complaining
>>         >>>>of
>>         >>>> 'no track information'.
>>         >>>>
>>         >>>> This would probably be easier for a MAKER developer to look
>> into.
>>         >>>>
>>         >>>>
>>         >>>> Robert Buels
>>         >>>> Lead Developer
>>         >>>> JBrowse -http://jbrowse.org
>>
>>         >>>>
>>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration
>> (much of
>>         >>>>> which is not backwards compatible with other Jbrowse
>> versions), as a
>>         >>>>> result the script maker2jbrowse has had to evolve with
>> Jbrowse (and
>>         >>>>>will
>>         >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing
>> behind). I can
>>         >>>>> have it working with whatever the most current repository
>> is if you
>>         >>>>>were
>>         >>>>> to give me a week, or you can try loading the GFF3's using
>> Jbrowse's
>>         >>>>>own
>>         >>>>> loader (tutorial here -->
>>         >>>>>http://gmod.org/wiki/**JBrowse_Tutorial_2012<http://gmod.org/wiki/JBrowse_Tutorial_2012>
>> ).
>>         >>>>>    Of course this tutorial is also likely to be somewhat
>> out of date
>>         >>>>> :-( But the 2013 version is supposed to be up and running
>> as part of
>>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>> generated
>>         >>>>> data for the tutorial, so it should be relevant to what you
>> are
>>         >>>>>doing.
>>         >>>>>
>>         >>>>> Thanks,
>>         >>>>> Carson
>>         >>>>>
>>         >>>>>
>>         >>>>>
>>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>         >>>>> To: <maker-devel at yandell-lab.org <mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>
>>         >>>>><mailto:maker-devel@**yandell-lab.org<maker-devel at yandell-lab.org><mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>>
>>
>>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>         >>>>>
>>         >>>>> Hi Maker team,
>>         >>>>>
>>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3)
>> on our
>>         >>>>> server, using the -d option for the index.log file.
>>  However, I am
>>         >>>>> getting this error for each contig:
>>         >>>>>
>>         >>>>> ERROR: No track information for source
>>         >>>>> 'AK_assembly_datastore/22/D4/**AK_contig_1/'
>>         >>>>>
>>         >>>>> Looking at the perl script, the file locations are getting
>> read, but
>>         >>>>> then the tracks aren't getting found in the hash of
>> commands.
>>         >>>>>
>>         >>>>> Any advice for getting past this will be most appreciated.
>>  Thank
>>         >>>>>you!
>>         >>>>>
>>         >>>>> Best,
>>         >>>>> Val
>>         >>>>> ______________________________**_________________
>> maker-devel mailing
>>         >>>>>list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>><mailto:maker-devel@**box290.bluehost.com<maker-devel at box290.bluehost.com>
>>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >>
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>>>
>>         >>>>> ______________________________**_________________
>>         >>>>> maker-devel mailing list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>
>>         >>>
>>         >>>
>>         >
>>         >
>>
>>
>>
>>
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From rbuels at gmail.com  Mon Jul 15 13:54:58 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 15 Jul 2013 14:54:58 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
Message-ID: <51E44582.9020100@gmail.com>

On 07/15/2013 01:57 PM, V Wong wrote:
> I tried adding an Alignment2 track in the format of the example to the
> browser with Maker tracks (those get viewed fine), but I am getting the
> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
> though the specified file is in that location.

If you visit that URL in your browser, is the bai file really there?

If so, is the BAI file on a different server from the one you're running 
JBrowse on?  If so, you'll need to enable CORS on the server for the BAI 
and BAM files.

Rob



From Michael.Li3 at AGR.GC.CA  Thu Jul 18 14:06:38 2013
From: Michael.Li3 at AGR.GC.CA (Li, Michael)
Date: Thu, 18 Jul 2013 19:06:38 +0000
Subject: [maker-devel] InterProScan v5
Message-ID: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for users. However, I noticed that maker's iprscan_batch, iprscan_wrap, ipr_update_gff and iprscan2gff3 are not compatible with this new version of IPR. Is there a workaround available or is the script easy to modify to suit the new version?
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From carsonhh at gmail.com  Thu Jul 18 14:18:20 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 18 Jul 2013 15:18:20 -0400
Subject: [maker-devel] InterProScan v5
In-Reply-To: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>
Message-ID: <CE0DB539.77E1%carsonhh@gmail.com>

All those tools were written for InterProScan 4.  We have plans to update
everything for InterProScan 5 sometime in the near future. Some will have to
be dropped or rewritten completely, while other like  ipr_update_gff and
iprscan2gff3 are both relatively simple and I could probably have those
included with the next MAKER release (current release is 2.28).  That would
be about 3 weeks from now.

--Carson



From:  "Li, Michael" <Michael.Li3 at AGR.GC.CA>
Date:  Thursday, July 18, 2013 3:06 PM
To:  "'maker-devel at yandell-lab.org'" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] InterProScan v5

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for
users. However, I noticed that maker?s iprscan_batch, iprscan_wrap,
ipr_update_gff and iprscan2gff3 are not compatible with this new version of
IPR. Is there a workaround available or is the script easy to modify to suit
the new version?
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From vwong at umn.edu  Fri Jul 19 16:36:03 2013
From: vwong at umn.edu (V Wong)
Date: Fri, 19 Jul 2013 17:36:03 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51E44582.9020100@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
	<51E44582.9020100@gmail.com>
Message-ID: <CAEi2voasDqTHLEe00+JDUgWgav-BYJuM+fPSAbK5ysZCKj6VTw@mail.gmail.com>

Ah, I just had some syntax inconsistencies between the file locations on
the server and the path for the web browser.  Thank you Rob!

Best,
Val


On Mon, Jul 15, 2013 at 2:54 PM, Robert Buels <rbuels at gmail.com> wrote:

> On 07/15/2013 01:57 PM, V Wong wrote:
>
>> I tried adding an Alignment2 track in the format of the example to the
>> browser with Maker tracks (those get viewed fine), but I am getting the
>> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
>> though the specified file is in that location.
>>
>
> If you visit that URL in your browser, is the bai file really there?
>
> If so, is the BAI file on a different server from the one you're running
> JBrowse on?  If so, you'll need to enable CORS on the server for the BAI
> and BAM files.
>
> Rob
>
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From jmdoyle at purdue.edu  Sun Jul 21 08:44:26 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Sun, 21 Jul 2013 09:44:26 -0400 (EDT)
Subject: [maker-devel] altest without MPI?
In-Reply-To: <1806377131.45449.1371745335968.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>

I just wanted to check in and say that this strategy worked really nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with protein2genome and my contigs greater than 1200000 bases.  Each of the training runs took less than 4 hours.  My final run with all my contigs (and altest) took about 5 and 1/2 days.  Not bad!   

----- Original Message -----
From: Carson Holt <carsonhh at gmail.com>
To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
Subject: Re: [maker-devel] altest without MPI?

The throughput is based on contig length, so long contigs will take longer
than short contigs.  Any contig less than 10kb is mostly useless for
annotation purposes (so you can filter those from your 800,000 right
away). Take your contigs that finish, and sum up their length to get a
better estimate of how long it will take to complete running.  Most
genomes can complete in a few days an a multi-core machine.  Bigger
genomes or bigger datasets take longer.  (note that altest evidence takes
3-4x longer to align than proteins).

The advantage of proteins is that the species do not have to be closely
related.  Nucleotide sequence diverges quickly and proteins slowly (that's
why proteins are used for phylogenetic trees).

A good strategy would be to get ~10Mb of sequence (use your longest
contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
protein2genome option to generate annotations.  Those annotations should
now be sufficient to train SNAP and Augustus.  Then you can finish by
running all your contigs with the same dataset (protein2genome now turned
off), use the newly trained snap and augustus files along with any altest
files you want to use. Note that the size of the dataset will determine
the total run time.

To get things to run faster, you can also run on your university's
computer cluster (then you will have hundreds of cpus available to you).
The purdue cluster supports MPI and with 30-50 cpus you could annotate
even large genomes in a reasonable time.  Alternatively you can request a
startup account at XSEDE, an NFS funded computer resource open to all US
institutions.  A startup allocation with 50,000 cpu hours only takes 2
weeks to approve. You should request an allocation on the Lonestar cluster
if you go that route, it has 64,000 cpus. I was able to annotate the Maize
genome (which is a very large genome at over 2 gigabases).  I used an
abnormally large EST and protein datasets (~4 gigabases of evidence which
is much more than a normal annotation job), and it completed in under 3
hours on 2,100 cpus.

--Carson


On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hi Carson (and whoever else might be reading this!)
>
>Thanks so much, I think splitting the files up using fasta_tool will
>definitely move things along.  I did a trial version with altest this
>weekend, and seemed to be averaging about an hour a scaffold (with 1
>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>seem like a reasonable estimate of the time it should take to annotate
>one sequence?  Could I be missing something in my maker_opts file?
>
>Let me back up for just a minute and describe the project a little more
>generally.  As I mentioned before, we have no protein sequences or ESTs
>for our species of interest, which is an avian species.  I could
>potentially use proteins from chicken or turkey, but neither is closely
>related to our species.  Time is a bit of an issue... do you have any
>thoughts on how much time per scaffold it should take to annotate using
>protein2genome?  If chicken and turkey are not closely related, is it
>worth the time investment?
>
>Let me finish by saying I think MAKER is wonderful, and I really
>appreciate the discussions on this group.
>
>Best wishes, Jackie 






From carsonhh at gmail.com  Sun Jul 21 16:09:12 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 21 Jul 2013 17:09:12 -0400
Subject: [maker-devel] altest without MPI?
In-Reply-To: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE11C4D7.7990%carsonhh@gmail.com>

Glad I could help. If you come across anything else, just let us know.

Thanks,
Carson



On 7/21/13 9:44 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>I just wanted to check in and say that this strategy worked really
>nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with
>protein2genome and my contigs greater than 1200000 bases.  Each of the
>training runs took less than 4 hours.  My final run with all my contigs
>(and altest) took about 5 and 1/2 days.  Not bad!
>
>----- Original Message -----
>From: Carson Holt <carsonhh at gmail.com>
>To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
>Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
>Subject: Re: [maker-devel] altest without MPI?
>
>The throughput is based on contig length, so long contigs will take longer
>than short contigs.  Any contig less than 10kb is mostly useless for
>annotation purposes (so you can filter those from your 800,000 right
>away). Take your contigs that finish, and sum up their length to get a
>better estimate of how long it will take to complete running.  Most
>genomes can complete in a few days an a multi-core machine.  Bigger
>genomes or bigger datasets take longer.  (note that altest evidence takes
>3-4x longer to align than proteins).
>
>The advantage of proteins is that the species do not have to be closely
>related.  Nucleotide sequence diverges quickly and proteins slowly (that's
>why proteins are used for phylogenetic trees).
>
>A good strategy would be to get ~10Mb of sequence (use your longest
>contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
>protein2genome option to generate annotations.  Those annotations should
>now be sufficient to train SNAP and Augustus.  Then you can finish by
>running all your contigs with the same dataset (protein2genome now turned
>off), use the newly trained snap and augustus files along with any altest
>files you want to use. Note that the size of the dataset will determine
>the total run time.
>
>To get things to run faster, you can also run on your university's
>computer cluster (then you will have hundreds of cpus available to you).
>The purdue cluster supports MPI and with 30-50 cpus you could annotate
>even large genomes in a reasonable time.  Alternatively you can request a
>startup account at XSEDE, an NFS funded computer resource open to all US
>institutions.  A startup allocation with 50,000 cpu hours only takes 2
>weeks to approve. You should request an allocation on the Lonestar cluster
>if you go that route, it has 64,000 cpus. I was able to annotate the Maize
>genome (which is a very large genome at over 2 gigabases).  I used an
>abnormally large EST and protein datasets (~4 gigabases of evidence which
>is much more than a normal annotation job), and it completed in under 3
>hours on 2,100 cpus.
>
>--Carson
>
>
>On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:
>
>>Hi Carson (and whoever else might be reading this!)
>>
>>Thanks so much, I think splitting the files up using fasta_tool will
>>definitely move things along.  I did a trial version with altest this
>>weekend, and seemed to be averaging about an hour a scaffold (with 1
>>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>>seem like a reasonable estimate of the time it should take to annotate
>>one sequence?  Could I be missing something in my maker_opts file?
>>
>>Let me back up for just a minute and describe the project a little more
>>generally.  As I mentioned before, we have no protein sequences or ESTs
>>for our species of interest, which is an avian species.  I could
>>potentially use proteins from chicken or turkey, but neither is closely
>>related to our species.  Time is a bit of an issue... do you have any
>>thoughts on how much time per scaffold it should take to annotate using
>>protein2genome?  If chicken and turkey are not closely related, is it
>>worth the time investment?
>>
>>Let me finish by saying I think MAKER is wonderful, and I really
>>appreciate the discussions on this group.
>>
>>Best wishes, Jackie
>
>
>





From Carson.Holt at oicr.on.ca  Tue Jul 23 14:00:27 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 23 Jul 2013 19:00:27 +0000
Subject: [maker-devel] Fwd: about running MAKER
In-Reply-To: <CAMNfi+gSdTtfBHD7ipTFJ08jvL3UtpbH3q+gCG-N-J-vV+Vpow@mail.gmail.com>
Message-ID: <CE143780.7AD6%carson.holt@oicr.on.ca>

If the log is growing then it is still working.  The time it takes is a function of the evidence dataset, genome size, and gene density.  Is there any way, you could try starting a second maker process in the same directory with additional CPUs to get it to complete sooner (each process will detect each other and avoid overlapping on their work, so it will still get divided up efficiently).  Also if you combine the length of all finished contigs, you will get a better idea of how much run time is remaining (i.e. See if contigs remaining are short or long compared to most contigs in the assembly).

Thanks,
Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 23, 2013 1:12 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Thanks Carson,

gephy.transcripts.fa is 64406072
geph_AS_masked.fa is 296693827

The log is growing. It finished 21700 scaffolds. I think we have nearly 38149 scaffolds. Is that means the program running good?

Sincerely,
Yunxi



2013/7/22 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Nothing looks out of the ordinary.  How big is this file --> gephy.transcripts.fa
How big is this file --> geph_AS_masked.fa

Also is the STDERR log growing or is it frozen?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, July 22, 2013 12:24 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Sorry to bother you again. I ran the MAKER for like around two weeks, but it is still running now. I attached my control files. Can you help me to see if I set something wrong? I used the masked genome as my input, so I skipped the repeatmasker in maker. I think it should be faster. I ran this mpiexec -n 8 maker

I'm running another maker using unmasked data in 16 threads, so I ran this in 8. I already got 34G data for this. Because the time cost in running already out of schedule. I'm worry about something wrong in the setting.

Thank you.
Yunxi


2013/7/14 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson.


2013/7/14 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
I would use the same data to train both.

More information here --> https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J

--Carson

From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Friday, July 12, 2013 9:04 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

One more is when I train the SNAP and Augustus, should I do them in the same time with the est2genome and protein2genome, or do them separately? Thank you.


2013/7/12 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Hi Carson

The MAKER is running fine right now. I'm confusing about using the CEGMA with MAKER to train the SNAP and Augustus.

I'm running the MAKER from est2genome with protein2genome without using the result from CEGMA. I think the data I already enough for generating the hmm.

And I got the zff from the result of CEGMA, and I followed the link last time you gave me to generate the file for SNAP and Augustus.

I'm not that clear how to combine the hmm model from CEGMA and MAKER.

Thank you for your help.

Sincerely,
Yunxi


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I think I should better to use the default, in case it occurs an error after several days' running.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Some operations are not NFS safe (NFS behaves different than normal file systems).  So maker performs those operations in the temporary directory.  If you redirect those files to an NFS location, you may get errors (basically MAKER just dies).  It won't necessarily happen, but the warning lets you know that, if it fails then you should set TMP= somewhere else before trying again.

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 3:22 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got an error message about this:
ERROR: Temporary directory set to an NFS location.
TMP=/home/lin11/tmp
The temporary directory in MAKER is specifically for
operations that are not NFS-safe. You must set TMP
to a locally mounted directory such as /tmp or add
--ignore_nfs_tmp to the maker command line to
override this error message.

Does the MAKER need a big temporary file? Because our system temporary directory may not have that much space. If it does not need that big tmp file, I can set it back to default. Or I just ignore the error message?

Thank you.


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Anything from maker under the ~/perl5/ should be deleted.  MAKER should be self contained in its own directory.  Do 'rm ~/perl5/bin/*maker*'.  If you see anything else that is maker related there delete it as well.

Example:
.../maker/bin/
.../maker/lib/
.../maker/exe/

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 1:40 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I installed the new version of MAKER. But right now have a problem of running it. Because I was missing perl dependencies, I installed the perl local library. And then I tried to run maker, it will automatically go to the one in local library called ~/perl5/bin/maker. Do you know how to get rid of this path? I found this path in .bashrc : export PATH="/home/lin11/perl5/bin:$PATH". If that ok to delete it?

Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It's been stable enough that I could remove the beta tag (no major updates in 2 months).  In fact I'll go ahead and do that.

--Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:21 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Is that the 2.28 only have the beta version?


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I'll try then let you know.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You could just install it in a new directory (I.e. maker_2.28 rather than maker).  The 2.1 version more than 2 years old (lots of changes and improvements since then).

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:11 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson
I think I may need to update MAKER too. My version is 2.1. Is the new version of MAKER changed a lot? Because someone running MAKER on the server now, can I just update it instead of delete the old one then reinstall the new version?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
If you are using MAKER 2.28, and let it do the install for you it will install mpich2 from this location --> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz

The installation will be in the .../maker/exe/mpich2 directory.

Alternatively, if you do the installation yourself, all you have to do set a few flags during install configuration.
--> ./configure --prefix=$path --enable-shared
Set $path to the location where you want MPICH2 to be installed.
Then run 'make install'

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:59 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I think it installed the 1.3.1 version. Can I update it?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It should be installed under .../maker/exe/mpich2.  Having it under ~/perl5/exe/mpich2 is odd as maker should do that.

Type 'which mpiexec' to see if there is another mpiexec installed somewhere.  Also run 'mpiexec --version'.  What does it give?  I ask because the error message you got before is the same as a bug in an old version of MPICH2 (version 1.3).  MAKER will install version 1.5.

Also run 'mpiexec -n 16 hostname'
What happens?

Thanks,
Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:17 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

How's the trip?

I did it followed your instruction. I ran ./build mpich2 first
It installed it into ~/perl5/exe/mpich2 directory.
And then i go back to maker/src ran perl build.pl<http://build.pl> and type Y to accept the MPI.
Then I ran ./build install
After that, I went to ~/.bash_profile to add the ~/perl5/exe/mpich2/bin into the PATH.
I used mpiexec -n 16 maker as the command.
Do I need to set some special variable in that three control file first?

Thank you.

Yunxi Lin

On Jul 2, 2013, at 7:44 AM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

Sorry for not responding sooner (it was a long holiday weekend in Canada).  Did you have maker install MPICH2 or did you install it yourself?  Also what is the exact command line you used to launch?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sunday, June 30, 2013 2:09 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got the errors like:
[mpiexec at bioinfo1] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file hydra_pmi_proxy (No such file or directory)
[mpiexec at bioinfo1] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:315): assert (!closed) failed
[mpiexec at bioinfo1] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec at bioinfo1] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event
[mpiexec at bioinfo1] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion

Is that means our server only has one cpu so I cannot use mpi?

Thank you.



2013/6/25 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.

When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only).  It will be in ?/maker/exe/mpich2.  This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having to get upgraded privileges.  So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.

--Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, 25 June, 2013 11:40 AM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>

Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu?  Because my school own the server, I only have the limit authorization.

Yunxi Lin

On Jun 24, 2013, at 5:39 PM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

You are most likely only getting 1 cpu of performance.

You should just install MPICH2.  It's easy just to let MAKER do it for you:
Go to the ?/maker/src/ directory
Run './Build mpich2'
Once it finishes installing, it will be in the ?/maker/exe/mpich2/bin/ directory.

Setup MAKER again to use MPICH2:
Go to the ?/maker/src/ directory
Run 'perl Build.PL'
Say yes to the "use MPI": question
Run './Build install'

Now run MAKER via 'mpiexec'.
Example --> ?/maker/exe/mpich2/bin/mpiexec -n 16 maker

The ?n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines.  You will get much better performance.

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, 24 June, 2013 7:11 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank your for your help.

My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER.

I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus.

Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way.

Sincerely,
Yunxi



2013/6/24 Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use.  If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time.  This is especially true if you use the alt_est option for evidence as these are aligned via tblastx  which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.

Also you do not need results from the entire genome to train SNAP.  If you get results from ~10Mb of the genome that is usually sufficient.  Also make sure you are taking advantage of parallelization.  Launch via MPI to get maximum performance.  I commonly launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.

--Carson


From: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Date: Sunday, 23 June, 2013 10:15 PM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Cc: <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Subject: [maker-devel] Fwd: about running MAKER

>From the GMOD helpdesk; please cc Lin, lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>.

---------- Forwarded message ----------
From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sun, Jun 23, 2013 at 4:14 PM
Subject: about running MAKER
To: "gmod-help at gmod.org<mailto:gmod-help at gmod.org>" <help at gmod.org<mailto:help at gmod.org>>


Hi

I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server.

Thank you.

Sincerely,
Lin



--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

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From grburke at uga.edu  Tue Jul 30 14:14:02 2013
From: grburke at uga.edu (Gaelen Burke)
Date: Tue, 30 Jul 2013 19:14:02 -0000
Subject: [maker-devel] unknown error
Message-ID: <602FA505-8A78-4006-8D8F-D3EC81A73FEC@uga.edu>

Hello,
I have an error that occurs in my MAKER run for 52 of several thousand scaffolds. The annotation of these scaffolds fails, even after 3 re-tries. I also pulled out the failed sequences and started a run from scratch, with the same result. Could anyone tell me what this error means and how I could possibly fix it?
Thanks,
Gaelen Burke

Here is the message that occurs:

Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
:411
STACK: PhatHit_utils::_adjust /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit_utils.pm:
880
STACK: PhatHit_utils::adjust_start_stop /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit
_utils.pm:776
STACK: maker::auto_annotator::load_transcript_struct /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/.
./lib/maker/auto_annotator.pm:1808
STACK: maker::auto_annotator::group_transcripts /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib
/maker/auto_annotator.pm:2163
STACK: maker::auto_annotator::annotate_genes /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/ma
ker/auto_annotator.pm:877
STACK: Process::MpiChunk::_go /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:2159
STACK: Process::MpiChunk::run /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:257
STACK: Process::MpiTiers::run_all /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiTi
ers.pm:193
STACK: /usr/local/maker/latest/bin/maker:276
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while clustering transcripts into genes for annotations!!

ERROR: Chunk failed at level 20
!!
FAILED CONTIG:scaffold_0040



From vwong at umn.edu  Tue Jul  2 09:38:26 2013
From: vwong at umn.edu (V Wong)
Date: Tue, 2 Jul 2013 10:38:26 -0500
Subject: [maker-devel] maker2jbrowse implementation
Message-ID: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
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From carsonhh at gmail.com  Tue Jul  2 10:27:19 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 12:27:19 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>
Message-ID: <CDF873FE.65B7%carsonhh@gmail.com>

The Jbrowse codebase tends to undergo very rapid alteration (much of which
is not backwards compatible with other Jbrowse versions), as a result the
script maker2jbrowse has had to evolve with Jbrowse (and will not work with
all versions).  I'm not sure if the script is currently behind or ahead of
Jbrowse version 1.9.3 (I'm guessing behind). I can have it working with
whatever the most current repository is if you were to give me a week, or
you can try loading the GFF3's using Jbrowse's own loader (tutorial here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012).  Of course this tutorial is
also likely to be somewhat out of date :-( But the 2013 version is supposed
to be up and running as part of this years GMOD summer school in ~3 weeks.
They use MAKER generated data for the tutorial, so it should be relevant to
what you are doing.

Thanks,
Carson



From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Tuesday, July 2, 2013 11:38 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker2jbrowse implementation

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From rbuels at gmail.com  Tue Jul  2 11:32:40 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 02 Jul 2013 13:32:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D30EB8.5090002@gmail.com>

One of my objectives has been maintaining complete backward 
compatibility with data formatted from JBrowse 1.2.1 onward.  I add 
capabilities, and the look and feel of the browser improves, but you can 
still view data in it that was formatted with JBrowse 1.2.1 (released 
March 17, 2011).

I would try to have a look at the maker2jbrowse implementation to 
troubleshoot further, but your source code doesn't seem to be public. 
Or at least the link to the source browser on the GMOD wiki page 
(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't 
find any kind of source code links under 
http://www.yandell-lab.org/software/maker.html.  Is the MAKER source 
code actually open?

Regarding the 2012 tutorial, the directions in the 2012 tutorial should 
still work, since I have been keeping backward compatibility with the 
scripts also.

Val, Carson, could you elaborate with details on the backward 
compatibility problems you're seeing?  Or could you give me access to 
the maker2jbrowse source code?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Tue Jul  2 13:19:40 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 15:19:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D30EB8.5090002@gmail.com>
Message-ID: <CDF89913.661B%carsonhh@gmail.com>

Good to know the tutorial is up to date.  I had to make several
consecutive updates to my script about a year ago with Jbrowse updates, so
I'm glad to know I can likely just fix whatever is wrong now and that will
be good for most previous and upcoming Jbrowse version :-)

It has more to do with converting data from GFF3.  maker2jbrowse is just a
script that wraps the flatfile-to-json.pl calls together with some css
files (all included in maker tar ball - it's open source).  So if anything
changes in flatfile-to-json.pl or the expected tags in css files then
maker2jbrowse won't work (the css files are where I usually get into
trouble). I just have to figure out what the changes are and then fix
them.  I know I had to do some updates for colors in Web Apollo recently
and I imagine I can just use that as a template.

Thanks,
Carson




On 7/2/13 1:32 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>One of my objectives has been maintaining complete backward
>compatibility with data formatted from JBrowse 1.2.1 onward.  I add
>capabilities, and the look and feel of the browser improves, but you can
>still view data in it that was formatted with JBrowse 1.2.1 (released
>March 17, 2011).
>
>I would try to have a look at the maker2jbrowse implementation to
>troubleshoot further, but your source code doesn't seem to be public.
>Or at least the link to the source browser on the GMOD wiki page
>(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't
>find any kind of source code links under
>http://www.yandell-lab.org/software/maker.html.  Is the MAKER source
>code actually open?
>
>Regarding the 2012 tutorial, the directions in the 2012 tutorial should
>still work, since I have been keeping backward compatibility with the
>scripts also.
>
>Val, Carson, could you elaborate with details on the backward
>compatibility problems you're seeing?  Or could you give me access to
>the maker2jbrowse source code?
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Jul  2 13:24:43 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 2 Jul 2013 13:24:43 -0600
Subject: [maker-devel] maker2jbrowse
References: <mailman.69.1372786364.6126.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <E031B282-253C-4DFE-9D08-ECC02501CCAD@genetics.utah.edu>

Hi Robert,

Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use.  You can download the code here:

http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.

Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)

B

> From: Robert Buels <rbuels at gmail.com>
> Subject: Re: [maker-devel] maker2jbrowse implementation
> Date: July 2, 2013 11:32:40 AM MDT
> To: <maker-devel at yandell-lab.org>
> 
> 
> One of my objectives has been maintaining complete backward compatibility with data formatted from JBrowse 1.2.1 onward.  I add capabilities, and the look and feel of the browser improves, but you can still view data in it that was formatted with JBrowse 1.2.1 (released March 17, 2011).
> 
> I would try to have a look at the maker2jbrowse implementation to troubleshoot further, but your source code doesn't seem to be public. Or at least the link to the source browser on the GMOD wiki page (http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't find any kind of source code links under http://www.yandell-lab.org/software/maker.html.  Is the MAKER source code actually open?
> 
> Regarding the 2012 tutorial, the directions in the 2012 tutorial should still work, since I have been keeping backward compatibility with the scripts also.
> 
> Val, Carson, could you elaborate with details on the backward compatibility problems you're seeing?  Or could you give me access to the maker2jbrowse source code?
> 
> 
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
> 
> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>  Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>> 
>> Hi Maker team,
>> 
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>> 
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> 
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>> 
>> Any advice for getting past this will be most appreciated.  Thank you!
>> 
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 
> 
> 
> From: <maker-devel-request at yandell-lab.org>
> Subject: confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc
> Date: July 2, 2013 11:32:44 AM MDT
> 
> 
> If you reply to this message, keeping the Subject: header intact,
> Mailman will discard the held message.  Do this if the message is
> spam.  If you reply to this message and include an Approved: header
> with the list password in it, the message will be approved for posting
> to the list.  The Approved: header can also appear in the first line
> of the body of the reply.
> 
> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From rbuels at gmail.com  Wed Jul  3 09:45:53 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 11:45:53 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D44731.6060308@gmail.com>

After looking at the maker2jbrowse source (thanks for giving me access), 
there seems to be some kind of problem with the way maker2jbrowse is 
parsing the MAKER datastore index, leading to the script complaining of 
'no track information'.

This would probably be easier for a MAKER developer to look into.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Wed Jul  3 10:02:23 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 12:02:23 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D44731.6060308@gmail.com>
Message-ID: <CDF9C28B.66AF%carsonhh@gmail.com>

I think you may not have it set up right.  If you run the example data,
you can then use that.  For me it populates the JSON data tracks
information, but nothing displays.  I think the problem is with the maker
genome.css.  It is very out of date.  I'll do some work on it and then get
your feedback.

Thanks,
Carson



On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:

>After looking at the maker2jbrowse source (thanks for giving me access),
>there seems to be some kind of problem with the way maker2jbrowse is
>parsing the MAKER datastore index, leading to the script complaining of
>'no track information'.
>
>This would probably be easier for a MAKER developer to look into.
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>





From rbuels at gmail.com  Wed Jul  3 10:14:49 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:14:49 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D44DF9.9050908@gmail.com>

How does this have anything to do with CSS?  The errors Val is talking 
about are coming from the maker2jbrowse script:

ERROR: No track information for source
 >>> 'AK_assembly_datastore/22/D4/AK_contig_1/'


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From vwong at umn.edu  Wed Jul  3 10:15:38 2013
From: vwong at umn.edu (V Wong)
Date: Wed, 3 Jul 2013 11:15:38 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <51D44731.6060308@gmail.com>
	<CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <CAEi2voZNLhwS=u2FvTukC6HoxMuF7_3p8K2y1VCy7RAFsw_xgw@mail.gmail.com>

Hi Carson and Robert,

Thank you for your feedback on this!  Carson, could you describe the set up
a little more?  For instance, are you running the script in a specific
location in the JBrowse directory?  I seem to be running into the same
problem as Robert.

Best,
Val


On Wed, Jul 3, 2013 at 11:02 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
> >After looking at the maker2jbrowse source (thanks for giving me access),
> >there seems to be some kind of problem with the way maker2jbrowse is
> >parsing the MAKER datastore index, leading to the script complaining of
> >'no track information'.
> >
> >This would probably be easier for a MAKER developer to look into.
> >
> >
> >Robert Buels
> >Lead Developer
> >JBrowse - http://jbrowse.org
> >
> >On 07/02/2013 12:27 PM, Carson Holt wrote:
> >> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >> which is not backwards compatible with other Jbrowse versions), as a
> >> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> >> not work with all versions).  I'm not sure if the script is currently
> >> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >> have it working with whatever the most current repository is if you were
> >> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> >> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>   Of course this tutorial is also likely to be somewhat out of date
> >> :-( But the 2013 version is supposed to be up and running as part of
> >> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >> data for the tutorial, so it should be relevant to what you are doing.
> >>
> >> Thanks,
> >> Carson
> >>
> >>
> >>
> >> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Date: Tuesday, July 2, 2013 11:38 AM
> >> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> >> Subject: [maker-devel] maker2jbrowse implementation
> >>
> >> Hi Maker team,
> >>
> >> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >> server, using the -d option for the index.log file.  However, I am
> >> getting this error for each contig:
> >>
> >> ERROR: No track information for source
> >> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>
> >> Looking at the perl script, the file locations are getting read, but
> >> then the tracks aren't getting found in the hash of commands.
> >>
> >> Any advice for getting past this will be most appreciated.  Thank you!
> >>
> >> Best,
> >> Val
> >> _______________________________________________ maker-devel mailing list
> >> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com
> >
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >>
> >> _______________________________________________
> >> maker-devel mailing list
> >> maker-devel at box290.bluehost.com
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
>
>
>
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From rbuels at gmail.com  Wed Jul  3 10:39:51 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:39:51 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D453D7.4070801@gmail.com>

Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what 
you're doing with that, but it appears to be a fork of a very old 
JBrowse main css file.  If that's overriding or being copied over the 
JBrowse released CSS, it will break pretty much everything.  It would be 
like me randomly replacing one of MAKER's Perl modules with my own old 
forked copy.

If what you're trying to accomplish is to add some custom styles, the 
best way to do that would be to do one of:

* add just your custom feature styles on the flatfile-to-json.pl command 
line
* add a "css": { "url": "http://url/of/your/custom.css" } to the
   JBrowse trackList.json someplace in the workflow (easy to add
   things to JSON files with JSON.pm) that loads your custom CSS
   (containing only your custom feature styles!)
* add all of the custom styles to the trackList.json as a
   string: "css": "string { of: lots and lots of; css: properties; }"


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From carsonhh at gmail.com  Wed Jul  3 13:26:32 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 15:26:32 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D453D7.4070801@gmail.com>
Message-ID: <CDF9E0AE.6703%carsonhh@gmail.com>

Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
documentation had you modify the genome.css file to create your own
tracks.  Version 1.2.1 looks like it is the last version where the
genome.css file that maker provided works. I can still get simple test
GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
But I need to fix some things, because they are all indistinguishable from
each other (so it is not the desired behavior).

Indepent of that issue though, to regenerate the original error, I do the
following -->
    maker2jbrowse  
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 
    ERROR: No track information for source
'dpp_contig_datastore/05/1F/contig-dpp-500-500/'

Basically you are missing the '-d' flag (whiteout that the script is
expecting a list of GFF3 files).

So this works -->
    maker2jbrowse -d
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 


Of course all tracks look the same though per the original issue I
mentioned.

Thanks,
Carson



Some versions of Jbrowse still load fine with the script as is Jbrowse
1.3, 

On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>you're doing with that, but it appears to be a fork of a very old
>JBrowse main css file.  If that's overriding or being copied over the
>JBrowse released CSS, it will break pretty much everything.  It would be
>like me randomly replacing one of MAKER's Perl modules with my own old
>forked copy.
>
>If what you're trying to accomplish is to add some custom styles, the
>best way to do that would be to do one of:
>
>* add just your custom feature styles on the flatfile-to-json.pl command
>line
>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>   JBrowse trackList.json someplace in the workflow (easy to add
>   things to JSON files with JSON.pm) that loads your custom CSS
>   (containing only your custom feature styles!)
>* add all of the custom styles to the trackList.json as a
>   string: "css": "string { of: lots and lots of; css: properties; }"
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> I think you may not have it set up right.  If you run the example data,
>> you can then use that.  For me it populates the JSON data tracks
>> information, but nothing displays.  I think the problem is with the
>>maker
>> genome.css.  It is very out of date.  I'll do some work on it and then
>>get
>> your feedback.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>
>>> After looking at the maker2jbrowse source (thanks for giving me
>>>access),
>>> there seems to be some kind of problem with the way maker2jbrowse is
>>> parsing the MAKER datastore index, leading to the script complaining of
>>> 'no track information'.
>>>
>>> This would probably be easier for a MAKER developer to look into.
>>>
>>>
>>> Robert Buels
>>> Lead Developer
>>> JBrowse - http://jbrowse.org
>>>
>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>will
>>>> not work with all versions).  I'm not sure if the script is currently
>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>> have it working with whatever the most current repository is if you
>>>>were
>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>own
>>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>> data for the tutorial, so it should be relevant to what you are doing.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>
>>>> Hi Maker team,
>>>>
>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>> server, using the -d option for the index.log file.  However, I am
>>>> getting this error for each contig:
>>>>
>>>> ERROR: No track information for source
>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>
>>>> Looking at the perl script, the file locations are getting read, but
>>>> then the tracks aren't getting found in the hash of commands.
>>>>
>>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>>
>>>> Best,
>>>> Val
>>>> _______________________________________________ maker-devel mailing
>>>>list
>>>> maker-devel at box290.bluehost.com
>>>><mailto:maker-devel at box290.bluehost.com>
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>
>>
>>





From benayoun at stanford.edu  Fri Jul  5 15:35:44 2013
From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:35:44 -0700
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
References: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
Message-ID: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
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From carsonhh at gmail.com  Mon Jul  8 08:20:53 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 10:20:53 -0400
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>
Message-ID: <CE00422F.6A5C%carsonhh@gmail.com>

In your MAKER STDERR (printed to screen or captured as part of run), search
for the word ERROR.  That will give a more specific explanation as to why it
is failing.  If you did not capture this on your first run, you may need to
redirect it to a file on a retry.

Example --> maker 2> error.log

Thanks,
Carson

From:  B?r?nice Benayoun <benayoun at stanford.edu>
Date:  Friday, July 5, 2013 5:35 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] FAILED contigs

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
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From berenice.benayoun at gmail.com  Fri Jul  5 15:33:35 2013
From: berenice.benayoun at gmail.com (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:33:35 -0700
Subject: [maker-devel] FAILED contigs
Message-ID: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice

-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/
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From onson001 at umn.edu  Mon Jul  8 16:12:06 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Mon, 8 Jul 2013 17:12:06 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
Message-ID: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>

Maker Developers,

I am testing Maker on a well annotated contig from the encode project and
in one of the genes, maker does not output an exon despite HSPs supporting
it. I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question.

I even set the parameters est2genome and protein2genome to 1 but still
Maker did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks,
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From carsonhh at gmail.com  Mon Jul  8 19:55:15 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 21:55:15 -0400
Subject: [maker-devel] Maker not outputting exons with EST and Protein
 Evidence
In-Reply-To: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
Message-ID: <CE00DF97.6C2A%carsonhh@gmail.com>

This is because augustus never calls it either without hints or after being
given hints by MAKER.  This may be because even though the exon has support
from ESTs and protein alignments, it breaks the open reading frame (you can
check using apollo ? just click and drag them into the annotation tier).  I
did this individually for each of the polished proteins and ESTs, and none
have proper open reading frame.

Perhaps the official annotation contains a frame shift or something to make
it work (augustus can't do that).  Such a thing is not all that uncommon.
There are many instances of RefSeq annotations for example where if you cut
out the exons and try and translate them, they won't translate.  This can
happen because the reference sequence changed or is incorrect, and if the
annotation was generated from a different assembly, then it just gets mapped
as best as possible to the current assembly and the correct protein
translation is saved elsewhere in the database (even though manual
translation won't directly reproduce it).  Genes where this happens make up
just under 1% of the human genome (but they can drive you nuts especially if
your analysis expects protein sequence to match the nucleotide sequence
translation).  It's really just an artifacts of the process used to move
annotations forward on the humans genome every time they update the
assembly.

Thanks,
Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Monday, July 8, 2013 6:12 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker not outputting exons with EST and Protein
Evidence

Maker Developers, 

I am testing Maker on a well annotated contig from the encode project and in
one of the genes, maker does not output an exon despite HSPs supporting it.
I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question. 

I even set the parameters est2genome and protein2genome to 1 but still Maker
did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks, 
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Tue Jul  9 09:57:09 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 09 Jul 2013 11:57:09 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9E0AE.6703%carsonhh@gmail.com>
Message-ID: <CE01A884.6C92%carsonhh@gmail.com>

Hi Val,

I've attached new files for you to test.  These will be bundled in the
next maker release pending successful tests (~ 1 week).

Instructions:
1. Place maker2jbrowse in your .../maker/bin/ directory and
.../maker/src/bin/ directory (this is just to ensure you don't
accidentally overwrite it if you reinstall at any time).
2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
3. You must be in the jbrowse installation directory when running
maker2jbrowse.  Run the script with the -d flag and the datastore index
file.

This new version will assign colors by copying maker.css to the jbrowse
installation as apposed to replacing the genome.css file, and it will also
edit the genome.css file to add the import call for maker.css.  In
addition I have updated command line flags in the wrapper to do what is
currently expected by flatfile-to-json.pl.

Could you test it out and let me know how it goes.

Thanks,
Carson



On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:

>Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>documentation had you modify the genome.css file to create your own
>tracks.  Version 1.2.1 looks like it is the last version where the
>genome.css file that maker provided works. I can still get simple test
>GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>But I need to fix some things, because they are all indistinguishable from
>each other (so it is not the desired behavior).
>
>Indepent of that issue though, to regenerate the original error, I do the
>following -->
>    maker2jbrowse 
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>    ERROR: No track information for source
>'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>
>Basically you are missing the '-d' flag (whiteout that the script is
>expecting a list of GFF3 files).
>
>So this works -->
>    maker2jbrowse -d
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>
>
>Of course all tracks look the same though per the original issue I
>mentioned.
>
>Thanks,
>Carson
>
>
>
>Some versions of Jbrowse still load fine with the script as is Jbrowse
>1.3, 
>
>On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>you're doing with that, but it appears to be a fork of a very old
>>JBrowse main css file.  If that's overriding or being copied over the
>>JBrowse released CSS, it will break pretty much everything.  It would be
>>like me randomly replacing one of MAKER's Perl modules with my own old
>>forked copy.
>>
>>If what you're trying to accomplish is to add some custom styles, the
>>best way to do that would be to do one of:
>>
>>* add just your custom feature styles on the flatfile-to-json.pl command
>>line
>>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>   JBrowse trackList.json someplace in the workflow (easy to add
>>   things to JSON files with JSON.pm) that loads your custom CSS
>>   (containing only your custom feature styles!)
>>* add all of the custom styles to the trackList.json as a
>>   string: "css": "string { of: lots and lots of; css: properties; }"
>>
>>
>>Robert Buels
>>Lead Developer
>>JBrowse - http://jbrowse.org
>>
>>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>> I think you may not have it set up right.  If you run the example data,
>>> you can then use that.  For me it populates the JSON data tracks
>>> information, but nothing displays.  I think the problem is with the
>>>maker
>>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>get
>>> your feedback.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>
>>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>access),
>>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>> parsing the MAKER datastore index, leading to the script complaining
>>>>of
>>>> 'no track information'.
>>>>
>>>> This would probably be easier for a MAKER developer to look into.
>>>>
>>>>
>>>> Robert Buels
>>>> Lead Developer
>>>> JBrowse - http://jbrowse.org
>>>>
>>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>will
>>>>> not work with all versions).  I'm not sure if the script is currently
>>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>>> have it working with whatever the most current repository is if you
>>>>>were
>>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>>own
>>>>> loader (tutorial here -->
>>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>>> data for the tutorial, so it should be relevant to what you are
>>>>>doing.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>> To: <maker-devel at yandell-lab.org
>>>>><mailto:maker-devel at yandell-lab.org>>
>>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>
>>>>> Hi Maker team,
>>>>>
>>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>> server, using the -d option for the index.log file.  However, I am
>>>>> getting this error for each contig:
>>>>>
>>>>> ERROR: No track information for source
>>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>
>>>>> Looking at the perl script, the file locations are getting read, but
>>>>> then the tracks aren't getting found in the hash of commands.
>>>>>
>>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>you!
>>>>>
>>>>> Best,
>>>>> Val
>>>>> _______________________________________________ maker-devel mailing
>>>>>list
>>>>> maker-devel at box290.bluehost.com
>>>>><mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>
>>>
>>>
>
>

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From Carson.Holt at oicr.on.ca  Tue Jul  9 13:19:14 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 9 Jul 2013 19:19:14 +0000
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE01D9F3.6CF4%carson.holt@oicr.on.ca>

It's perfectly safe to kill.

If you are constantly getting FAIL in the datastore index, then something
is wrong.  If you are capturing the jobs STDERR, try looking for the term
ERROR or FATAL for a better explanation as to why it's failing and send
the error to me.

Thanks,
Carson


On 7/9/13 2:47 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hello Maker Developers!
>
>I have a quick question... I've been using MAKER to annotate a genome (it
>has been running for about 6 days with 48 cpus).  Many of my contigs have
>failed, surely because most of them are smaller than the 10 kb limit I
>set, which is fine.  My concern is that although I've set tries = 2, the
>index log seems to indicate that MAKER is on its fourth try for some of
>the contigs (see attached).  Is is safe to shut MAKER down, or are there
>clean-up steps at the end of the annotation process that need to be
>allowed to occur?  Oh, and I'm using MAKER 2.28.
>
>Best, Jacqueline
>
>




From onson001 at umn.edu  Tue Jul  9 15:29:21 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Tue, 9 Jul 2013 16:29:21 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
In-Reply-To: <CE00DF97.6C2A%carsonhh@gmail.com>
References: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
	<CE00DF97.6C2A%carsonhh@gmail.com>
Message-ID: <CACFwDdLkUR3A-j8dzFj=GujNz6oKmL0RpXjpH6bZhr53Tr1rcg@mail.gmail.com>

Thanks for the insight.


On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> This is because augustus never calls it either without hints or after
> being given hints by MAKER.  This may be because even though the exon has
> support from ESTs and protein alignments, it breaks the open reading frame
> (you can check using apollo ? just click and drag them into the annotation
> tier).  I did this individually for each of the polished proteins and ESTs,
> and none have proper open reading frame.
>
> Perhaps the official annotation contains a frame shift or something to
> make it work (augustus can't do that).  Such a thing is not all that
> uncommon.  There are many instances of RefSeq annotations for example where
> if you cut out the exons and try and translate them, they won't translate.
>  This can happen because the reference sequence changed or is incorrect,
> and if the annotation was generated from a different assembly, then it just
> gets mapped as best as possible to the current assembly and the correct
> protein translation is saved elsewhere in the database (even though manual
> translation won't directly reproduce it).  Genes where this happens make up
> just under 1% of the human genome (but they can drive you nuts especially
> if your analysis expects protein sequence to match the nucleotide sequence
> translation).  It's really just an artifacts of the process used to move
> annotations forward on the humans genome every time they update the
> assembly.
>
> Thanks,
> Carson
>
>
> From: Innocent Onsongo <onson001 at umn.edu>
> Date: Monday, July 8, 2013 6:12 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker not outputting exons with EST and Protein
> Evidence
>
> Maker Developers,
>
> I am testing Maker on a well annotated contig from the encode project and
> in one of the genes, maker does not output an exon despite HSPs supporting
> it. I have attached a compressed folder with
>
> ENr122_genes.gff: The validated genes as per encode
> ENr122.gff: Makers output
> maker_opts.ctl: The control file I used
> ENr122_98669-134249.pptx: A power point visually illustrated the exon in
> question.
>
> I even set the parameters est2genome and protein2genome to 1 but still
> Maker did not output this exon.
>
> Is there a good reason Maker does no have this exon in its final model
> despite the HSPs supporting it?
>
> Thanks,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From jmdoyle at purdue.edu  Tue Jul  9 12:47:46 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Tue, 9 Jul 2013 14:47:46 -0400 (EDT)
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <53458481.77205.1373395049899.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>

Hello Maker Developers!

I have a quick question... I've been using MAKER to annotate a genome (it has been running for about 6 days with 48 cpus).  Many of my contigs have failed, surely because most of them are smaller than the 10 kb limit I set, which is fine.  My concern is that although I've set tries = 2, the index log seems to indicate that MAKER is on its fourth try for some of the contigs (see attached).  Is is safe to shut MAKER down, or are there clean-up steps at the end of the annotation process that need to be allowed to occur?  Oh, and I'm using MAKER 2.28.

Best, Jacqueline


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From yuharas at takara-bio.co.jp  Wed Jul 10 20:27:12 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 11:27:12 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>

Dear developers

I'm considering using MAKER2 to annotate plant genome (~1Gb) I've assembled using illumina HiSeq data.
And I'm planning to obtain mRNA-seq data by using HiSeq.
Do you have any recommendation of sequencing depth of RNA-seq data for using MAKER2 annotation pipeline?

Thanks,
Satoshi




From carsonhh at gmail.com  Wed Jul 10 20:40:52 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 10 Jul 2013 22:40:52 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
Message-ID: <CE039117.6E22%carsonhh@gmail.com>

As far as total depth I don't know, but I'd recommend using something like
trinity to assemble the reads and supply them to the est= option in fasta
format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From yuharas at takara-bio.co.jp  Wed Jul 10 22:47:10 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 13:47:10 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE039117.6E22%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
	<CE039117.6E22%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>

Dear Carson

Thank you for your quick reply.
Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
although the tutorial contains information about Tophat and Cufflinks?

Satoshi


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 11:41 AM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

As far as total depth I don't know, but I'd recommend using something like trinity to assemble the reads and supply them to the est= option in fasta format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for 
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From vwong at umn.edu  Wed Jul 10 23:10:52 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 00:10:52 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE01A884.6C92%carsonhh@gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
Message-ID: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser,
but that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Val,
>
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
>
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
>
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl.
>
> Could you test it out and let me know how it goes.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
> >documentation had you modify the genome.css file to create your own
> >tracks.  Version 1.2.1 looks like it is the last version where the
> >genome.css file that maker provided works. I can still get simple test
> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
> >But I need to fix some things, because they are all indistinguishable from
> >each other (so it is not the desired behavior).
> >
> >Indepent of that issue though, to regenerate the original error, I do the
> >following -->
> >    maker2jbrowse
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >    ERROR: No track information for source
> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
> >
> >Basically you are missing the '-d' flag (whiteout that the script is
> >expecting a list of GFF3 files).
> >
> >So this works -->
> >    maker2jbrowse -d
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >
> >
> >Of course all tracks look the same though per the original issue I
> >mentioned.
> >
> >Thanks,
> >Carson
> >
> >
> >
> >Some versions of Jbrowse still load fine with the script as is Jbrowse
> >1.3,
> >
> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
> >
> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
> >>you're doing with that, but it appears to be a fork of a very old
> >>JBrowse main css file.  If that's overriding or being copied over the
> >>JBrowse released CSS, it will break pretty much everything.  It would be
> >>like me randomly replacing one of MAKER's Perl modules with my own old
> >>forked copy.
> >>
> >>If what you're trying to accomplish is to add some custom styles, the
> >>best way to do that would be to do one of:
> >>
> >>* add just your custom feature styles on the flatfile-to-json.pl command
> >>line
> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
> >>   JBrowse trackList.json someplace in the workflow (easy to add
> >>   things to JSON files with JSON.pm) that loads your custom CSS
> >>   (containing only your custom feature styles!)
> >>* add all of the custom styles to the trackList.json as a
> >>   string: "css": "string { of: lots and lots of; css: properties; }"
> >>
> >>
> >>Robert Buels
> >>Lead Developer
> >>JBrowse - http://jbrowse.org
> >>
> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
> >>> I think you may not have it set up right.  If you run the example data,
> >>> you can then use that.  For me it populates the JSON data tracks
> >>> information, but nothing displays.  I think the problem is with the
> >>>maker
> >>> genome.css.  It is very out of date.  I'll do some work on it and then
> >>>get
> >>> your feedback.
> >>>
> >>> Thanks,
> >>> Carson
> >>>
> >>>
> >>>
> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
> >>>
> >>>> After looking at the maker2jbrowse source (thanks for giving me
> >>>>access),
> >>>> there seems to be some kind of problem with the way maker2jbrowse is
> >>>> parsing the MAKER datastore index, leading to the script complaining
> >>>>of
> >>>> 'no track information'.
> >>>>
> >>>> This would probably be easier for a MAKER developer to look into.
> >>>>
> >>>>
> >>>> Robert Buels
> >>>> Lead Developer
> >>>> JBrowse - http://jbrowse.org
> >>>>
> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >>>>> which is not backwards compatible with other Jbrowse versions), as a
> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
> >>>>>will
> >>>>> not work with all versions).  I'm not sure if the script is currently
> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >>>>> have it working with whatever the most current repository is if you
> >>>>>were
> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
> >>>>>own
> >>>>> loader (tutorial here -->
> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>>>>    Of course this tutorial is also likely to be somewhat out of date
> >>>>> :-( But the 2013 version is supposed to be up and running as part of
> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >>>>> data for the tutorial, so it should be relevant to what you are
> >>>>>doing.
> >>>>>
> >>>>> Thanks,
> >>>>> Carson
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
> >>>>> To: <maker-devel at yandell-lab.org
> >>>>><mailto:maker-devel at yandell-lab.org>>
> >>>>> Subject: [maker-devel] maker2jbrowse implementation
> >>>>>
> >>>>> Hi Maker team,
> >>>>>
> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >>>>> server, using the -d option for the index.log file.  However, I am
> >>>>> getting this error for each contig:
> >>>>>
> >>>>> ERROR: No track information for source
> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>>>>
> >>>>> Looking at the perl script, the file locations are getting read, but
> >>>>> then the tracks aren't getting found in the hash of commands.
> >>>>>
> >>>>> Any advice for getting past this will be most appreciated.  Thank
> >>>>>you!
> >>>>>
> >>>>> Best,
> >>>>> Val
> >>>>> _______________________________________________ maker-devel mailing
> >>>>>list
> >>>>> maker-devel at box290.bluehost.com
> >>>>><mailto:maker-devel at box290.bluehost.com>
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> maker-devel mailing list
> >>>>> maker-devel at box290.bluehost.com
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>
> >>>
> >>>
> >
> >
>
>
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From carsonhh at gmail.com  Thu Jul 11 05:37:13 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:37:13 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
Message-ID: <CE0410D8.6E4A%carsonhh@gmail.com>

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to
cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks,
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something
>like trinity to assemble the reads and supply them to the est= option in
>fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>





From carsonhh at gmail.com  Thu Jul 11 05:44:07 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:44:07 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <CE04120C.6E55%carsonhh@gmail.com>

You next put the entire JBrowse directory into the /var/www/html/ directory
or wherever you have apache set up to load from (if it's not already there).
Then it will be accessible as a webpage (browser is inside the JBrowse
directory).

Example /var/www/html/Jbrowse/
Webpage --> http://localhost/Jbrowse/

--Carson

From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:10 AM
To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser, but
that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Hi Val,
> 
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
> 
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
> 
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
> 
> Could you test it out and let me know how it goes.
> 
> Thanks,
> Carson
> 
> 
> 
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>> >>you're doing with that, but it appears to be a fork of a very old
>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>> >>forked copy.
>>> >>
>>> >>If what you're trying to accomplish is to add some custom styles, the
>>> >>best way to do that would be to do one of:
>>> >>
>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>> <http://flatfile-to-json.pl>  command
>>> >>line
>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>> >>   (containing only your custom feature styles!)
>>> >>* add all of the custom styles to the trackList.json as a
>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>> >>
>>> >>
>>> >>Robert Buels
>>> >>Lead Developer
>>> >>JBrowse - http://jbrowse.org
>>> >>
>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>> >>> I think you may not have it set up right.  If you run the example data,
>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>> >>> information, but nothing displays.  I think the problem is with the
>>>> >>>maker
>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>> >>>get
>>>> >>> your feedback.
>>>> >>>
>>>> >>> Thanks,
>>>> >>> Carson
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>> >>>
>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>> >>>>access),
>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>> >>>>of
>>>>> >>>> 'no track information'.
>>>>> >>>>
>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>> >>>>
>>>>> >>>>
>>>>> >>>> Robert Buels
>>>>> >>>> Lead Developer
>>>>> >>>> JBrowse - http://jbrowse.org
>>>>> >>>>
>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>> >>>>>will
>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>> currently
>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>> >>>>> have it working with whatever the most current repository is if you
>>>>>> >>>>>were
>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>> Jbrowse's
>>>>>> >>>>>own
>>>>>> >>>>> loader (tutorial here -->
>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>> generated
>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>> >>>>>doing.
>>>>>> >>>>>
>>>>>> >>>>> Thanks,
>>>>>> >>>>> Carson
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>> >>>>>
>>>>>> >>>>> Hi Maker team,
>>>>>> >>>>>
>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>> >>>>> getting this error for each contig:
>>>>>> >>>>>
>>>>>> >>>>> ERROR: No track information for source
>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>> >>>>>
>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>> >>>>>
>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>> >>>>>you!
>>>>>> >>>>>
>>>>>> >>>>> Best,
>>>>>> >>>>> Val
>>>>>> >>>>> _______________________________________________ maker-devel mailing
>>>>>> >>>>>list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> maker-devel mailing list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>> >
>> >
> 



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From vwong at umn.edu  Thu Jul 11 11:58:42 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 12:58:42 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE04120C.6E55%carsonhh@gmail.com>
References: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
	<CE04120C.6E55%carsonhh@gmail.com>
Message-ID: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl is doing the job.  Is it possible to merge these tracks
into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You next put the entire JBrowse directory into the /var/www/html/
> directory or wherever you have apache set up to load from (if it's not
> already there).  Then it will be accessible as a webpage (browser is inside
> the JBrowse directory).
>
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
>
> --Carson
>
> From: V Wong <vwong at umn.edu>
> Reply-To: <vwong at umn.edu>
> Date: Thursday, July 11, 2013 1:10 AM
> To: Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc: <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Thanks!  I followed your instructions, and maker2jbrowse, and it
> successfully populated the ../JBrowse/data/tracks directory with
> RepeatMasker, Augustus, and GeneMark predictions.
>
> I'm not entirely sure how to get these numerous tracks into the browser,
> but that may be something to work out with JBrowse rather than Maker.
>
> Best,
> Val
>
>
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Hi Val,
>>
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>>
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>>
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl.
>>
>> Could you test it out and let me know how it goes.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>>
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable
>> from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>> >>you're doing with that, but it appears to be a fork of a very old
>> >>JBrowse main css file.  If that's overriding or being copied over the
>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>> >>forked copy.
>> >>
>> >>If what you're trying to accomplish is to add some custom styles, the
>> >>best way to do that would be to do one of:
>> >>
>> >>* add just your custom feature styles on the flatfile-to-json.plcommand
>> >>line
>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>> >>   (containing only your custom feature styles!)
>> >>* add all of the custom styles to the trackList.json as a
>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>> >>
>> >>
>> >>Robert Buels
>> >>Lead Developer
>> >>JBrowse - http://jbrowse.org
>> >>
>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> >>> I think you may not have it set up right.  If you run the example
>> data,
>> >>> you can then use that.  For me it populates the JSON data tracks
>> >>> information, but nothing displays.  I think the problem is with the
>> >>>maker
>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>> >>>get
>> >>> your feedback.
>> >>>
>> >>> Thanks,
>> >>> Carson
>> >>>
>> >>>
>> >>>
>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >>>
>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>> >>>>access),
>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>> >>>> parsing the MAKER datastore index, leading to the script complaining
>> >>>>of
>> >>>> 'no track information'.
>> >>>>
>> >>>> This would probably be easier for a MAKER developer to look into.
>> >>>>
>> >>>>
>> >>>> Robert Buels
>> >>>> Lead Developer
>> >>>> JBrowse - http://jbrowse.org
>> >>>>
>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> >>>>> which is not backwards compatible with other Jbrowse versions), as a
>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>> >>>>>will
>> >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
>> can
>> >>>>> have it working with whatever the most current repository is if you
>> >>>>>were
>> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>> >>>>>own
>> >>>>> loader (tutorial here -->
>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>> >>>>>    Of course this tutorial is also likely to be somewhat out of date
>> >>>>> :-( But the 2013 version is supposed to be up and running as part of
>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> >>>>> data for the tutorial, so it should be relevant to what you are
>> >>>>>doing.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Carson
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>> >>>>> To: <maker-devel at yandell-lab.org
>> >>>>><mailto:maker-devel at yandell-lab.org>>
>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>> >>>>>
>> >>>>> Hi Maker team,
>> >>>>>
>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> >>>>> server, using the -d option for the index.log file.  However, I am
>> >>>>> getting this error for each contig:
>> >>>>>
>> >>>>> ERROR: No track information for source
>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> >>>>>
>> >>>>> Looking at the perl script, the file locations are getting read, but
>> >>>>> then the tracks aren't getting found in the hash of commands.
>> >>>>>
>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>> >>>>>you!
>> >>>>>
>> >>>>> Best,
>> >>>>> Val
>> >>>>> _______________________________________________ maker-devel mailing
>> >>>>>list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>><mailto:maker-devel at box290.bluehost.com>
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> maker-devel mailing list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>
>> >>>
>> >>>
>> >
>> >
>>
>>
>
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From carsonhh at gmail.com  Thu Jul 11 12:23:04 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 14:23:04 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>
Message-ID: <CE046E99.6E7F%carsonhh@gmail.com>

If you have a previous Jbrowse with already populated tracks you can just,
run maker2jbrowse in that directory instead of the new Jbrowse directory,
then the maker features will be added there.  Make a backup copy of the
directory before you do this of course incase you need to roll back the
changes.

Alternatively you will have to add those to the new Jbrowse directory using
bin/bam-to-json.pl and following the instructions here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data

I guess Robert can chime in here as well, since we have now moved outside of
MAKER scripts and fully into JBrowse.

--Carson


From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:58 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Ignazio Carbone <icarbon at ncsu.edu>, <maker-devel at yandell-lab.org>,
Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl <http://add-track-json.pl>  is doing the job.  Is it
possible to merge these tracks into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:
> You next put the entire JBrowse directory into the /var/www/html/ directory or
> wherever you have apache set up to load from (if it's not already there).
> Then it will be accessible as a webpage (browser is inside the JBrowse
> directory).
> 
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
> 
> --Carson
> 
> From:  V Wong <vwong at umn.edu>
> Reply-To:  <vwong at umn.edu>
> Date:  Thursday, July 11, 2013 1:10 AM
> To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
> 
> Subject:  Re: [maker-devel] maker2jbrowse implementation
> 
> Hi Carson,
> 
> Thanks!  I followed your instructions, and maker2jbrowse, and it successfully
> populated the ../JBrowse/data/tracks directory with RepeatMasker, Augustus,
> and GeneMark predictions.
> 
> I'm not entirely sure how to get these numerous tracks into the browser, but
> that may be something to work out with JBrowse rather than Maker.
> 
> Best,
> Val
> 
> 
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> Hi Val,
>> 
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>> 
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>> 
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
>> 
>> Could you test it out and let me know how it goes.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>>> >documentation had you modify the genome.css file to create your own
>>> >tracks.  Version 1.2.1 looks like it is the last version where the
>>> >genome.css file that maker provided works. I can still get simple test
>>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>>> >But I need to fix some things, because they are all indistinguishable from
>>> >each other (so it is not the desired behavior).
>>> >
>>> >Indepent of that issue though, to regenerate the original error, I do the
>>> >following -->
>>> >    maker2jbrowse
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >    ERROR: No track information for source
>>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>>> >
>>> >Basically you are missing the '-d' flag (whiteout that the script is
>>> >expecting a list of GFF3 files).
>>> >
>>> >So this works -->
>>> >    maker2jbrowse -d
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >
>>> >
>>> >Of course all tracks look the same though per the original issue I
>>> >mentioned.
>>> >
>>> >Thanks,
>>> >Carson
>>> >
>>> >
>>> >
>>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>>> >1.3,
>>> >
>>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>>> >
>>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>>> >>you're doing with that, but it appears to be a fork of a very old
>>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>>> >>forked copy.
>>>> >>
>>>> >>If what you're trying to accomplish is to add some custom styles, the
>>>> >>best way to do that would be to do one of:
>>>> >>
>>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>>> <http://flatfile-to-json.pl>  command
>>>> >>line
>>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>>> >>   (containing only your custom feature styles!)
>>>> >>* add all of the custom styles to the trackList.json as a
>>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>>> >>
>>>> >>
>>>> >>Robert Buels
>>>> >>Lead Developer
>>>> >>JBrowse - http://jbrowse.org
>>>> >>
>>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>>> >>> I think you may not have it set up right.  If you run the example
>>>>> data,
>>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>>> >>> information, but nothing displays.  I think the problem is with the
>>>>> >>>maker
>>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>>> >>>get
>>>>> >>> your feedback.
>>>>> >>>
>>>>> >>> Thanks,
>>>>> >>> Carson
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>>> >>>
>>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>>> >>>>access),
>>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>>> >>>>of
>>>>>> >>>> 'no track information'.
>>>>>> >>>>
>>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>> Robert Buels
>>>>>> >>>> Lead Developer
>>>>>> >>>> JBrowse - http://jbrowse.org
>>>>>> >>>>
>>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse
(and
>>>>>>> >>>>>will
>>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>>> currently
>>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>>> >>>>> have it working with whatever the most current repository is if
you
>>>>>>> >>>>>were
>>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>>> Jbrowse's
>>>>>>> >>>>>own
>>>>>>> >>>>> loader (tutorial here -->
>>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>>> generated
>>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>>> >>>>>doing.
>>>>>>> >>>>>
>>>>>>> >>>>> Thanks,
>>>>>>> >>>>> Carson
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>>> >>>>>
>>>>>>> >>>>> Hi Maker team,
>>>>>>> >>>>>
>>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>>> >>>>> getting this error for each contig:
>>>>>>> >>>>>
>>>>>>> >>>>> ERROR: No track information for source
>>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>>> >>>>>
>>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>>> >>>>>
>>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>>> >>>>>you!
>>>>>>> >>>>>
>>>>>>> >>>>> Best,
>>>>>>> >>>>> Val
>>>>>>> >>>>> _______________________________________________ maker-devel
>>>>>>> mailing
>>>>>>> >>>>>list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> _______________________________________________
>>>>>>> >>>>> maker-devel mailing list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>> >
>>> >
>> 
> 



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From rbuels at gmail.com  Thu Jul 11 12:27:10 2013
From: rbuels at gmail.com (Robert Buels)
Date: Thu, 11 Jul 2013 14:27:10 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE046E99.6E7F%carsonhh@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
Message-ID: <51DEF8FE.2000907@gmail.com>

These days, it's better to use direct BAM access.  bam-to-json.pl still 
works, but the direct BAM access is much better.

See 
http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/11/2013 02:23 PM, Carson Holt wrote:
> If you have a previous Jbrowse with already populated tracks you can
> just, run maker2jbrowse in that directory instead of the new Jbrowse
> directory, then the maker features will be added there.  Make a backup
> copy of the directory before you do this of course incase you need to
> roll back the changes.
>
> Alternatively you will have to add those to the new Jbrowse directory
> using bin/bam-to-json.pl and following the instructions here -->
> http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data
>
> I guess Robert can chime in here as well, since we have now moved
> outside of MAKER scripts and fully into JBrowse.
>
> --Carson
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Thursday, July 11, 2013 1:58 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>,
> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
> directory, the Maker tracks are now on view.
>
> However, I'm having some trouble getting our older tracks (bam
> alignments and coverage tracks) into the same browser.  Neither 1.
> copying and pasting the tracks from the previous trackList.json to the
> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
> doing the job.  Is it possible to merge these tracks into one browser?
>
> Best,
> Val
>
>
> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
> <mailto:carsonhh at gmail.com>> wrote:
>
>     You next put the entire JBrowse directory into the /var/www/html/
>     directory or wherever you have apache set up to load from (if it's
>     not already there).  Then it will be accessible as a webpage
>     (browser is inside the JBrowse directory).
>
>     Example /var/www/html/Jbrowse/
>     Webpage --> http://localhost/Jbrowse/
>
>     --Carson
>
>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Date: Thursday, July 11, 2013 1:10 AM
>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>     Cc: <maker-devel at yandell-lab.org
>     <mailto:maker-devel at yandell-lab.org>>, Robert Buels
>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>
>     Subject: Re: [maker-devel] maker2jbrowse implementation
>
>     Hi Carson,
>
>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>     successfully populated the ../JBrowse/data/tracks directory with
>     RepeatMasker, Augustus, and GeneMark predictions.
>
>     I'm not entirely sure how to get these numerous tracks into the
>     browser, but that may be something to work out with JBrowse rather
>     than Maker.
>
>     Best,
>     Val
>
>
>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>     <mailto:carsonhh at gmail.com>> wrote:
>
>         Hi Val,
>
>         I've attached new files for you to test.  These will be bundled
>         in the
>         next maker release pending successful tests (~ 1 week).
>
>         Instructions:
>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>         .../maker/src/bin/ directory (this is just to ensure you don't
>         accidentally overwrite it if you reinstall at any time).
>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>         3. You must be in the jbrowse installation directory when running
>         maker2jbrowse.  Run the script with the -d flag and the
>         datastore index
>         file.
>
>         This new version will assign colors by copying maker.css to the
>         jbrowse
>         installation as apposed to replacing the genome.css file, and it
>         will also
>         edit the genome.css file to add the import call for maker.css.  In
>         addition I have updated command line flags in the wrapper to do
>         what is
>         currently expected by flatfile-to-json.pl
>         <http://flatfile-to-json.pl>.
>
>         Could you test it out and let me know how it goes.
>
>         Thanks,
>         Carson
>
>
>
>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>         <mailto:carsonhh at gmail.com>> wrote:
>
>         >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>         >documentation had you modify the genome.css file to create your own
>         >tracks.  Version 1.2.1 looks like it is the last version where the
>         >genome.css file that maker provided works. I can still get simple test
>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>         >But I need to fix some things, because they are all indistinguishable from
>         >each other (so it is not the desired behavior).
>         >
>         >Indepent of that issue though, to regenerate the original error, I do the
>         >following -->
>         >    maker2jbrowse
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >    ERROR: No track information for source
>         >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>         >
>         >Basically you are missing the '-d' flag (whiteout that the script is
>         >expecting a list of GFF3 files).
>         >
>         >So this works -->
>         >    maker2jbrowse -d
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >
>         >
>         >Of course all tracks look the same though per the original issue I
>         >mentioned.
>         >
>         >Thanks,
>         >Carson
>         >
>         >
>         >
>         >Some versions of Jbrowse still load fine with the script as is Jbrowse
>         >1.3,
>         >
>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >
>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>         >>you're doing with that, but it appears to be a fork of a very old
>         >>JBrowse main css file.  If that's overriding or being copied over the
>         >>JBrowse released CSS, it will break pretty much everything.  It would be
>         >>like me randomly replacing one of MAKER's Perl modules with my own old
>         >>forked copy.
>         >>
>         >>If what you're trying to accomplish is to add some custom styles, the
>         >>best way to do that would be to do one of:
>         >>
>         >>* add just your custom feature styles on theflatfile-to-json.pl <http://flatfile-to-json.pl> command
>         >>line
>         >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>         >>   (containing only your custom feature styles!)
>         >>* add all of the custom styles to the trackList.json as a
>         >>   string: "css": "string { of: lots and lots of; css: properties; }"
>         >>
>         >>
>         >>Robert Buels
>         >>Lead Developer
>         >>JBrowse -http://jbrowse.org
>         >>
>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>         >>> I think you may not have it set up right.  If you run the example data,
>         >>> you can then use that.  For me it populates the JSON data tracks
>         >>> information, but nothing displays.  I think the problem is with the
>         >>>maker
>         >>> genome.css.  It is very out of date.  I'll do some work on it and then
>         >>>get
>         >>> your feedback.
>         >>>
>         >>> Thanks,
>         >>> Carson
>         >>>
>         >>>
>         >>>
>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >>>
>         >>>> After looking at the maker2jbrowse source (thanks for giving me
>         >>>>access),
>         >>>> there seems to be some kind of problem with the way maker2jbrowse is
>         >>>> parsing the MAKER datastore index, leading to the script complaining
>         >>>>of
>         >>>> 'no track information'.
>         >>>>
>         >>>> This would probably be easier for a MAKER developer to look into.
>         >>>>
>         >>>>
>         >>>> Robert Buels
>         >>>> Lead Developer
>         >>>> JBrowse -http://jbrowse.org
>         >>>>
>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>         >>>>> which is not backwards compatible with other Jbrowse versions), as a
>         >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>         >>>>>will
>         >>>>> not work with all versions).  I'm not sure if the script is currently
>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>         >>>>> have it working with whatever the most current repository is if you
>         >>>>>were
>         >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>         >>>>>own
>         >>>>> loader (tutorial here -->
>         >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>         >>>>>    Of course this tutorial is also likely to be somewhat out of date
>         >>>>> :-( But the 2013 version is supposed to be up and running as part of
>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>         >>>>> data for the tutorial, so it should be relevant to what you are
>         >>>>>doing.
>         >>>>>
>         >>>>> Thanks,
>         >>>>> Carson
>         >>>>>
>         >>>>>
>         >>>>>
>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>         >>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>         >>>>><mailto:maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>>
>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>         >>>>>
>         >>>>> Hi Maker team,
>         >>>>>
>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>         >>>>> server, using the -d option for the index.log file.  However, I am
>         >>>>> getting this error for each contig:
>         >>>>>
>         >>>>> ERROR: No track information for source
>         >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>         >>>>>
>         >>>>> Looking at the perl script, the file locations are getting read, but
>         >>>>> then the tracks aren't getting found in the hash of commands.
>         >>>>>
>         >>>>> Any advice for getting past this will be most appreciated.  Thank
>         >>>>>you!
>         >>>>>
>         >>>>> Best,
>         >>>>> Val
>         >>>>> _______________________________________________ maker-devel mailing
>         >>>>>list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>><mailto:maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>>>
>         >>>>> _______________________________________________
>         >>>>> maker-devel mailing list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>
>         >>>
>         >>>
>         >
>         >
>
>
>



From yuharas at takara-bio.co.jp  Fri Jul 12 00:19:39 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Fri, 12 Jul 2013 15:19:39 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE0410D8.6E4A%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
	<CE0410D8.6E4A%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3F37@TKREXMB3.central.takara.co.jp>

I understand?
Thank you for your useful information.

Satoshi

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 8:37 PM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something 
>like trinity to assemble the reads and supply them to the est= option 
>in fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" 
><yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for 
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>





From Carson.Holt at oicr.on.ca  Fri Jul 12 07:34:06 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Fri, 12 Jul 2013 13:34:06 +0000
Subject: [maker-devel] failed contigs error report
In-Reply-To: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>
Message-ID: <CE05726A.6EBE%carson.holt@oicr.on.ca>

Could you pack up and send me this directory (use dropbox if they are too
big) -->
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.m
aker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_co
ntig_12295/

And this file -->
AG1-IA_China_Prot.fasta

--Carson


On 7/12/13 6:47 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have collected my failed contigs and I have rerun them in Maker v. 2.28
>but they have failed again. I don't know what the error codes mean but I
>have attached the run log for your review. Any help would be appreciated.
>
>Cheers
>Ian
>
>
>




From ianmisner at my.uri.edu  Fri Jul 12 04:47:39 2013
From: ianmisner at my.uri.edu (Ian Misner)
Date: Fri, 12 Jul 2013 06:47:39 -0400
Subject: [maker-devel] failed contigs error report
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
	<CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>

Hello,

I have collected my failed contigs and I have rerun them in Maker v. 2.28 but they have failed again. I don't know what the error codes mean but I have attached the run log for your review. Any help would be appreciated. 

Cheers
Ian

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From vwong at umn.edu  Mon Jul 15 11:57:30 2013
From: vwong at umn.edu (V Wong)
Date: Mon, 15 Jul 2013 12:57:30 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51DEF8FE.2000907@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
	<51DEF8FE.2000907@gmail.com>
Message-ID: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>

Hi Carson,

I tried running maker2jbrowse in the browser directory with existing
tracks, but the script expects to be run in the JBrowse directory and
printed this error:

FATAL: Can not find ./bin/flatfile-to-json.pl

Make sure you are running inside the JBrowse directory


Hi Robert,

I tried adding an Alignment2 track in the format of the example to the
browser with Maker tracks (those get viewed fine), but I am getting the
error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
though the specified file is in that location.


Thank you both for your continued aid.

Since this is departing Maker for strictly JBrowse territory, would it be
more appropriate to move to the JBrowse list?

Best,

Val


On Thu, Jul 11, 2013 at 1:27 PM, Robert Buels <rbuels at gmail.com> wrote:

> These days, it's better to use direct BAM access.  bam-to-json.pl still
> works, but the direct BAM access is much better.
>
> See http://gmod.org/wiki/JBrowse_**Configuration_Guide#Alignment_**
> Tracks_.28BAM.29<http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29>
>
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 07/11/2013 02:23 PM, Carson Holt wrote:
>
>> If you have a previous Jbrowse with already populated tracks you can
>> just, run maker2jbrowse in that directory instead of the new Jbrowse
>> directory, then the maker features will be added there.  Make a backup
>> copy of the directory before you do this of course incase you need to
>> roll back the changes.
>>
>> Alternatively you will have to add those to the new Jbrowse directory
>> using bin/bam-to-json.pl and following the instructions here -->
>> http://gmod.org/wiki/JBrowse_**Tutorial_2012#BAM_data<http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data>
>>
>> I guess Robert can chime in here as well, since we have now moved
>> outside of MAKER scripts and fully into JBrowse.
>>
>> --Carson
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Thursday, July 11, 2013 1:58 PM
>> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
>> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-**lab.org<maker-devel at yandell-lab.org>
>> >>,
>> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>> Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>> Hi Carson,
>>
>> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
>> directory, the Maker tracks are now on view.
>>
>> However, I'm having some trouble getting our older tracks (bam
>> alignments and coverage tracks) into the same browser.  Neither 1.
>> copying and pasting the tracks from the previous trackList.json to the
>> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
>>
>> doing the job.  Is it possible to merge these tracks into one browser?
>>
>> Best,
>> Val
>>
>>
>> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
>> <mailto:carsonhh at gmail.com>> wrote:
>>
>>     You next put the entire JBrowse directory into the /var/www/html/
>>     directory or wherever you have apache set up to load from (if it's
>>     not already there).  Then it will be accessible as a webpage
>>     (browser is inside the JBrowse directory).
>>
>>     Example /var/www/html/Jbrowse/
>>     Webpage --> http://localhost/Jbrowse/
>>
>>     --Carson
>>
>>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Date: Thursday, July 11, 2013 1:10 AM
>>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>>     Cc: <maker-devel at yandell-lab.org
>>     <mailto:maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>,
>> Robert Buels
>>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>>
>>     Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>>     Hi Carson,
>>
>>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>>     successfully populated the ../JBrowse/data/tracks directory with
>>     RepeatMasker, Augustus, and GeneMark predictions.
>>
>>     I'm not entirely sure how to get these numerous tracks into the
>>     browser, but that may be something to work out with JBrowse rather
>>     than Maker.
>>
>>     Best,
>>     Val
>>
>>
>>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>>     <mailto:carsonhh at gmail.com>> wrote:
>>
>>         Hi Val,
>>
>>         I've attached new files for you to test.  These will be bundled
>>         in the
>>         next maker release pending successful tests (~ 1 week).
>>
>>         Instructions:
>>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>>         .../maker/src/bin/ directory (this is just to ensure you don't
>>         accidentally overwrite it if you reinstall at any time).
>>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>>         3. You must be in the jbrowse installation directory when running
>>         maker2jbrowse.  Run the script with the -d flag and the
>>         datastore index
>>         file.
>>
>>         This new version will assign colors by copying maker.css to the
>>         jbrowse
>>         installation as apposed to replacing the genome.css file, and it
>>         will also
>>         edit the genome.css file to add the import call for maker.css.  In
>>         addition I have updated command line flags in the wrapper to do
>>         what is
>>         currently expected by flatfile-to-json.pl
>>         <http://flatfile-to-json.pl>.
>>
>>
>>         Could you test it out and let me know how it goes.
>>
>>         Thanks,
>>         Carson
>>
>>
>>
>>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>>         <mailto:carsonhh at gmail.com>> wrote:
>>
>>         >Like I said that css file is ~1 year old.  Once upon a time the
>> Jbrowse
>>         >documentation had you modify the genome.css file to create your
>> own
>>         >tracks.  Version 1.2.1 looks like it is the last version where
>> the
>>         >genome.css file that maker provided works. I can still get
>> simple test
>>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse
>> script.
>>         >But I need to fix some things, because they are all
>> indistinguishable from
>>         >each other (so it is not the desired behavior).
>>         >
>>         >Indepent of that issue though, to regenerate the original error,
>> I do the
>>         >following -->
>>         >    maker2jbrowse
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >    ERROR: No track information for source
>>         >'dpp_contig_datastore/05/1F/**contig-dpp-500-500/'
>>         >
>>         >Basically you are missing the '-d' flag (whiteout that the
>> script is
>>         >expecting a list of GFF3 files).
>>         >
>>         >So this works -->
>>         >    maker2jbrowse -d
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >
>>         >
>>         >Of course all tracks look the same though per the original issue
>> I
>>         >mentioned.
>>         >
>>         >Thanks,
>>         >Carson
>>         >
>>         >
>>         >
>>         >Some versions of Jbrowse still load fine with the script as is
>> Jbrowse
>>         >1.3,
>>         >
>>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >
>>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not
>> sure what
>>         >>you're doing with that, but it appears to be a fork of a very
>> old
>>         >>JBrowse main css file.  If that's overriding or being copied
>> over the
>>         >>JBrowse released CSS, it will break pretty much everything.  It
>> would be
>>         >>like me randomly replacing one of MAKER's Perl modules with my
>> own old
>>         >>forked copy.
>>         >>
>>         >>If what you're trying to accomplish is to add some custom
>> styles, the
>>         >>best way to do that would be to do one of:
>>         >>
>>         >>* add just your custom feature styles on theflatfile-to-json.pl<
>> http://flatfile-to-json.pl> command
>>
>>         >>line
>>         >>* add a "css": { "url": "http://url/of/your/custom.css**" } to
>> the
>>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>>         >>   (containing only your custom feature styles!)
>>         >>* add all of the custom styles to the trackList.json as a
>>         >>   string: "css": "string { of: lots and lots of; css:
>> properties; }"
>>         >>
>>         >>
>>         >>Robert Buels
>>         >>Lead Developer
>>         >>JBrowse -http://jbrowse.org
>>
>>         >>
>>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>         >>> I think you may not have it set up right.  If you run the
>> example data,
>>         >>> you can then use that.  For me it populates the JSON data
>> tracks
>>         >>> information, but nothing displays.  I think the problem is
>> with the
>>         >>>maker
>>         >>> genome.css.  It is very out of date.  I'll do some work on it
>> and then
>>         >>>get
>>         >>> your feedback.
>>         >>>
>>         >>> Thanks,
>>         >>> Carson
>>         >>>
>>         >>>
>>         >>>
>>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >>>
>>         >>>> After looking at the maker2jbrowse source (thanks for giving
>> me
>>         >>>>access),
>>         >>>> there seems to be some kind of problem with the way
>> maker2jbrowse is
>>         >>>> parsing the MAKER datastore index, leading to the script
>> complaining
>>         >>>>of
>>         >>>> 'no track information'.
>>         >>>>
>>         >>>> This would probably be easier for a MAKER developer to look
>> into.
>>         >>>>
>>         >>>>
>>         >>>> Robert Buels
>>         >>>> Lead Developer
>>         >>>> JBrowse -http://jbrowse.org
>>
>>         >>>>
>>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration
>> (much of
>>         >>>>> which is not backwards compatible with other Jbrowse
>> versions), as a
>>         >>>>> result the script maker2jbrowse has had to evolve with
>> Jbrowse (and
>>         >>>>>will
>>         >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing
>> behind). I can
>>         >>>>> have it working with whatever the most current repository
>> is if you
>>         >>>>>were
>>         >>>>> to give me a week, or you can try loading the GFF3's using
>> Jbrowse's
>>         >>>>>own
>>         >>>>> loader (tutorial here -->
>>         >>>>>http://gmod.org/wiki/**JBrowse_Tutorial_2012<http://gmod.org/wiki/JBrowse_Tutorial_2012>
>> ).
>>         >>>>>    Of course this tutorial is also likely to be somewhat
>> out of date
>>         >>>>> :-( But the 2013 version is supposed to be up and running
>> as part of
>>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>> generated
>>         >>>>> data for the tutorial, so it should be relevant to what you
>> are
>>         >>>>>doing.
>>         >>>>>
>>         >>>>> Thanks,
>>         >>>>> Carson
>>         >>>>>
>>         >>>>>
>>         >>>>>
>>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>         >>>>> To: <maker-devel at yandell-lab.org <mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>
>>         >>>>><mailto:maker-devel@**yandell-lab.org<maker-devel at yandell-lab.org><mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>>
>>
>>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>         >>>>>
>>         >>>>> Hi Maker team,
>>         >>>>>
>>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3)
>> on our
>>         >>>>> server, using the -d option for the index.log file.
>>  However, I am
>>         >>>>> getting this error for each contig:
>>         >>>>>
>>         >>>>> ERROR: No track information for source
>>         >>>>> 'AK_assembly_datastore/22/D4/**AK_contig_1/'
>>         >>>>>
>>         >>>>> Looking at the perl script, the file locations are getting
>> read, but
>>         >>>>> then the tracks aren't getting found in the hash of
>> commands.
>>         >>>>>
>>         >>>>> Any advice for getting past this will be most appreciated.
>>  Thank
>>         >>>>>you!
>>         >>>>>
>>         >>>>> Best,
>>         >>>>> Val
>>         >>>>> ______________________________**_________________
>> maker-devel mailing
>>         >>>>>list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>><mailto:maker-devel@**box290.bluehost.com<maker-devel at box290.bluehost.com>
>>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >>
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>>>
>>         >>>>> ______________________________**_________________
>>         >>>>> maker-devel mailing list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>
>>         >>>
>>         >>>
>>         >
>>         >
>>
>>
>>
>>
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From rbuels at gmail.com  Mon Jul 15 12:54:58 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 15 Jul 2013 14:54:58 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
Message-ID: <51E44582.9020100@gmail.com>

On 07/15/2013 01:57 PM, V Wong wrote:
> I tried adding an Alignment2 track in the format of the example to the
> browser with Maker tracks (those get viewed fine), but I am getting the
> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
> though the specified file is in that location.

If you visit that URL in your browser, is the bai file really there?

If so, is the BAI file on a different server from the one you're running 
JBrowse on?  If so, you'll need to enable CORS on the server for the BAI 
and BAM files.

Rob



From Michael.Li3 at AGR.GC.CA  Thu Jul 18 13:06:38 2013
From: Michael.Li3 at AGR.GC.CA (Li, Michael)
Date: Thu, 18 Jul 2013 19:06:38 +0000
Subject: [maker-devel] InterProScan v5
Message-ID: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for users. However, I noticed that maker's iprscan_batch, iprscan_wrap, ipr_update_gff and iprscan2gff3 are not compatible with this new version of IPR. Is there a workaround available or is the script easy to modify to suit the new version?
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From carsonhh at gmail.com  Thu Jul 18 13:18:20 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 18 Jul 2013 15:18:20 -0400
Subject: [maker-devel] InterProScan v5
In-Reply-To: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>
Message-ID: <CE0DB539.77E1%carsonhh@gmail.com>

All those tools were written for InterProScan 4.  We have plans to update
everything for InterProScan 5 sometime in the near future. Some will have to
be dropped or rewritten completely, while other like  ipr_update_gff and
iprscan2gff3 are both relatively simple and I could probably have those
included with the next MAKER release (current release is 2.28).  That would
be about 3 weeks from now.

--Carson



From:  "Li, Michael" <Michael.Li3 at AGR.GC.CA>
Date:  Thursday, July 18, 2013 3:06 PM
To:  "'maker-devel at yandell-lab.org'" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] InterProScan v5

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for
users. However, I noticed that maker?s iprscan_batch, iprscan_wrap,
ipr_update_gff and iprscan2gff3 are not compatible with this new version of
IPR. Is there a workaround available or is the script easy to modify to suit
the new version?
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From vwong at umn.edu  Fri Jul 19 15:36:03 2013
From: vwong at umn.edu (V Wong)
Date: Fri, 19 Jul 2013 17:36:03 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51E44582.9020100@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
	<51E44582.9020100@gmail.com>
Message-ID: <CAEi2voasDqTHLEe00+JDUgWgav-BYJuM+fPSAbK5ysZCKj6VTw@mail.gmail.com>

Ah, I just had some syntax inconsistencies between the file locations on
the server and the path for the web browser.  Thank you Rob!

Best,
Val


On Mon, Jul 15, 2013 at 2:54 PM, Robert Buels <rbuels at gmail.com> wrote:

> On 07/15/2013 01:57 PM, V Wong wrote:
>
>> I tried adding an Alignment2 track in the format of the example to the
>> browser with Maker tracks (those get viewed fine), but I am getting the
>> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
>> though the specified file is in that location.
>>
>
> If you visit that URL in your browser, is the bai file really there?
>
> If so, is the BAI file on a different server from the one you're running
> JBrowse on?  If so, you'll need to enable CORS on the server for the BAI
> and BAM files.
>
> Rob
>
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From jmdoyle at purdue.edu  Sun Jul 21 07:44:26 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Sun, 21 Jul 2013 09:44:26 -0400 (EDT)
Subject: [maker-devel] altest without MPI?
In-Reply-To: <1806377131.45449.1371745335968.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>

I just wanted to check in and say that this strategy worked really nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with protein2genome and my contigs greater than 1200000 bases.  Each of the training runs took less than 4 hours.  My final run with all my contigs (and altest) took about 5 and 1/2 days.  Not bad!   

----- Original Message -----
From: Carson Holt <carsonhh at gmail.com>
To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
Subject: Re: [maker-devel] altest without MPI?

The throughput is based on contig length, so long contigs will take longer
than short contigs.  Any contig less than 10kb is mostly useless for
annotation purposes (so you can filter those from your 800,000 right
away). Take your contigs that finish, and sum up their length to get a
better estimate of how long it will take to complete running.  Most
genomes can complete in a few days an a multi-core machine.  Bigger
genomes or bigger datasets take longer.  (note that altest evidence takes
3-4x longer to align than proteins).

The advantage of proteins is that the species do not have to be closely
related.  Nucleotide sequence diverges quickly and proteins slowly (that's
why proteins are used for phylogenetic trees).

A good strategy would be to get ~10Mb of sequence (use your longest
contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
protein2genome option to generate annotations.  Those annotations should
now be sufficient to train SNAP and Augustus.  Then you can finish by
running all your contigs with the same dataset (protein2genome now turned
off), use the newly trained snap and augustus files along with any altest
files you want to use. Note that the size of the dataset will determine
the total run time.

To get things to run faster, you can also run on your university's
computer cluster (then you will have hundreds of cpus available to you).
The purdue cluster supports MPI and with 30-50 cpus you could annotate
even large genomes in a reasonable time.  Alternatively you can request a
startup account at XSEDE, an NFS funded computer resource open to all US
institutions.  A startup allocation with 50,000 cpu hours only takes 2
weeks to approve. You should request an allocation on the Lonestar cluster
if you go that route, it has 64,000 cpus. I was able to annotate the Maize
genome (which is a very large genome at over 2 gigabases).  I used an
abnormally large EST and protein datasets (~4 gigabases of evidence which
is much more than a normal annotation job), and it completed in under 3
hours on 2,100 cpus.

--Carson


On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hi Carson (and whoever else might be reading this!)
>
>Thanks so much, I think splitting the files up using fasta_tool will
>definitely move things along.  I did a trial version with altest this
>weekend, and seemed to be averaging about an hour a scaffold (with 1
>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>seem like a reasonable estimate of the time it should take to annotate
>one sequence?  Could I be missing something in my maker_opts file?
>
>Let me back up for just a minute and describe the project a little more
>generally.  As I mentioned before, we have no protein sequences or ESTs
>for our species of interest, which is an avian species.  I could
>potentially use proteins from chicken or turkey, but neither is closely
>related to our species.  Time is a bit of an issue... do you have any
>thoughts on how much time per scaffold it should take to annotate using
>protein2genome?  If chicken and turkey are not closely related, is it
>worth the time investment?
>
>Let me finish by saying I think MAKER is wonderful, and I really
>appreciate the discussions on this group.
>
>Best wishes, Jackie 






From carsonhh at gmail.com  Sun Jul 21 15:09:12 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 21 Jul 2013 17:09:12 -0400
Subject: [maker-devel] altest without MPI?
In-Reply-To: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE11C4D7.7990%carsonhh@gmail.com>

Glad I could help. If you come across anything else, just let us know.

Thanks,
Carson



On 7/21/13 9:44 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>I just wanted to check in and say that this strategy worked really
>nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with
>protein2genome and my contigs greater than 1200000 bases.  Each of the
>training runs took less than 4 hours.  My final run with all my contigs
>(and altest) took about 5 and 1/2 days.  Not bad!
>
>----- Original Message -----
>From: Carson Holt <carsonhh at gmail.com>
>To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
>Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
>Subject: Re: [maker-devel] altest without MPI?
>
>The throughput is based on contig length, so long contigs will take longer
>than short contigs.  Any contig less than 10kb is mostly useless for
>annotation purposes (so you can filter those from your 800,000 right
>away). Take your contigs that finish, and sum up their length to get a
>better estimate of how long it will take to complete running.  Most
>genomes can complete in a few days an a multi-core machine.  Bigger
>genomes or bigger datasets take longer.  (note that altest evidence takes
>3-4x longer to align than proteins).
>
>The advantage of proteins is that the species do not have to be closely
>related.  Nucleotide sequence diverges quickly and proteins slowly (that's
>why proteins are used for phylogenetic trees).
>
>A good strategy would be to get ~10Mb of sequence (use your longest
>contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
>protein2genome option to generate annotations.  Those annotations should
>now be sufficient to train SNAP and Augustus.  Then you can finish by
>running all your contigs with the same dataset (protein2genome now turned
>off), use the newly trained snap and augustus files along with any altest
>files you want to use. Note that the size of the dataset will determine
>the total run time.
>
>To get things to run faster, you can also run on your university's
>computer cluster (then you will have hundreds of cpus available to you).
>The purdue cluster supports MPI and with 30-50 cpus you could annotate
>even large genomes in a reasonable time.  Alternatively you can request a
>startup account at XSEDE, an NFS funded computer resource open to all US
>institutions.  A startup allocation with 50,000 cpu hours only takes 2
>weeks to approve. You should request an allocation on the Lonestar cluster
>if you go that route, it has 64,000 cpus. I was able to annotate the Maize
>genome (which is a very large genome at over 2 gigabases).  I used an
>abnormally large EST and protein datasets (~4 gigabases of evidence which
>is much more than a normal annotation job), and it completed in under 3
>hours on 2,100 cpus.
>
>--Carson
>
>
>On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:
>
>>Hi Carson (and whoever else might be reading this!)
>>
>>Thanks so much, I think splitting the files up using fasta_tool will
>>definitely move things along.  I did a trial version with altest this
>>weekend, and seemed to be averaging about an hour a scaffold (with 1
>>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>>seem like a reasonable estimate of the time it should take to annotate
>>one sequence?  Could I be missing something in my maker_opts file?
>>
>>Let me back up for just a minute and describe the project a little more
>>generally.  As I mentioned before, we have no protein sequences or ESTs
>>for our species of interest, which is an avian species.  I could
>>potentially use proteins from chicken or turkey, but neither is closely
>>related to our species.  Time is a bit of an issue... do you have any
>>thoughts on how much time per scaffold it should take to annotate using
>>protein2genome?  If chicken and turkey are not closely related, is it
>>worth the time investment?
>>
>>Let me finish by saying I think MAKER is wonderful, and I really
>>appreciate the discussions on this group.
>>
>>Best wishes, Jackie
>
>
>





From Carson.Holt at oicr.on.ca  Tue Jul 23 13:00:27 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 23 Jul 2013 19:00:27 +0000
Subject: [maker-devel] Fwd: about running MAKER
In-Reply-To: <CAMNfi+gSdTtfBHD7ipTFJ08jvL3UtpbH3q+gCG-N-J-vV+Vpow@mail.gmail.com>
Message-ID: <CE143780.7AD6%carson.holt@oicr.on.ca>

If the log is growing then it is still working.  The time it takes is a function of the evidence dataset, genome size, and gene density.  Is there any way, you could try starting a second maker process in the same directory with additional CPUs to get it to complete sooner (each process will detect each other and avoid overlapping on their work, so it will still get divided up efficiently).  Also if you combine the length of all finished contigs, you will get a better idea of how much run time is remaining (i.e. See if contigs remaining are short or long compared to most contigs in the assembly).

Thanks,
Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 23, 2013 1:12 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Thanks Carson,

gephy.transcripts.fa is 64406072
geph_AS_masked.fa is 296693827

The log is growing. It finished 21700 scaffolds. I think we have nearly 38149 scaffolds. Is that means the program running good?

Sincerely,
Yunxi



2013/7/22 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Nothing looks out of the ordinary.  How big is this file --> gephy.transcripts.fa
How big is this file --> geph_AS_masked.fa

Also is the STDERR log growing or is it frozen?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, July 22, 2013 12:24 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Sorry to bother you again. I ran the MAKER for like around two weeks, but it is still running now. I attached my control files. Can you help me to see if I set something wrong? I used the masked genome as my input, so I skipped the repeatmasker in maker. I think it should be faster. I ran this mpiexec -n 8 maker

I'm running another maker using unmasked data in 16 threads, so I ran this in 8. I already got 34G data for this. Because the time cost in running already out of schedule. I'm worry about something wrong in the setting.

Thank you.
Yunxi


2013/7/14 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson.


2013/7/14 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
I would use the same data to train both.

More information here --> https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J

--Carson

From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Friday, July 12, 2013 9:04 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

One more is when I train the SNAP and Augustus, should I do them in the same time with the est2genome and protein2genome, or do them separately? Thank you.


2013/7/12 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Hi Carson

The MAKER is running fine right now. I'm confusing about using the CEGMA with MAKER to train the SNAP and Augustus.

I'm running the MAKER from est2genome with protein2genome without using the result from CEGMA. I think the data I already enough for generating the hmm.

And I got the zff from the result of CEGMA, and I followed the link last time you gave me to generate the file for SNAP and Augustus.

I'm not that clear how to combine the hmm model from CEGMA and MAKER.

Thank you for your help.

Sincerely,
Yunxi


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I think I should better to use the default, in case it occurs an error after several days' running.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Some operations are not NFS safe (NFS behaves different than normal file systems).  So maker performs those operations in the temporary directory.  If you redirect those files to an NFS location, you may get errors (basically MAKER just dies).  It won't necessarily happen, but the warning lets you know that, if it fails then you should set TMP= somewhere else before trying again.

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 3:22 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got an error message about this:
ERROR: Temporary directory set to an NFS location.
TMP=/home/lin11/tmp
The temporary directory in MAKER is specifically for
operations that are not NFS-safe. You must set TMP
to a locally mounted directory such as /tmp or add
--ignore_nfs_tmp to the maker command line to
override this error message.

Does the MAKER need a big temporary file? Because our system temporary directory may not have that much space. If it does not need that big tmp file, I can set it back to default. Or I just ignore the error message?

Thank you.


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Anything from maker under the ~/perl5/ should be deleted.  MAKER should be self contained in its own directory.  Do 'rm ~/perl5/bin/*maker*'.  If you see anything else that is maker related there delete it as well.

Example:
.../maker/bin/
.../maker/lib/
.../maker/exe/

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 1:40 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I installed the new version of MAKER. But right now have a problem of running it. Because I was missing perl dependencies, I installed the perl local library. And then I tried to run maker, it will automatically go to the one in local library called ~/perl5/bin/maker. Do you know how to get rid of this path? I found this path in .bashrc : export PATH="/home/lin11/perl5/bin:$PATH". If that ok to delete it?

Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It's been stable enough that I could remove the beta tag (no major updates in 2 months).  In fact I'll go ahead and do that.

--Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:21 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Is that the 2.28 only have the beta version?


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I'll try then let you know.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You could just install it in a new directory (I.e. maker_2.28 rather than maker).  The 2.1 version more than 2 years old (lots of changes and improvements since then).

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:11 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson
I think I may need to update MAKER too. My version is 2.1. Is the new version of MAKER changed a lot? Because someone running MAKER on the server now, can I just update it instead of delete the old one then reinstall the new version?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
If you are using MAKER 2.28, and let it do the install for you it will install mpich2 from this location --> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz

The installation will be in the .../maker/exe/mpich2 directory.

Alternatively, if you do the installation yourself, all you have to do set a few flags during install configuration.
--> ./configure --prefix=$path --enable-shared
Set $path to the location where you want MPICH2 to be installed.
Then run 'make install'

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:59 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I think it installed the 1.3.1 version. Can I update it?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It should be installed under .../maker/exe/mpich2.  Having it under ~/perl5/exe/mpich2 is odd as maker should do that.

Type 'which mpiexec' to see if there is another mpiexec installed somewhere.  Also run 'mpiexec --version'.  What does it give?  I ask because the error message you got before is the same as a bug in an old version of MPICH2 (version 1.3).  MAKER will install version 1.5.

Also run 'mpiexec -n 16 hostname'
What happens?

Thanks,
Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:17 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

How's the trip?

I did it followed your instruction. I ran ./build mpich2 first
It installed it into ~/perl5/exe/mpich2 directory.
And then i go back to maker/src ran perl build.pl<http://build.pl> and type Y to accept the MPI.
Then I ran ./build install
After that, I went to ~/.bash_profile to add the ~/perl5/exe/mpich2/bin into the PATH.
I used mpiexec -n 16 maker as the command.
Do I need to set some special variable in that three control file first?

Thank you.

Yunxi Lin

On Jul 2, 2013, at 7:44 AM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

Sorry for not responding sooner (it was a long holiday weekend in Canada).  Did you have maker install MPICH2 or did you install it yourself?  Also what is the exact command line you used to launch?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sunday, June 30, 2013 2:09 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got the errors like:
[mpiexec at bioinfo1] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file hydra_pmi_proxy (No such file or directory)
[mpiexec at bioinfo1] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:315): assert (!closed) failed
[mpiexec at bioinfo1] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec at bioinfo1] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event
[mpiexec at bioinfo1] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion

Is that means our server only has one cpu so I cannot use mpi?

Thank you.



2013/6/25 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.

When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only).  It will be in ?/maker/exe/mpich2.  This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having to get upgraded privileges.  So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.

--Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, 25 June, 2013 11:40 AM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>

Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu?  Because my school own the server, I only have the limit authorization.

Yunxi Lin

On Jun 24, 2013, at 5:39 PM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

You are most likely only getting 1 cpu of performance.

You should just install MPICH2.  It's easy just to let MAKER do it for you:
Go to the ?/maker/src/ directory
Run './Build mpich2'
Once it finishes installing, it will be in the ?/maker/exe/mpich2/bin/ directory.

Setup MAKER again to use MPICH2:
Go to the ?/maker/src/ directory
Run 'perl Build.PL'
Say yes to the "use MPI": question
Run './Build install'

Now run MAKER via 'mpiexec'.
Example --> ?/maker/exe/mpich2/bin/mpiexec -n 16 maker

The ?n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines.  You will get much better performance.

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, 24 June, 2013 7:11 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank your for your help.

My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER.

I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus.

Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way.

Sincerely,
Yunxi



2013/6/24 Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use.  If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time.  This is especially true if you use the alt_est option for evidence as these are aligned via tblastx  which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.

Also you do not need results from the entire genome to train SNAP.  If you get results from ~10Mb of the genome that is usually sufficient.  Also make sure you are taking advantage of parallelization.  Launch via MPI to get maximum performance.  I commonly launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.

--Carson


From: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Date: Sunday, 23 June, 2013 10:15 PM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Cc: <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Subject: [maker-devel] Fwd: about running MAKER

>From the GMOD helpdesk; please cc Lin, lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>.

---------- Forwarded message ----------
From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sun, Jun 23, 2013 at 4:14 PM
Subject: about running MAKER
To: "gmod-help at gmod.org<mailto:gmod-help at gmod.org>" <help at gmod.org<mailto:help at gmod.org>>


Hi

I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server.

Thank you.

Sincerely,
Lin



--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org















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From grburke at uga.edu  Tue Jul 30 13:14:02 2013
From: grburke at uga.edu (Gaelen Burke)
Date: Tue, 30 Jul 2013 19:14:02 -0000
Subject: [maker-devel] unknown error
Message-ID: <602FA505-8A78-4006-8D8F-D3EC81A73FEC@uga.edu>

Hello,
I have an error that occurs in my MAKER run for 52 of several thousand scaffolds. The annotation of these scaffolds fails, even after 3 re-tries. I also pulled out the failed sequences and started a run from scratch, with the same result. Could anyone tell me what this error means and how I could possibly fix it?
Thanks,
Gaelen Burke

Here is the message that occurs:

Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
:411
STACK: PhatHit_utils::_adjust /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit_utils.pm:
880
STACK: PhatHit_utils::adjust_start_stop /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit
_utils.pm:776
STACK: maker::auto_annotator::load_transcript_struct /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/.
./lib/maker/auto_annotator.pm:1808
STACK: maker::auto_annotator::group_transcripts /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib
/maker/auto_annotator.pm:2163
STACK: maker::auto_annotator::annotate_genes /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/ma
ker/auto_annotator.pm:877
STACK: Process::MpiChunk::_go /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:2159
STACK: Process::MpiChunk::run /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:257
STACK: Process::MpiTiers::run_all /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiTi
ers.pm:193
STACK: /usr/local/maker/latest/bin/maker:276
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while clustering transcripts into genes for annotations!!

ERROR: Chunk failed at level 20
!!
FAILED CONTIG:scaffold_0040



From vwong at umn.edu  Tue Jul  2 09:38:26 2013
From: vwong at umn.edu (V Wong)
Date: Tue, 2 Jul 2013 10:38:26 -0500
Subject: [maker-devel] maker2jbrowse implementation
Message-ID: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
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From carsonhh at gmail.com  Tue Jul  2 10:27:19 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 12:27:19 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>
Message-ID: <CDF873FE.65B7%carsonhh@gmail.com>

The Jbrowse codebase tends to undergo very rapid alteration (much of which
is not backwards compatible with other Jbrowse versions), as a result the
script maker2jbrowse has had to evolve with Jbrowse (and will not work with
all versions).  I'm not sure if the script is currently behind or ahead of
Jbrowse version 1.9.3 (I'm guessing behind). I can have it working with
whatever the most current repository is if you were to give me a week, or
you can try loading the GFF3's using Jbrowse's own loader (tutorial here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012).  Of course this tutorial is
also likely to be somewhat out of date :-( But the 2013 version is supposed
to be up and running as part of this years GMOD summer school in ~3 weeks.
They use MAKER generated data for the tutorial, so it should be relevant to
what you are doing.

Thanks,
Carson



From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Tuesday, July 2, 2013 11:38 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker2jbrowse implementation

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From rbuels at gmail.com  Tue Jul  2 11:32:40 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 02 Jul 2013 13:32:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D30EB8.5090002@gmail.com>

One of my objectives has been maintaining complete backward 
compatibility with data formatted from JBrowse 1.2.1 onward.  I add 
capabilities, and the look and feel of the browser improves, but you can 
still view data in it that was formatted with JBrowse 1.2.1 (released 
March 17, 2011).

I would try to have a look at the maker2jbrowse implementation to 
troubleshoot further, but your source code doesn't seem to be public. 
Or at least the link to the source browser on the GMOD wiki page 
(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't 
find any kind of source code links under 
http://www.yandell-lab.org/software/maker.html.  Is the MAKER source 
code actually open?

Regarding the 2012 tutorial, the directions in the 2012 tutorial should 
still work, since I have been keeping backward compatibility with the 
scripts also.

Val, Carson, could you elaborate with details on the backward 
compatibility problems you're seeing?  Or could you give me access to 
the maker2jbrowse source code?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Tue Jul  2 13:19:40 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 15:19:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D30EB8.5090002@gmail.com>
Message-ID: <CDF89913.661B%carsonhh@gmail.com>

Good to know the tutorial is up to date.  I had to make several
consecutive updates to my script about a year ago with Jbrowse updates, so
I'm glad to know I can likely just fix whatever is wrong now and that will
be good for most previous and upcoming Jbrowse version :-)

It has more to do with converting data from GFF3.  maker2jbrowse is just a
script that wraps the flatfile-to-json.pl calls together with some css
files (all included in maker tar ball - it's open source).  So if anything
changes in flatfile-to-json.pl or the expected tags in css files then
maker2jbrowse won't work (the css files are where I usually get into
trouble). I just have to figure out what the changes are and then fix
them.  I know I had to do some updates for colors in Web Apollo recently
and I imagine I can just use that as a template.

Thanks,
Carson




On 7/2/13 1:32 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>One of my objectives has been maintaining complete backward
>compatibility with data formatted from JBrowse 1.2.1 onward.  I add
>capabilities, and the look and feel of the browser improves, but you can
>still view data in it that was formatted with JBrowse 1.2.1 (released
>March 17, 2011).
>
>I would try to have a look at the maker2jbrowse implementation to
>troubleshoot further, but your source code doesn't seem to be public.
>Or at least the link to the source browser on the GMOD wiki page
>(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't
>find any kind of source code links under
>http://www.yandell-lab.org/software/maker.html.  Is the MAKER source
>code actually open?
>
>Regarding the 2012 tutorial, the directions in the 2012 tutorial should
>still work, since I have been keeping backward compatibility with the
>scripts also.
>
>Val, Carson, could you elaborate with details on the backward
>compatibility problems you're seeing?  Or could you give me access to
>the maker2jbrowse source code?
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Jul  2 13:24:43 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 2 Jul 2013 13:24:43 -0600
Subject: [maker-devel] maker2jbrowse
References: <mailman.69.1372786364.6126.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <E031B282-253C-4DFE-9D08-ECC02501CCAD@genetics.utah.edu>

Hi Robert,

Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use.  You can download the code here:

http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.

Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)

B

> From: Robert Buels <rbuels at gmail.com>
> Subject: Re: [maker-devel] maker2jbrowse implementation
> Date: July 2, 2013 11:32:40 AM MDT
> To: <maker-devel at yandell-lab.org>
> 
> 
> One of my objectives has been maintaining complete backward compatibility with data formatted from JBrowse 1.2.1 onward.  I add capabilities, and the look and feel of the browser improves, but you can still view data in it that was formatted with JBrowse 1.2.1 (released March 17, 2011).
> 
> I would try to have a look at the maker2jbrowse implementation to troubleshoot further, but your source code doesn't seem to be public. Or at least the link to the source browser on the GMOD wiki page (http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't find any kind of source code links under http://www.yandell-lab.org/software/maker.html.  Is the MAKER source code actually open?
> 
> Regarding the 2012 tutorial, the directions in the 2012 tutorial should still work, since I have been keeping backward compatibility with the scripts also.
> 
> Val, Carson, could you elaborate with details on the backward compatibility problems you're seeing?  Or could you give me access to the maker2jbrowse source code?
> 
> 
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
> 
> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>  Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>> 
>> Hi Maker team,
>> 
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>> 
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> 
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>> 
>> Any advice for getting past this will be most appreciated.  Thank you!
>> 
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 
> 
> 
> From: <maker-devel-request at yandell-lab.org>
> Subject: confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc
> Date: July 2, 2013 11:32:44 AM MDT
> 
> 
> If you reply to this message, keeping the Subject: header intact,
> Mailman will discard the held message.  Do this if the message is
> spam.  If you reply to this message and include an Approved: header
> with the list password in it, the message will be approved for posting
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> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
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From rbuels at gmail.com  Wed Jul  3 09:45:53 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 11:45:53 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D44731.6060308@gmail.com>

After looking at the maker2jbrowse source (thanks for giving me access), 
there seems to be some kind of problem with the way maker2jbrowse is 
parsing the MAKER datastore index, leading to the script complaining of 
'no track information'.

This would probably be easier for a MAKER developer to look into.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Wed Jul  3 10:02:23 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 12:02:23 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D44731.6060308@gmail.com>
Message-ID: <CDF9C28B.66AF%carsonhh@gmail.com>

I think you may not have it set up right.  If you run the example data,
you can then use that.  For me it populates the JSON data tracks
information, but nothing displays.  I think the problem is with the maker
genome.css.  It is very out of date.  I'll do some work on it and then get
your feedback.

Thanks,
Carson



On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:

>After looking at the maker2jbrowse source (thanks for giving me access),
>there seems to be some kind of problem with the way maker2jbrowse is
>parsing the MAKER datastore index, leading to the script complaining of
>'no track information'.
>
>This would probably be easier for a MAKER developer to look into.
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>





From rbuels at gmail.com  Wed Jul  3 10:14:49 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:14:49 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D44DF9.9050908@gmail.com>

How does this have anything to do with CSS?  The errors Val is talking 
about are coming from the maker2jbrowse script:

ERROR: No track information for source
 >>> 'AK_assembly_datastore/22/D4/AK_contig_1/'


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From vwong at umn.edu  Wed Jul  3 10:15:38 2013
From: vwong at umn.edu (V Wong)
Date: Wed, 3 Jul 2013 11:15:38 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <51D44731.6060308@gmail.com>
	<CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <CAEi2voZNLhwS=u2FvTukC6HoxMuF7_3p8K2y1VCy7RAFsw_xgw@mail.gmail.com>

Hi Carson and Robert,

Thank you for your feedback on this!  Carson, could you describe the set up
a little more?  For instance, are you running the script in a specific
location in the JBrowse directory?  I seem to be running into the same
problem as Robert.

Best,
Val


On Wed, Jul 3, 2013 at 11:02 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
> >After looking at the maker2jbrowse source (thanks for giving me access),
> >there seems to be some kind of problem with the way maker2jbrowse is
> >parsing the MAKER datastore index, leading to the script complaining of
> >'no track information'.
> >
> >This would probably be easier for a MAKER developer to look into.
> >
> >
> >Robert Buels
> >Lead Developer
> >JBrowse - http://jbrowse.org
> >
> >On 07/02/2013 12:27 PM, Carson Holt wrote:
> >> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >> which is not backwards compatible with other Jbrowse versions), as a
> >> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> >> not work with all versions).  I'm not sure if the script is currently
> >> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >> have it working with whatever the most current repository is if you were
> >> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> >> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>   Of course this tutorial is also likely to be somewhat out of date
> >> :-( But the 2013 version is supposed to be up and running as part of
> >> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >> data for the tutorial, so it should be relevant to what you are doing.
> >>
> >> Thanks,
> >> Carson
> >>
> >>
> >>
> >> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Date: Tuesday, July 2, 2013 11:38 AM
> >> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> >> Subject: [maker-devel] maker2jbrowse implementation
> >>
> >> Hi Maker team,
> >>
> >> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >> server, using the -d option for the index.log file.  However, I am
> >> getting this error for each contig:
> >>
> >> ERROR: No track information for source
> >> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>
> >> Looking at the perl script, the file locations are getting read, but
> >> then the tracks aren't getting found in the hash of commands.
> >>
> >> Any advice for getting past this will be most appreciated.  Thank you!
> >>
> >> Best,
> >> Val
> >> _______________________________________________ maker-devel mailing list
> >> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com
> >
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >>
> >> _______________________________________________
> >> maker-devel mailing list
> >> maker-devel at box290.bluehost.com
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
>
>
>
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From rbuels at gmail.com  Wed Jul  3 10:39:51 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:39:51 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D453D7.4070801@gmail.com>

Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what 
you're doing with that, but it appears to be a fork of a very old 
JBrowse main css file.  If that's overriding or being copied over the 
JBrowse released CSS, it will break pretty much everything.  It would be 
like me randomly replacing one of MAKER's Perl modules with my own old 
forked copy.

If what you're trying to accomplish is to add some custom styles, the 
best way to do that would be to do one of:

* add just your custom feature styles on the flatfile-to-json.pl command 
line
* add a "css": { "url": "http://url/of/your/custom.css" } to the
   JBrowse trackList.json someplace in the workflow (easy to add
   things to JSON files with JSON.pm) that loads your custom CSS
   (containing only your custom feature styles!)
* add all of the custom styles to the trackList.json as a
   string: "css": "string { of: lots and lots of; css: properties; }"


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From carsonhh at gmail.com  Wed Jul  3 13:26:32 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 15:26:32 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D453D7.4070801@gmail.com>
Message-ID: <CDF9E0AE.6703%carsonhh@gmail.com>

Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
documentation had you modify the genome.css file to create your own
tracks.  Version 1.2.1 looks like it is the last version where the
genome.css file that maker provided works. I can still get simple test
GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
But I need to fix some things, because they are all indistinguishable from
each other (so it is not the desired behavior).

Indepent of that issue though, to regenerate the original error, I do the
following -->
    maker2jbrowse  
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 
    ERROR: No track information for source
'dpp_contig_datastore/05/1F/contig-dpp-500-500/'

Basically you are missing the '-d' flag (whiteout that the script is
expecting a list of GFF3 files).

So this works -->
    maker2jbrowse -d
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 


Of course all tracks look the same though per the original issue I
mentioned.

Thanks,
Carson



Some versions of Jbrowse still load fine with the script as is Jbrowse
1.3, 

On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>you're doing with that, but it appears to be a fork of a very old
>JBrowse main css file.  If that's overriding or being copied over the
>JBrowse released CSS, it will break pretty much everything.  It would be
>like me randomly replacing one of MAKER's Perl modules with my own old
>forked copy.
>
>If what you're trying to accomplish is to add some custom styles, the
>best way to do that would be to do one of:
>
>* add just your custom feature styles on the flatfile-to-json.pl command
>line
>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>   JBrowse trackList.json someplace in the workflow (easy to add
>   things to JSON files with JSON.pm) that loads your custom CSS
>   (containing only your custom feature styles!)
>* add all of the custom styles to the trackList.json as a
>   string: "css": "string { of: lots and lots of; css: properties; }"
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> I think you may not have it set up right.  If you run the example data,
>> you can then use that.  For me it populates the JSON data tracks
>> information, but nothing displays.  I think the problem is with the
>>maker
>> genome.css.  It is very out of date.  I'll do some work on it and then
>>get
>> your feedback.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>
>>> After looking at the maker2jbrowse source (thanks for giving me
>>>access),
>>> there seems to be some kind of problem with the way maker2jbrowse is
>>> parsing the MAKER datastore index, leading to the script complaining of
>>> 'no track information'.
>>>
>>> This would probably be easier for a MAKER developer to look into.
>>>
>>>
>>> Robert Buels
>>> Lead Developer
>>> JBrowse - http://jbrowse.org
>>>
>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>will
>>>> not work with all versions).  I'm not sure if the script is currently
>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>> have it working with whatever the most current repository is if you
>>>>were
>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>own
>>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>> data for the tutorial, so it should be relevant to what you are doing.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>
>>>> Hi Maker team,
>>>>
>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>> server, using the -d option for the index.log file.  However, I am
>>>> getting this error for each contig:
>>>>
>>>> ERROR: No track information for source
>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>
>>>> Looking at the perl script, the file locations are getting read, but
>>>> then the tracks aren't getting found in the hash of commands.
>>>>
>>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>>
>>>> Best,
>>>> Val
>>>> _______________________________________________ maker-devel mailing
>>>>list
>>>> maker-devel at box290.bluehost.com
>>>><mailto:maker-devel at box290.bluehost.com>
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>
>>
>>





From benayoun at stanford.edu  Fri Jul  5 15:35:44 2013
From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:35:44 -0700
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
References: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
Message-ID: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
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From carsonhh at gmail.com  Mon Jul  8 08:20:53 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 10:20:53 -0400
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>
Message-ID: <CE00422F.6A5C%carsonhh@gmail.com>

In your MAKER STDERR (printed to screen or captured as part of run), search
for the word ERROR.  That will give a more specific explanation as to why it
is failing.  If you did not capture this on your first run, you may need to
redirect it to a file on a retry.

Example --> maker 2> error.log

Thanks,
Carson

From:  B?r?nice Benayoun <benayoun at stanford.edu>
Date:  Friday, July 5, 2013 5:35 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] FAILED contigs

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From berenice.benayoun at gmail.com  Fri Jul  5 15:33:35 2013
From: berenice.benayoun at gmail.com (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:33:35 -0700
Subject: [maker-devel] FAILED contigs
Message-ID: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice

-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/
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From onson001 at umn.edu  Mon Jul  8 16:12:06 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Mon, 8 Jul 2013 17:12:06 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
Message-ID: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>

Maker Developers,

I am testing Maker on a well annotated contig from the encode project and
in one of the genes, maker does not output an exon despite HSPs supporting
it. I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question.

I even set the parameters est2genome and protein2genome to 1 but still
Maker did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks,
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From carsonhh at gmail.com  Mon Jul  8 19:55:15 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 21:55:15 -0400
Subject: [maker-devel] Maker not outputting exons with EST and Protein
 Evidence
In-Reply-To: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
Message-ID: <CE00DF97.6C2A%carsonhh@gmail.com>

This is because augustus never calls it either without hints or after being
given hints by MAKER.  This may be because even though the exon has support
from ESTs and protein alignments, it breaks the open reading frame (you can
check using apollo ? just click and drag them into the annotation tier).  I
did this individually for each of the polished proteins and ESTs, and none
have proper open reading frame.

Perhaps the official annotation contains a frame shift or something to make
it work (augustus can't do that).  Such a thing is not all that uncommon.
There are many instances of RefSeq annotations for example where if you cut
out the exons and try and translate them, they won't translate.  This can
happen because the reference sequence changed or is incorrect, and if the
annotation was generated from a different assembly, then it just gets mapped
as best as possible to the current assembly and the correct protein
translation is saved elsewhere in the database (even though manual
translation won't directly reproduce it).  Genes where this happens make up
just under 1% of the human genome (but they can drive you nuts especially if
your analysis expects protein sequence to match the nucleotide sequence
translation).  It's really just an artifacts of the process used to move
annotations forward on the humans genome every time they update the
assembly.

Thanks,
Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Monday, July 8, 2013 6:12 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker not outputting exons with EST and Protein
Evidence

Maker Developers, 

I am testing Maker on a well annotated contig from the encode project and in
one of the genes, maker does not output an exon despite HSPs supporting it.
I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question. 

I even set the parameters est2genome and protein2genome to 1 but still Maker
did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks, 
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Tue Jul  9 09:57:09 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 09 Jul 2013 11:57:09 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9E0AE.6703%carsonhh@gmail.com>
Message-ID: <CE01A884.6C92%carsonhh@gmail.com>

Hi Val,

I've attached new files for you to test.  These will be bundled in the
next maker release pending successful tests (~ 1 week).

Instructions:
1. Place maker2jbrowse in your .../maker/bin/ directory and
.../maker/src/bin/ directory (this is just to ensure you don't
accidentally overwrite it if you reinstall at any time).
2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
3. You must be in the jbrowse installation directory when running
maker2jbrowse.  Run the script with the -d flag and the datastore index
file.

This new version will assign colors by copying maker.css to the jbrowse
installation as apposed to replacing the genome.css file, and it will also
edit the genome.css file to add the import call for maker.css.  In
addition I have updated command line flags in the wrapper to do what is
currently expected by flatfile-to-json.pl.

Could you test it out and let me know how it goes.

Thanks,
Carson



On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:

>Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>documentation had you modify the genome.css file to create your own
>tracks.  Version 1.2.1 looks like it is the last version where the
>genome.css file that maker provided works. I can still get simple test
>GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>But I need to fix some things, because they are all indistinguishable from
>each other (so it is not the desired behavior).
>
>Indepent of that issue though, to regenerate the original error, I do the
>following -->
>    maker2jbrowse 
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>    ERROR: No track information for source
>'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>
>Basically you are missing the '-d' flag (whiteout that the script is
>expecting a list of GFF3 files).
>
>So this works -->
>    maker2jbrowse -d
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>
>
>Of course all tracks look the same though per the original issue I
>mentioned.
>
>Thanks,
>Carson
>
>
>
>Some versions of Jbrowse still load fine with the script as is Jbrowse
>1.3, 
>
>On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>you're doing with that, but it appears to be a fork of a very old
>>JBrowse main css file.  If that's overriding or being copied over the
>>JBrowse released CSS, it will break pretty much everything.  It would be
>>like me randomly replacing one of MAKER's Perl modules with my own old
>>forked copy.
>>
>>If what you're trying to accomplish is to add some custom styles, the
>>best way to do that would be to do one of:
>>
>>* add just your custom feature styles on the flatfile-to-json.pl command
>>line
>>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>   JBrowse trackList.json someplace in the workflow (easy to add
>>   things to JSON files with JSON.pm) that loads your custom CSS
>>   (containing only your custom feature styles!)
>>* add all of the custom styles to the trackList.json as a
>>   string: "css": "string { of: lots and lots of; css: properties; }"
>>
>>
>>Robert Buels
>>Lead Developer
>>JBrowse - http://jbrowse.org
>>
>>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>> I think you may not have it set up right.  If you run the example data,
>>> you can then use that.  For me it populates the JSON data tracks
>>> information, but nothing displays.  I think the problem is with the
>>>maker
>>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>get
>>> your feedback.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>
>>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>access),
>>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>> parsing the MAKER datastore index, leading to the script complaining
>>>>of
>>>> 'no track information'.
>>>>
>>>> This would probably be easier for a MAKER developer to look into.
>>>>
>>>>
>>>> Robert Buels
>>>> Lead Developer
>>>> JBrowse - http://jbrowse.org
>>>>
>>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>will
>>>>> not work with all versions).  I'm not sure if the script is currently
>>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>>> have it working with whatever the most current repository is if you
>>>>>were
>>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>>own
>>>>> loader (tutorial here -->
>>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>>> data for the tutorial, so it should be relevant to what you are
>>>>>doing.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>> To: <maker-devel at yandell-lab.org
>>>>><mailto:maker-devel at yandell-lab.org>>
>>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>
>>>>> Hi Maker team,
>>>>>
>>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>> server, using the -d option for the index.log file.  However, I am
>>>>> getting this error for each contig:
>>>>>
>>>>> ERROR: No track information for source
>>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>
>>>>> Looking at the perl script, the file locations are getting read, but
>>>>> then the tracks aren't getting found in the hash of commands.
>>>>>
>>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>you!
>>>>>
>>>>> Best,
>>>>> Val
>>>>> _______________________________________________ maker-devel mailing
>>>>>list
>>>>> maker-devel at box290.bluehost.com
>>>>><mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>
>>>
>>>
>
>

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From Carson.Holt at oicr.on.ca  Tue Jul  9 13:19:14 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 9 Jul 2013 19:19:14 +0000
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE01D9F3.6CF4%carson.holt@oicr.on.ca>

It's perfectly safe to kill.

If you are constantly getting FAIL in the datastore index, then something
is wrong.  If you are capturing the jobs STDERR, try looking for the term
ERROR or FATAL for a better explanation as to why it's failing and send
the error to me.

Thanks,
Carson


On 7/9/13 2:47 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hello Maker Developers!
>
>I have a quick question... I've been using MAKER to annotate a genome (it
>has been running for about 6 days with 48 cpus).  Many of my contigs have
>failed, surely because most of them are smaller than the 10 kb limit I
>set, which is fine.  My concern is that although I've set tries = 2, the
>index log seems to indicate that MAKER is on its fourth try for some of
>the contigs (see attached).  Is is safe to shut MAKER down, or are there
>clean-up steps at the end of the annotation process that need to be
>allowed to occur?  Oh, and I'm using MAKER 2.28.
>
>Best, Jacqueline
>
>




From onson001 at umn.edu  Tue Jul  9 15:29:21 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Tue, 9 Jul 2013 16:29:21 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
In-Reply-To: <CE00DF97.6C2A%carsonhh@gmail.com>
References: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
	<CE00DF97.6C2A%carsonhh@gmail.com>
Message-ID: <CACFwDdLkUR3A-j8dzFj=GujNz6oKmL0RpXjpH6bZhr53Tr1rcg@mail.gmail.com>

Thanks for the insight.


On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> This is because augustus never calls it either without hints or after
> being given hints by MAKER.  This may be because even though the exon has
> support from ESTs and protein alignments, it breaks the open reading frame
> (you can check using apollo ? just click and drag them into the annotation
> tier).  I did this individually for each of the polished proteins and ESTs,
> and none have proper open reading frame.
>
> Perhaps the official annotation contains a frame shift or something to
> make it work (augustus can't do that).  Such a thing is not all that
> uncommon.  There are many instances of RefSeq annotations for example where
> if you cut out the exons and try and translate them, they won't translate.
>  This can happen because the reference sequence changed or is incorrect,
> and if the annotation was generated from a different assembly, then it just
> gets mapped as best as possible to the current assembly and the correct
> protein translation is saved elsewhere in the database (even though manual
> translation won't directly reproduce it).  Genes where this happens make up
> just under 1% of the human genome (but they can drive you nuts especially
> if your analysis expects protein sequence to match the nucleotide sequence
> translation).  It's really just an artifacts of the process used to move
> annotations forward on the humans genome every time they update the
> assembly.
>
> Thanks,
> Carson
>
>
> From: Innocent Onsongo <onson001 at umn.edu>
> Date: Monday, July 8, 2013 6:12 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker not outputting exons with EST and Protein
> Evidence
>
> Maker Developers,
>
> I am testing Maker on a well annotated contig from the encode project and
> in one of the genes, maker does not output an exon despite HSPs supporting
> it. I have attached a compressed folder with
>
> ENr122_genes.gff: The validated genes as per encode
> ENr122.gff: Makers output
> maker_opts.ctl: The control file I used
> ENr122_98669-134249.pptx: A power point visually illustrated the exon in
> question.
>
> I even set the parameters est2genome and protein2genome to 1 but still
> Maker did not output this exon.
>
> Is there a good reason Maker does no have this exon in its final model
> despite the HSPs supporting it?
>
> Thanks,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From jmdoyle at purdue.edu  Tue Jul  9 12:47:46 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Tue, 9 Jul 2013 14:47:46 -0400 (EDT)
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <53458481.77205.1373395049899.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>

Hello Maker Developers!

I have a quick question... I've been using MAKER to annotate a genome (it has been running for about 6 days with 48 cpus).  Many of my contigs have failed, surely because most of them are smaller than the 10 kb limit I set, which is fine.  My concern is that although I've set tries = 2, the index log seems to indicate that MAKER is on its fourth try for some of the contigs (see attached).  Is is safe to shut MAKER down, or are there clean-up steps at the end of the annotation process that need to be allowed to occur?  Oh, and I'm using MAKER 2.28.

Best, Jacqueline


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From yuharas at takara-bio.co.jp  Wed Jul 10 20:27:12 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 11:27:12 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>

Dear developers

I'm considering using MAKER2 to annotate plant genome (~1Gb) I've assembled using illumina HiSeq data.
And I'm planning to obtain mRNA-seq data by using HiSeq.
Do you have any recommendation of sequencing depth of RNA-seq data for using MAKER2 annotation pipeline?

Thanks,
Satoshi




From carsonhh at gmail.com  Wed Jul 10 20:40:52 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 10 Jul 2013 22:40:52 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
Message-ID: <CE039117.6E22%carsonhh@gmail.com>

As far as total depth I don't know, but I'd recommend using something like
trinity to assemble the reads and supply them to the est= option in fasta
format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From yuharas at takara-bio.co.jp  Wed Jul 10 22:47:10 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 13:47:10 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE039117.6E22%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
	<CE039117.6E22%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>

Dear Carson

Thank you for your quick reply.
Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
although the tutorial contains information about Tophat and Cufflinks?

Satoshi


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 11:41 AM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

As far as total depth I don't know, but I'd recommend using something like trinity to assemble the reads and supply them to the est= option in fasta format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for 
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From vwong at umn.edu  Wed Jul 10 23:10:52 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 00:10:52 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE01A884.6C92%carsonhh@gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
Message-ID: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser,
but that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Val,
>
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
>
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
>
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl.
>
> Could you test it out and let me know how it goes.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
> >documentation had you modify the genome.css file to create your own
> >tracks.  Version 1.2.1 looks like it is the last version where the
> >genome.css file that maker provided works. I can still get simple test
> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
> >But I need to fix some things, because they are all indistinguishable from
> >each other (so it is not the desired behavior).
> >
> >Indepent of that issue though, to regenerate the original error, I do the
> >following -->
> >    maker2jbrowse
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >    ERROR: No track information for source
> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
> >
> >Basically you are missing the '-d' flag (whiteout that the script is
> >expecting a list of GFF3 files).
> >
> >So this works -->
> >    maker2jbrowse -d
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >
> >
> >Of course all tracks look the same though per the original issue I
> >mentioned.
> >
> >Thanks,
> >Carson
> >
> >
> >
> >Some versions of Jbrowse still load fine with the script as is Jbrowse
> >1.3,
> >
> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
> >
> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
> >>you're doing with that, but it appears to be a fork of a very old
> >>JBrowse main css file.  If that's overriding or being copied over the
> >>JBrowse released CSS, it will break pretty much everything.  It would be
> >>like me randomly replacing one of MAKER's Perl modules with my own old
> >>forked copy.
> >>
> >>If what you're trying to accomplish is to add some custom styles, the
> >>best way to do that would be to do one of:
> >>
> >>* add just your custom feature styles on the flatfile-to-json.pl command
> >>line
> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
> >>   JBrowse trackList.json someplace in the workflow (easy to add
> >>   things to JSON files with JSON.pm) that loads your custom CSS
> >>   (containing only your custom feature styles!)
> >>* add all of the custom styles to the trackList.json as a
> >>   string: "css": "string { of: lots and lots of; css: properties; }"
> >>
> >>
> >>Robert Buels
> >>Lead Developer
> >>JBrowse - http://jbrowse.org
> >>
> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
> >>> I think you may not have it set up right.  If you run the example data,
> >>> you can then use that.  For me it populates the JSON data tracks
> >>> information, but nothing displays.  I think the problem is with the
> >>>maker
> >>> genome.css.  It is very out of date.  I'll do some work on it and then
> >>>get
> >>> your feedback.
> >>>
> >>> Thanks,
> >>> Carson
> >>>
> >>>
> >>>
> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
> >>>
> >>>> After looking at the maker2jbrowse source (thanks for giving me
> >>>>access),
> >>>> there seems to be some kind of problem with the way maker2jbrowse is
> >>>> parsing the MAKER datastore index, leading to the script complaining
> >>>>of
> >>>> 'no track information'.
> >>>>
> >>>> This would probably be easier for a MAKER developer to look into.
> >>>>
> >>>>
> >>>> Robert Buels
> >>>> Lead Developer
> >>>> JBrowse - http://jbrowse.org
> >>>>
> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >>>>> which is not backwards compatible with other Jbrowse versions), as a
> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
> >>>>>will
> >>>>> not work with all versions).  I'm not sure if the script is currently
> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >>>>> have it working with whatever the most current repository is if you
> >>>>>were
> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
> >>>>>own
> >>>>> loader (tutorial here -->
> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>>>>    Of course this tutorial is also likely to be somewhat out of date
> >>>>> :-( But the 2013 version is supposed to be up and running as part of
> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >>>>> data for the tutorial, so it should be relevant to what you are
> >>>>>doing.
> >>>>>
> >>>>> Thanks,
> >>>>> Carson
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
> >>>>> To: <maker-devel at yandell-lab.org
> >>>>><mailto:maker-devel at yandell-lab.org>>
> >>>>> Subject: [maker-devel] maker2jbrowse implementation
> >>>>>
> >>>>> Hi Maker team,
> >>>>>
> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >>>>> server, using the -d option for the index.log file.  However, I am
> >>>>> getting this error for each contig:
> >>>>>
> >>>>> ERROR: No track information for source
> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>>>>
> >>>>> Looking at the perl script, the file locations are getting read, but
> >>>>> then the tracks aren't getting found in the hash of commands.
> >>>>>
> >>>>> Any advice for getting past this will be most appreciated.  Thank
> >>>>>you!
> >>>>>
> >>>>> Best,
> >>>>> Val
> >>>>> _______________________________________________ maker-devel mailing
> >>>>>list
> >>>>> maker-devel at box290.bluehost.com
> >>>>><mailto:maker-devel at box290.bluehost.com>
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> maker-devel mailing list
> >>>>> maker-devel at box290.bluehost.com
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>
> >>>
> >>>
> >
> >
>
>
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From carsonhh at gmail.com  Thu Jul 11 05:37:13 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:37:13 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
Message-ID: <CE0410D8.6E4A%carsonhh@gmail.com>

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to
cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks,
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something
>like trinity to assemble the reads and supply them to the est= option in
>fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>





From carsonhh at gmail.com  Thu Jul 11 05:44:07 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:44:07 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <CE04120C.6E55%carsonhh@gmail.com>

You next put the entire JBrowse directory into the /var/www/html/ directory
or wherever you have apache set up to load from (if it's not already there).
Then it will be accessible as a webpage (browser is inside the JBrowse
directory).

Example /var/www/html/Jbrowse/
Webpage --> http://localhost/Jbrowse/

--Carson

From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:10 AM
To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser, but
that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Hi Val,
> 
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
> 
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
> 
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
> 
> Could you test it out and let me know how it goes.
> 
> Thanks,
> Carson
> 
> 
> 
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>> >>you're doing with that, but it appears to be a fork of a very old
>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>> >>forked copy.
>>> >>
>>> >>If what you're trying to accomplish is to add some custom styles, the
>>> >>best way to do that would be to do one of:
>>> >>
>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>> <http://flatfile-to-json.pl>  command
>>> >>line
>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>> >>   (containing only your custom feature styles!)
>>> >>* add all of the custom styles to the trackList.json as a
>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>> >>
>>> >>
>>> >>Robert Buels
>>> >>Lead Developer
>>> >>JBrowse - http://jbrowse.org
>>> >>
>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>> >>> I think you may not have it set up right.  If you run the example data,
>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>> >>> information, but nothing displays.  I think the problem is with the
>>>> >>>maker
>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>> >>>get
>>>> >>> your feedback.
>>>> >>>
>>>> >>> Thanks,
>>>> >>> Carson
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>> >>>
>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>> >>>>access),
>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>> >>>>of
>>>>> >>>> 'no track information'.
>>>>> >>>>
>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>> >>>>
>>>>> >>>>
>>>>> >>>> Robert Buels
>>>>> >>>> Lead Developer
>>>>> >>>> JBrowse - http://jbrowse.org
>>>>> >>>>
>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>> >>>>>will
>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>> currently
>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>> >>>>> have it working with whatever the most current repository is if you
>>>>>> >>>>>were
>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>> Jbrowse's
>>>>>> >>>>>own
>>>>>> >>>>> loader (tutorial here -->
>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>> generated
>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>> >>>>>doing.
>>>>>> >>>>>
>>>>>> >>>>> Thanks,
>>>>>> >>>>> Carson
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>> >>>>>
>>>>>> >>>>> Hi Maker team,
>>>>>> >>>>>
>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>> >>>>> getting this error for each contig:
>>>>>> >>>>>
>>>>>> >>>>> ERROR: No track information for source
>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>> >>>>>
>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>> >>>>>
>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>> >>>>>you!
>>>>>> >>>>>
>>>>>> >>>>> Best,
>>>>>> >>>>> Val
>>>>>> >>>>> _______________________________________________ maker-devel mailing
>>>>>> >>>>>list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> maker-devel mailing list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>> >
>> >
> 



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From vwong at umn.edu  Thu Jul 11 11:58:42 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 12:58:42 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE04120C.6E55%carsonhh@gmail.com>
References: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
	<CE04120C.6E55%carsonhh@gmail.com>
Message-ID: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl is doing the job.  Is it possible to merge these tracks
into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You next put the entire JBrowse directory into the /var/www/html/
> directory or wherever you have apache set up to load from (if it's not
> already there).  Then it will be accessible as a webpage (browser is inside
> the JBrowse directory).
>
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
>
> --Carson
>
> From: V Wong <vwong at umn.edu>
> Reply-To: <vwong at umn.edu>
> Date: Thursday, July 11, 2013 1:10 AM
> To: Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc: <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Thanks!  I followed your instructions, and maker2jbrowse, and it
> successfully populated the ../JBrowse/data/tracks directory with
> RepeatMasker, Augustus, and GeneMark predictions.
>
> I'm not entirely sure how to get these numerous tracks into the browser,
> but that may be something to work out with JBrowse rather than Maker.
>
> Best,
> Val
>
>
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Hi Val,
>>
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>>
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>>
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl.
>>
>> Could you test it out and let me know how it goes.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>>
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable
>> from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>> >>you're doing with that, but it appears to be a fork of a very old
>> >>JBrowse main css file.  If that's overriding or being copied over the
>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>> >>forked copy.
>> >>
>> >>If what you're trying to accomplish is to add some custom styles, the
>> >>best way to do that would be to do one of:
>> >>
>> >>* add just your custom feature styles on the flatfile-to-json.plcommand
>> >>line
>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>> >>   (containing only your custom feature styles!)
>> >>* add all of the custom styles to the trackList.json as a
>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>> >>
>> >>
>> >>Robert Buels
>> >>Lead Developer
>> >>JBrowse - http://jbrowse.org
>> >>
>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> >>> I think you may not have it set up right.  If you run the example
>> data,
>> >>> you can then use that.  For me it populates the JSON data tracks
>> >>> information, but nothing displays.  I think the problem is with the
>> >>>maker
>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>> >>>get
>> >>> your feedback.
>> >>>
>> >>> Thanks,
>> >>> Carson
>> >>>
>> >>>
>> >>>
>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >>>
>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>> >>>>access),
>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>> >>>> parsing the MAKER datastore index, leading to the script complaining
>> >>>>of
>> >>>> 'no track information'.
>> >>>>
>> >>>> This would probably be easier for a MAKER developer to look into.
>> >>>>
>> >>>>
>> >>>> Robert Buels
>> >>>> Lead Developer
>> >>>> JBrowse - http://jbrowse.org
>> >>>>
>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> >>>>> which is not backwards compatible with other Jbrowse versions), as a
>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>> >>>>>will
>> >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
>> can
>> >>>>> have it working with whatever the most current repository is if you
>> >>>>>were
>> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>> >>>>>own
>> >>>>> loader (tutorial here -->
>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>> >>>>>    Of course this tutorial is also likely to be somewhat out of date
>> >>>>> :-( But the 2013 version is supposed to be up and running as part of
>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> >>>>> data for the tutorial, so it should be relevant to what you are
>> >>>>>doing.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Carson
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>> >>>>> To: <maker-devel at yandell-lab.org
>> >>>>><mailto:maker-devel at yandell-lab.org>>
>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>> >>>>>
>> >>>>> Hi Maker team,
>> >>>>>
>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> >>>>> server, using the -d option for the index.log file.  However, I am
>> >>>>> getting this error for each contig:
>> >>>>>
>> >>>>> ERROR: No track information for source
>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> >>>>>
>> >>>>> Looking at the perl script, the file locations are getting read, but
>> >>>>> then the tracks aren't getting found in the hash of commands.
>> >>>>>
>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>> >>>>>you!
>> >>>>>
>> >>>>> Best,
>> >>>>> Val
>> >>>>> _______________________________________________ maker-devel mailing
>> >>>>>list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>><mailto:maker-devel at box290.bluehost.com>
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> maker-devel mailing list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>
>> >>>
>> >>>
>> >
>> >
>>
>>
>
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From carsonhh at gmail.com  Thu Jul 11 12:23:04 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 14:23:04 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>
Message-ID: <CE046E99.6E7F%carsonhh@gmail.com>

If you have a previous Jbrowse with already populated tracks you can just,
run maker2jbrowse in that directory instead of the new Jbrowse directory,
then the maker features will be added there.  Make a backup copy of the
directory before you do this of course incase you need to roll back the
changes.

Alternatively you will have to add those to the new Jbrowse directory using
bin/bam-to-json.pl and following the instructions here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data

I guess Robert can chime in here as well, since we have now moved outside of
MAKER scripts and fully into JBrowse.

--Carson


From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:58 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Ignazio Carbone <icarbon at ncsu.edu>, <maker-devel at yandell-lab.org>,
Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl <http://add-track-json.pl>  is doing the job.  Is it
possible to merge these tracks into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:
> You next put the entire JBrowse directory into the /var/www/html/ directory or
> wherever you have apache set up to load from (if it's not already there).
> Then it will be accessible as a webpage (browser is inside the JBrowse
> directory).
> 
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
> 
> --Carson
> 
> From:  V Wong <vwong at umn.edu>
> Reply-To:  <vwong at umn.edu>
> Date:  Thursday, July 11, 2013 1:10 AM
> To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
> 
> Subject:  Re: [maker-devel] maker2jbrowse implementation
> 
> Hi Carson,
> 
> Thanks!  I followed your instructions, and maker2jbrowse, and it successfully
> populated the ../JBrowse/data/tracks directory with RepeatMasker, Augustus,
> and GeneMark predictions.
> 
> I'm not entirely sure how to get these numerous tracks into the browser, but
> that may be something to work out with JBrowse rather than Maker.
> 
> Best,
> Val
> 
> 
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> Hi Val,
>> 
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>> 
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>> 
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
>> 
>> Could you test it out and let me know how it goes.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>>> >documentation had you modify the genome.css file to create your own
>>> >tracks.  Version 1.2.1 looks like it is the last version where the
>>> >genome.css file that maker provided works. I can still get simple test
>>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>>> >But I need to fix some things, because they are all indistinguishable from
>>> >each other (so it is not the desired behavior).
>>> >
>>> >Indepent of that issue though, to regenerate the original error, I do the
>>> >following -->
>>> >    maker2jbrowse
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >    ERROR: No track information for source
>>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>>> >
>>> >Basically you are missing the '-d' flag (whiteout that the script is
>>> >expecting a list of GFF3 files).
>>> >
>>> >So this works -->
>>> >    maker2jbrowse -d
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >
>>> >
>>> >Of course all tracks look the same though per the original issue I
>>> >mentioned.
>>> >
>>> >Thanks,
>>> >Carson
>>> >
>>> >
>>> >
>>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>>> >1.3,
>>> >
>>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>>> >
>>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>>> >>you're doing with that, but it appears to be a fork of a very old
>>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>>> >>forked copy.
>>>> >>
>>>> >>If what you're trying to accomplish is to add some custom styles, the
>>>> >>best way to do that would be to do one of:
>>>> >>
>>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>>> <http://flatfile-to-json.pl>  command
>>>> >>line
>>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>>> >>   (containing only your custom feature styles!)
>>>> >>* add all of the custom styles to the trackList.json as a
>>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>>> >>
>>>> >>
>>>> >>Robert Buels
>>>> >>Lead Developer
>>>> >>JBrowse - http://jbrowse.org
>>>> >>
>>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>>> >>> I think you may not have it set up right.  If you run the example
>>>>> data,
>>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>>> >>> information, but nothing displays.  I think the problem is with the
>>>>> >>>maker
>>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>>> >>>get
>>>>> >>> your feedback.
>>>>> >>>
>>>>> >>> Thanks,
>>>>> >>> Carson
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>>> >>>
>>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>>> >>>>access),
>>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>>> >>>>of
>>>>>> >>>> 'no track information'.
>>>>>> >>>>
>>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>> Robert Buels
>>>>>> >>>> Lead Developer
>>>>>> >>>> JBrowse - http://jbrowse.org
>>>>>> >>>>
>>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse
(and
>>>>>>> >>>>>will
>>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>>> currently
>>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>>> >>>>> have it working with whatever the most current repository is if
you
>>>>>>> >>>>>were
>>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>>> Jbrowse's
>>>>>>> >>>>>own
>>>>>>> >>>>> loader (tutorial here -->
>>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>>> generated
>>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>>> >>>>>doing.
>>>>>>> >>>>>
>>>>>>> >>>>> Thanks,
>>>>>>> >>>>> Carson
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>>> >>>>>
>>>>>>> >>>>> Hi Maker team,
>>>>>>> >>>>>
>>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>>> >>>>> getting this error for each contig:
>>>>>>> >>>>>
>>>>>>> >>>>> ERROR: No track information for source
>>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>>> >>>>>
>>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>>> >>>>>
>>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>>> >>>>>you!
>>>>>>> >>>>>
>>>>>>> >>>>> Best,
>>>>>>> >>>>> Val
>>>>>>> >>>>> _______________________________________________ maker-devel
>>>>>>> mailing
>>>>>>> >>>>>list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> _______________________________________________
>>>>>>> >>>>> maker-devel mailing list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>> >
>>> >
>> 
> 



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From rbuels at gmail.com  Thu Jul 11 12:27:10 2013
From: rbuels at gmail.com (Robert Buels)
Date: Thu, 11 Jul 2013 14:27:10 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE046E99.6E7F%carsonhh@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
Message-ID: <51DEF8FE.2000907@gmail.com>

These days, it's better to use direct BAM access.  bam-to-json.pl still 
works, but the direct BAM access is much better.

See 
http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/11/2013 02:23 PM, Carson Holt wrote:
> If you have a previous Jbrowse with already populated tracks you can
> just, run maker2jbrowse in that directory instead of the new Jbrowse
> directory, then the maker features will be added there.  Make a backup
> copy of the directory before you do this of course incase you need to
> roll back the changes.
>
> Alternatively you will have to add those to the new Jbrowse directory
> using bin/bam-to-json.pl and following the instructions here -->
> http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data
>
> I guess Robert can chime in here as well, since we have now moved
> outside of MAKER scripts and fully into JBrowse.
>
> --Carson
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Thursday, July 11, 2013 1:58 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>,
> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
> directory, the Maker tracks are now on view.
>
> However, I'm having some trouble getting our older tracks (bam
> alignments and coverage tracks) into the same browser.  Neither 1.
> copying and pasting the tracks from the previous trackList.json to the
> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
> doing the job.  Is it possible to merge these tracks into one browser?
>
> Best,
> Val
>
>
> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
> <mailto:carsonhh at gmail.com>> wrote:
>
>     You next put the entire JBrowse directory into the /var/www/html/
>     directory or wherever you have apache set up to load from (if it's
>     not already there).  Then it will be accessible as a webpage
>     (browser is inside the JBrowse directory).
>
>     Example /var/www/html/Jbrowse/
>     Webpage --> http://localhost/Jbrowse/
>
>     --Carson
>
>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Date: Thursday, July 11, 2013 1:10 AM
>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>     Cc: <maker-devel at yandell-lab.org
>     <mailto:maker-devel at yandell-lab.org>>, Robert Buels
>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>
>     Subject: Re: [maker-devel] maker2jbrowse implementation
>
>     Hi Carson,
>
>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>     successfully populated the ../JBrowse/data/tracks directory with
>     RepeatMasker, Augustus, and GeneMark predictions.
>
>     I'm not entirely sure how to get these numerous tracks into the
>     browser, but that may be something to work out with JBrowse rather
>     than Maker.
>
>     Best,
>     Val
>
>
>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>     <mailto:carsonhh at gmail.com>> wrote:
>
>         Hi Val,
>
>         I've attached new files for you to test.  These will be bundled
>         in the
>         next maker release pending successful tests (~ 1 week).
>
>         Instructions:
>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>         .../maker/src/bin/ directory (this is just to ensure you don't
>         accidentally overwrite it if you reinstall at any time).
>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>         3. You must be in the jbrowse installation directory when running
>         maker2jbrowse.  Run the script with the -d flag and the
>         datastore index
>         file.
>
>         This new version will assign colors by copying maker.css to the
>         jbrowse
>         installation as apposed to replacing the genome.css file, and it
>         will also
>         edit the genome.css file to add the import call for maker.css.  In
>         addition I have updated command line flags in the wrapper to do
>         what is
>         currently expected by flatfile-to-json.pl
>         <http://flatfile-to-json.pl>.
>
>         Could you test it out and let me know how it goes.
>
>         Thanks,
>         Carson
>
>
>
>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>         <mailto:carsonhh at gmail.com>> wrote:
>
>         >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>         >documentation had you modify the genome.css file to create your own
>         >tracks.  Version 1.2.1 looks like it is the last version where the
>         >genome.css file that maker provided works. I can still get simple test
>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>         >But I need to fix some things, because they are all indistinguishable from
>         >each other (so it is not the desired behavior).
>         >
>         >Indepent of that issue though, to regenerate the original error, I do the
>         >following -->
>         >    maker2jbrowse
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >    ERROR: No track information for source
>         >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>         >
>         >Basically you are missing the '-d' flag (whiteout that the script is
>         >expecting a list of GFF3 files).
>         >
>         >So this works -->
>         >    maker2jbrowse -d
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >
>         >
>         >Of course all tracks look the same though per the original issue I
>         >mentioned.
>         >
>         >Thanks,
>         >Carson
>         >
>         >
>         >
>         >Some versions of Jbrowse still load fine with the script as is Jbrowse
>         >1.3,
>         >
>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >
>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>         >>you're doing with that, but it appears to be a fork of a very old
>         >>JBrowse main css file.  If that's overriding or being copied over the
>         >>JBrowse released CSS, it will break pretty much everything.  It would be
>         >>like me randomly replacing one of MAKER's Perl modules with my own old
>         >>forked copy.
>         >>
>         >>If what you're trying to accomplish is to add some custom styles, the
>         >>best way to do that would be to do one of:
>         >>
>         >>* add just your custom feature styles on theflatfile-to-json.pl <http://flatfile-to-json.pl> command
>         >>line
>         >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>         >>   (containing only your custom feature styles!)
>         >>* add all of the custom styles to the trackList.json as a
>         >>   string: "css": "string { of: lots and lots of; css: properties; }"
>         >>
>         >>
>         >>Robert Buels
>         >>Lead Developer
>         >>JBrowse -http://jbrowse.org
>         >>
>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>         >>> I think you may not have it set up right.  If you run the example data,
>         >>> you can then use that.  For me it populates the JSON data tracks
>         >>> information, but nothing displays.  I think the problem is with the
>         >>>maker
>         >>> genome.css.  It is very out of date.  I'll do some work on it and then
>         >>>get
>         >>> your feedback.
>         >>>
>         >>> Thanks,
>         >>> Carson
>         >>>
>         >>>
>         >>>
>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >>>
>         >>>> After looking at the maker2jbrowse source (thanks for giving me
>         >>>>access),
>         >>>> there seems to be some kind of problem with the way maker2jbrowse is
>         >>>> parsing the MAKER datastore index, leading to the script complaining
>         >>>>of
>         >>>> 'no track information'.
>         >>>>
>         >>>> This would probably be easier for a MAKER developer to look into.
>         >>>>
>         >>>>
>         >>>> Robert Buels
>         >>>> Lead Developer
>         >>>> JBrowse -http://jbrowse.org
>         >>>>
>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>         >>>>> which is not backwards compatible with other Jbrowse versions), as a
>         >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>         >>>>>will
>         >>>>> not work with all versions).  I'm not sure if the script is currently
>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>         >>>>> have it working with whatever the most current repository is if you
>         >>>>>were
>         >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>         >>>>>own
>         >>>>> loader (tutorial here -->
>         >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>         >>>>>    Of course this tutorial is also likely to be somewhat out of date
>         >>>>> :-( But the 2013 version is supposed to be up and running as part of
>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>         >>>>> data for the tutorial, so it should be relevant to what you are
>         >>>>>doing.
>         >>>>>
>         >>>>> Thanks,
>         >>>>> Carson
>         >>>>>
>         >>>>>
>         >>>>>
>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>         >>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>         >>>>><mailto:maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>>
>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>         >>>>>
>         >>>>> Hi Maker team,
>         >>>>>
>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>         >>>>> server, using the -d option for the index.log file.  However, I am
>         >>>>> getting this error for each contig:
>         >>>>>
>         >>>>> ERROR: No track information for source
>         >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>         >>>>>
>         >>>>> Looking at the perl script, the file locations are getting read, but
>         >>>>> then the tracks aren't getting found in the hash of commands.
>         >>>>>
>         >>>>> Any advice for getting past this will be most appreciated.  Thank
>         >>>>>you!
>         >>>>>
>         >>>>> Best,
>         >>>>> Val
>         >>>>> _______________________________________________ maker-devel mailing
>         >>>>>list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>><mailto:maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>>>
>         >>>>> _______________________________________________
>         >>>>> maker-devel mailing list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>
>         >>>
>         >>>
>         >
>         >
>
>
>



From yuharas at takara-bio.co.jp  Fri Jul 12 00:19:39 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Fri, 12 Jul 2013 15:19:39 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE0410D8.6E4A%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
	<CE0410D8.6E4A%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3F37@TKREXMB3.central.takara.co.jp>

I understand?
Thank you for your useful information.

Satoshi

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 8:37 PM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something 
>like trinity to assemble the reads and supply them to the est= option 
>in fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" 
><yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for 
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>





From Carson.Holt at oicr.on.ca  Fri Jul 12 07:34:06 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Fri, 12 Jul 2013 13:34:06 +0000
Subject: [maker-devel] failed contigs error report
In-Reply-To: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>
Message-ID: <CE05726A.6EBE%carson.holt@oicr.on.ca>

Could you pack up and send me this directory (use dropbox if they are too
big) -->
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.m
aker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_co
ntig_12295/

And this file -->
AG1-IA_China_Prot.fasta

--Carson


On 7/12/13 6:47 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have collected my failed contigs and I have rerun them in Maker v. 2.28
>but they have failed again. I don't know what the error codes mean but I
>have attached the run log for your review. Any help would be appreciated.
>
>Cheers
>Ian
>
>
>




From ianmisner at my.uri.edu  Fri Jul 12 04:47:39 2013
From: ianmisner at my.uri.edu (Ian Misner)
Date: Fri, 12 Jul 2013 06:47:39 -0400
Subject: [maker-devel] failed contigs error report
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
	<CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>

Hello,

I have collected my failed contigs and I have rerun them in Maker v. 2.28 but they have failed again. I don't know what the error codes mean but I have attached the run log for your review. Any help would be appreciated. 

Cheers
Ian

-------------- next part --------------
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore

To access files for individual sequences use the datastore index:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917043%7Cgb%7CELU37906%2E1%7C.for.650-2882.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.gi%7C443917043%7Cgb%7CELU37906%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	173	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926460%7Cgb%7CELU45116%2E1%7C.for.1-1765.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.gi%7C443926460%7Cgb%7CELU45116%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926461%7Cgb%7CELU45117%2E1%7C.for.1462-7346.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.gi%7C443926461%7Cgb%7CELU45117%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912614%7Cgb%7CELU35926%2E1%7C.for.4446-5532.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.gi%7C443912614%7Cgb%7CELU35926%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916327%7Cgb%7CELU37443%2E1%7C.for.1450-6472.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.gi%7C443916327%7Cgb%7CELU37443%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912636%7Cgb%7CELU35932%2E1%7C.for.1832-6106.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.gi%7C443912636%7Cgb%7CELU35932%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916324%7Cgb%7CELU37441%2E1%7C.for.1618-7085.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.gi%7C443916324%7Cgb%7CELU37441%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926454%7Cgb%7CELU45111%2E1%7C.for.3156-7343.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.gi%7C443926454%7Cgb%7CELU45111%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912965%7Cgb%7CELU36010%2E1%7C.for.1462-5499.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.gi%7C443912965%7Cgb%7CELU36010%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926455%7Cgb%7CELU45112%2E1%7C.for.7818-9781.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.gi%7C443926455%7Cgb%7CELU45112%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 14
 ...processing 1 of 14
 ...processing 2 of 14
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
 ...processing 9 of 14
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	109	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924210%7Cgb%7CELU43269%2E1%7C.for.1-1171.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.gi%7C443924210%7Cgb%7CELU43269%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926803%7Cgb%7CELU45366%2E1%7C.for.1-1446.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.gi%7C443926803%7Cgb%7CELU45366%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926802%7Cgb%7CELU45365%2E1%7C.for.1965-3272.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.gi%7C443926802%7Cgb%7CELU45365%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	216	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3821
Length: 7594
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922723%7Cgb%7CELU42120%2E1%7C.for.2325-6375.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.gi%7C443922723%7Cgb%7CELU42120%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4802
Length: 7225
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914461%7Cgb%7CELU36415%2E1%7C.for.5310-7225.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.gi%7C443914461%7Cgb%7CELU36415%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4885
Length: 2762
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925371%7Cgb%7CELU44224%2E1%7C.for.1-1052.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.gi%7C443925371%7Cgb%7CELU44224%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:2 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925319%7Cgb%7CELU44178%2E1%7C.for.1-1315.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.gi%7C443925319%7Cgb%7CELU44178%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923087%7Cgb%7CELU42401%2E1%7C.for.1-1712.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.gi%7C443923087%7Cgb%7CELU42401%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916516%7Cgb%7CELU37570%2E1%7C.for.1-1705.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.gi%7C443916516%7Cgb%7CELU37570%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916517%7Cgb%7CELU37571%2E1%7C.for.1422-2768.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.gi%7C443916517%7Cgb%7CELU37571%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916518%7Cgb%7CELU37572%2E1%7C.for.2243-6168.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.gi%7C443916518%7Cgb%7CELU37572%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
total clusters:3 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	313	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919777%7Cgb%7CELU39849%2E1%7C.for.1-1825.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.gi%7C443919777%7Cgb%7CELU39849%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919779%7Cgb%7CELU39851%2E1%7C.for.4180-5237.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.gi%7C443919779%7Cgb%7CELU39851%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919366%7Cgb%7CELU39560%2E1%7C.for.701-2706.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.gi%7C443919366%7Cgb%7CELU39560%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	93	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925858%7Cgb%7CELU44619%2E1%7C.for.3225-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.gi%7C443925858%7Cgb%7CELU44619%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926070%7Cgb%7CELU44813%2E1%7C.for.1-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.gi%7C443926070%7Cgb%7CELU44813%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918793%7Cgb%7CELU39161%2E1%7C.for.3207-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.gi%7C443918793%7Cgb%7CELU39161%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	195	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7871
Length: 3828
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915640%7Cgb%7CELU37016%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443915640%7Cgb%7CELU37016%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925409%7Cgb%7CELU44250%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443925409%7Cgb%7CELU44250%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:5 now processing 0
total clusters:5 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:5 now processing 0
total clusters:5 now processing 0
total clusters:5 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-2576.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	194	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915594%7Cgb%7CELU36979%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915594%7Cgb%7CELU36979%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915591%7Cgb%7CELU36976%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915591%7Cgb%7CELU36976%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926575%7Cgb%7CELU45191%2E1%7C.for.1373-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.gi%7C443926575%7Cgb%7CELU45191%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	494	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926761%7Cgb%7CELU45333%2E1%7C.for.1-1216.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.gi%7C443926761%7Cgb%7CELU45333%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	782	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926230%7Cgb%7CELU44941%2E1%7C.for.1-813.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.gi%7C443926230%7Cgb%7CELU44941%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926228%7Cgb%7CELU44939%2E1%7C.for.5427-6593.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.gi%7C443926228%7Cgb%7CELU44939%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	201	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918707%7Cgb%7CELU39101%2E1%7C.for.1-1581.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.gi%7C443918707%7Cgb%7CELU39101%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	967	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920490%7Cgb%7CELU40399%2E1%7C.for.1-933.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.gi%7C443920490%7Cgb%7CELU40399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-6	166	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18734
Length: 1555
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:7 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:6 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:6 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915003%7Cgb%7CELU36646%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915003%7Cgb%7CELU36646%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921070%7Cgb%7CELU40845%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443921070%7Cgb%7CELU40845%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915001%7Cgb%7CELU36644%2E1%7C.for.1-1507.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.gi%7C443915001%7Cgb%7CELU36644%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923632%7Cgb%7CELU42812%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443923632%7Cgb%7CELU42812%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915695%7Cgb%7CELU37052%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915695%7Cgb%7CELU37052%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924765%7Cgb%7CELU43732%2E1%7C.for.1-976.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.gi%7C443924765%7Cgb%7CELU43732%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917077%7Cgb%7CELU37931%2E1%7C.for.1-838.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.gi%7C443917077%7Cgb%7CELU37931%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916648%7Cgb%7CELU37640%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443916648%7Cgb%7CELU37640%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19042
Length: 1697
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926334%7Cgb%7CELU45026%2E1%7C.for.1-1697.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.gi%7C443926334%7Cgb%7CELU45026%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-1079.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-4	179	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19560
Length: 1347
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924504%7Cgb%7CELU43508%2E1%7C.for.1-982.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.gi%7C443924504%7Cgb%7CELU43508%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	154	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923085%7Cgb%7CELU42399%2E1%7C.for.76-1596.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.gi%7C443923085%7Cgb%7CELU42399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	228	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21166
Length: 2541
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912610%7Cgb%7CELU35925%2E1%7C.for.1700-2541.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.gi%7C443912610%7Cgb%7CELU35925%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917001%7Cgb%7CELU37876%2E1%7C.for.1-1497.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.gi%7C443917001%7Cgb%7CELU37876%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	1025	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918865%7Cgb%7CELU39212%2E1%7C.for.1-1139.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.gi%7C443918865%7Cgb%7CELU39212%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	760	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	295	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23198
Length: 2379
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915448%7Cgb%7CELU36902%2E1%7C.for.1-2379.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.gi%7C443915448%7Cgb%7CELU36902%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23332
Length: 1024
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924676%7Cgb%7CELU43665%2E1%7C.for.1-1024.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.gi%7C443924676%7Cgb%7CELU43665%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_24240
Length: 1060
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26300
Length: 1034
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26955
Length: 1407
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917806%7Cgb%7CELU38443%2E1%7C.for.379-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.gi%7C443917806%7Cgb%7CELU38443%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917814%7Cgb%7CELU38450%2E1%7C.for.442-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.gi%7C443917814%7Cgb%7CELU38450%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27128
Length: 2040
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919020%7Cgb%7CELU39318%2E1%7C.for.1-941.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.gi%7C443919020%7Cgb%7CELU39318%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923430%7Cgb%7CELU42674%2E1%7C.for.1-1055.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.gi%7C443923430%7Cgb%7CELU42674%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443927136%7Cgb%7CELU45660%2E1%7C.for.1096-2040.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.gi%7C443927136%7Cgb%7CELU45660%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27180
Length: 1087
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915961%7Cgb%7CELU37227%2E1%7C.for.1-1087.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.gi%7C443915961%7Cgb%7CELU37227%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27507
Length: 2741
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914358%7Cgb%7CELU36379%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443914358%7Cgb%7CELU36379%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912830%7Cgb%7CELU35979%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443912830%7Cgb%7CELU35979%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918905%7Cgb%7CELU39238%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443918905%7Cgb%7CELU39238%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916513%7Cgb%7CELU37568%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916513%7Cgb%7CELU37568%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915770%7Cgb%7CELU37108%2E1%7C.for.1-787.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.gi%7C443915770%7Cgb%7CELU37108%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913539%7Cgb%7CELU36157%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443913539%7Cgb%7CELU36157%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913039%7Cgb%7CELU36027%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443913039%7Cgb%7CELU36027%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443911450%7Cgb%7CELU35667%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443911450%7Cgb%7CELU35667%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915845%7Cgb%7CELU37156%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443915845%7Cgb%7CELU37156%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915742%7Cgb%7CELU37086%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443915742%7Cgb%7CELU37086%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924323%7Cgb%7CELU43365%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443924323%7Cgb%7CELU43365%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914832%7Cgb%7CELU36565%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914832%7Cgb%7CELU36565%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913337%7Cgb%7CELU36105%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443913337%7Cgb%7CELU36105%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916857%7Cgb%7CELU37794%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916857%7Cgb%7CELU37794%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915502%7Cgb%7CELU36924%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443915502%7Cgb%7CELU36924%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921084%7Cgb%7CELU40854%2E1%7C.for.1-799.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.gi%7C443921084%7Cgb%7CELU40854%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915712%7Cgb%7CELU37064%2E1%7C.for.2201-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.gi%7C443915712%7Cgb%7CELU37064%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922842%7Cgb%7CELU42213%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922842%7Cgb%7CELU42213%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918751%7Cgb%7CELU39123%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443918751%7Cgb%7CELU39123%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912860%7Cgb%7CELU35983%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443912860%7Cgb%7CELU35983%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922901%7Cgb%7CELU42252%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922901%7Cgb%7CELU42252%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913566%7Cgb%7CELU36162%2E1%7C.for.1157-2601.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.gi%7C443913566%7Cgb%7CELU36162%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914292%7Cgb%7CELU36361%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914292%7Cgb%7CELU36361%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917664%7Cgb%7CELU38330%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443917664%7Cgb%7CELU38330%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921379%7Cgb%7CELU41050%2E1%7C.for.2069-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.gi%7C443921379%7Cgb%7CELU41050%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 14
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total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
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 ...processing 21 of 38
 ...trimming the rest
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
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 ...trimming the rest
 ...processing 0 of 12
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cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
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running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
 ...processing 19 of 20
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_28349
Length: 1535
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926253%7Cgb%7CELU44961%2E1%7C.for.535-1535.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.gi%7C443926253%7Cgb%7CELU44961%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921201%7Cgb%7CELU40930%2E1%7C.for.1-1427.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.gi%7C443921201%7Cgb%7CELU40930%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29160
Length: 1830
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924283%7Cgb%7CELU43333%2E1%7C.for.652-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.gi%7C443924283%7Cgb%7CELU43333%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924238%7Cgb%7CELU43291%2E1%7C.for.589-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.gi%7C443924238%7Cgb%7CELU43291%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924237%7Cgb%7CELU43290%2E1%7C.for.547-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.gi%7C443924237%7Cgb%7CELU43290%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29352
Length: 1073
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925337%7Cgb%7CELU44194%2E1%7C.for.1-1073.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.gi%7C443925337%7Cgb%7CELU44194%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29511
Length: 1330
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923460%7Cgb%7CELU42699%2E1%7C.for.1-1229.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.gi%7C443923460%7Cgb%7CELU42699%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_32665
Length: 1132
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	173	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 14
 ...processing 1 of 14
 ...processing 2 of 14
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
 ...processing 9 of 14
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	109	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	216	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	313	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	93	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	195	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	194	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	494	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	782	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	201	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	967	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-6	166	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-4	179	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	154	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	228	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	1025	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	760	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	295	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased


Maker is now finished!!!

-------------- next part --------------



From vwong at umn.edu  Mon Jul 15 11:57:30 2013
From: vwong at umn.edu (V Wong)
Date: Mon, 15 Jul 2013 12:57:30 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51DEF8FE.2000907@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
	<51DEF8FE.2000907@gmail.com>
Message-ID: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>

Hi Carson,

I tried running maker2jbrowse in the browser directory with existing
tracks, but the script expects to be run in the JBrowse directory and
printed this error:

FATAL: Can not find ./bin/flatfile-to-json.pl

Make sure you are running inside the JBrowse directory


Hi Robert,

I tried adding an Alignment2 track in the format of the example to the
browser with Maker tracks (those get viewed fine), but I am getting the
error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
though the specified file is in that location.


Thank you both for your continued aid.

Since this is departing Maker for strictly JBrowse territory, would it be
more appropriate to move to the JBrowse list?

Best,

Val


On Thu, Jul 11, 2013 at 1:27 PM, Robert Buels <rbuels at gmail.com> wrote:

> These days, it's better to use direct BAM access.  bam-to-json.pl still
> works, but the direct BAM access is much better.
>
> See http://gmod.org/wiki/JBrowse_**Configuration_Guide#Alignment_**
> Tracks_.28BAM.29<http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29>
>
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 07/11/2013 02:23 PM, Carson Holt wrote:
>
>> If you have a previous Jbrowse with already populated tracks you can
>> just, run maker2jbrowse in that directory instead of the new Jbrowse
>> directory, then the maker features will be added there.  Make a backup
>> copy of the directory before you do this of course incase you need to
>> roll back the changes.
>>
>> Alternatively you will have to add those to the new Jbrowse directory
>> using bin/bam-to-json.pl and following the instructions here -->
>> http://gmod.org/wiki/JBrowse_**Tutorial_2012#BAM_data<http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data>
>>
>> I guess Robert can chime in here as well, since we have now moved
>> outside of MAKER scripts and fully into JBrowse.
>>
>> --Carson
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Thursday, July 11, 2013 1:58 PM
>> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
>> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-**lab.org<maker-devel at yandell-lab.org>
>> >>,
>> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>> Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>> Hi Carson,
>>
>> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
>> directory, the Maker tracks are now on view.
>>
>> However, I'm having some trouble getting our older tracks (bam
>> alignments and coverage tracks) into the same browser.  Neither 1.
>> copying and pasting the tracks from the previous trackList.json to the
>> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
>>
>> doing the job.  Is it possible to merge these tracks into one browser?
>>
>> Best,
>> Val
>>
>>
>> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
>> <mailto:carsonhh at gmail.com>> wrote:
>>
>>     You next put the entire JBrowse directory into the /var/www/html/
>>     directory or wherever you have apache set up to load from (if it's
>>     not already there).  Then it will be accessible as a webpage
>>     (browser is inside the JBrowse directory).
>>
>>     Example /var/www/html/Jbrowse/
>>     Webpage --> http://localhost/Jbrowse/
>>
>>     --Carson
>>
>>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Date: Thursday, July 11, 2013 1:10 AM
>>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>>     Cc: <maker-devel at yandell-lab.org
>>     <mailto:maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>,
>> Robert Buels
>>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>>
>>     Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>>     Hi Carson,
>>
>>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>>     successfully populated the ../JBrowse/data/tracks directory with
>>     RepeatMasker, Augustus, and GeneMark predictions.
>>
>>     I'm not entirely sure how to get these numerous tracks into the
>>     browser, but that may be something to work out with JBrowse rather
>>     than Maker.
>>
>>     Best,
>>     Val
>>
>>
>>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>>     <mailto:carsonhh at gmail.com>> wrote:
>>
>>         Hi Val,
>>
>>         I've attached new files for you to test.  These will be bundled
>>         in the
>>         next maker release pending successful tests (~ 1 week).
>>
>>         Instructions:
>>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>>         .../maker/src/bin/ directory (this is just to ensure you don't
>>         accidentally overwrite it if you reinstall at any time).
>>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>>         3. You must be in the jbrowse installation directory when running
>>         maker2jbrowse.  Run the script with the -d flag and the
>>         datastore index
>>         file.
>>
>>         This new version will assign colors by copying maker.css to the
>>         jbrowse
>>         installation as apposed to replacing the genome.css file, and it
>>         will also
>>         edit the genome.css file to add the import call for maker.css.  In
>>         addition I have updated command line flags in the wrapper to do
>>         what is
>>         currently expected by flatfile-to-json.pl
>>         <http://flatfile-to-json.pl>.
>>
>>
>>         Could you test it out and let me know how it goes.
>>
>>         Thanks,
>>         Carson
>>
>>
>>
>>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>>         <mailto:carsonhh at gmail.com>> wrote:
>>
>>         >Like I said that css file is ~1 year old.  Once upon a time the
>> Jbrowse
>>         >documentation had you modify the genome.css file to create your
>> own
>>         >tracks.  Version 1.2.1 looks like it is the last version where
>> the
>>         >genome.css file that maker provided works. I can still get
>> simple test
>>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse
>> script.
>>         >But I need to fix some things, because they are all
>> indistinguishable from
>>         >each other (so it is not the desired behavior).
>>         >
>>         >Indepent of that issue though, to regenerate the original error,
>> I do the
>>         >following -->
>>         >    maker2jbrowse
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >    ERROR: No track information for source
>>         >'dpp_contig_datastore/05/1F/**contig-dpp-500-500/'
>>         >
>>         >Basically you are missing the '-d' flag (whiteout that the
>> script is
>>         >expecting a list of GFF3 files).
>>         >
>>         >So this works -->
>>         >    maker2jbrowse -d
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >
>>         >
>>         >Of course all tracks look the same though per the original issue
>> I
>>         >mentioned.
>>         >
>>         >Thanks,
>>         >Carson
>>         >
>>         >
>>         >
>>         >Some versions of Jbrowse still load fine with the script as is
>> Jbrowse
>>         >1.3,
>>         >
>>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >
>>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not
>> sure what
>>         >>you're doing with that, but it appears to be a fork of a very
>> old
>>         >>JBrowse main css file.  If that's overriding or being copied
>> over the
>>         >>JBrowse released CSS, it will break pretty much everything.  It
>> would be
>>         >>like me randomly replacing one of MAKER's Perl modules with my
>> own old
>>         >>forked copy.
>>         >>
>>         >>If what you're trying to accomplish is to add some custom
>> styles, the
>>         >>best way to do that would be to do one of:
>>         >>
>>         >>* add just your custom feature styles on theflatfile-to-json.pl<
>> http://flatfile-to-json.pl> command
>>
>>         >>line
>>         >>* add a "css": { "url": "http://url/of/your/custom.css**" } to
>> the
>>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>>         >>   (containing only your custom feature styles!)
>>         >>* add all of the custom styles to the trackList.json as a
>>         >>   string: "css": "string { of: lots and lots of; css:
>> properties; }"
>>         >>
>>         >>
>>         >>Robert Buels
>>         >>Lead Developer
>>         >>JBrowse -http://jbrowse.org
>>
>>         >>
>>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>         >>> I think you may not have it set up right.  If you run the
>> example data,
>>         >>> you can then use that.  For me it populates the JSON data
>> tracks
>>         >>> information, but nothing displays.  I think the problem is
>> with the
>>         >>>maker
>>         >>> genome.css.  It is very out of date.  I'll do some work on it
>> and then
>>         >>>get
>>         >>> your feedback.
>>         >>>
>>         >>> Thanks,
>>         >>> Carson
>>         >>>
>>         >>>
>>         >>>
>>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >>>
>>         >>>> After looking at the maker2jbrowse source (thanks for giving
>> me
>>         >>>>access),
>>         >>>> there seems to be some kind of problem with the way
>> maker2jbrowse is
>>         >>>> parsing the MAKER datastore index, leading to the script
>> complaining
>>         >>>>of
>>         >>>> 'no track information'.
>>         >>>>
>>         >>>> This would probably be easier for a MAKER developer to look
>> into.
>>         >>>>
>>         >>>>
>>         >>>> Robert Buels
>>         >>>> Lead Developer
>>         >>>> JBrowse -http://jbrowse.org
>>
>>         >>>>
>>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration
>> (much of
>>         >>>>> which is not backwards compatible with other Jbrowse
>> versions), as a
>>         >>>>> result the script maker2jbrowse has had to evolve with
>> Jbrowse (and
>>         >>>>>will
>>         >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing
>> behind). I can
>>         >>>>> have it working with whatever the most current repository
>> is if you
>>         >>>>>were
>>         >>>>> to give me a week, or you can try loading the GFF3's using
>> Jbrowse's
>>         >>>>>own
>>         >>>>> loader (tutorial here -->
>>         >>>>>http://gmod.org/wiki/**JBrowse_Tutorial_2012<http://gmod.org/wiki/JBrowse_Tutorial_2012>
>> ).
>>         >>>>>    Of course this tutorial is also likely to be somewhat
>> out of date
>>         >>>>> :-( But the 2013 version is supposed to be up and running
>> as part of
>>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>> generated
>>         >>>>> data for the tutorial, so it should be relevant to what you
>> are
>>         >>>>>doing.
>>         >>>>>
>>         >>>>> Thanks,
>>         >>>>> Carson
>>         >>>>>
>>         >>>>>
>>         >>>>>
>>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>         >>>>> To: <maker-devel at yandell-lab.org <mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>
>>         >>>>><mailto:maker-devel@**yandell-lab.org<maker-devel at yandell-lab.org><mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>>
>>
>>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>         >>>>>
>>         >>>>> Hi Maker team,
>>         >>>>>
>>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3)
>> on our
>>         >>>>> server, using the -d option for the index.log file.
>>  However, I am
>>         >>>>> getting this error for each contig:
>>         >>>>>
>>         >>>>> ERROR: No track information for source
>>         >>>>> 'AK_assembly_datastore/22/D4/**AK_contig_1/'
>>         >>>>>
>>         >>>>> Looking at the perl script, the file locations are getting
>> read, but
>>         >>>>> then the tracks aren't getting found in the hash of
>> commands.
>>         >>>>>
>>         >>>>> Any advice for getting past this will be most appreciated.
>>  Thank
>>         >>>>>you!
>>         >>>>>
>>         >>>>> Best,
>>         >>>>> Val
>>         >>>>> ______________________________**_________________
>> maker-devel mailing
>>         >>>>>list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>><mailto:maker-devel@**box290.bluehost.com<maker-devel at box290.bluehost.com>
>>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >>
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>>>
>>         >>>>> ______________________________**_________________
>>         >>>>> maker-devel mailing list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>
>>         >>>
>>         >>>
>>         >
>>         >
>>
>>
>>
>>
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From rbuels at gmail.com  Mon Jul 15 12:54:58 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 15 Jul 2013 14:54:58 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
Message-ID: <51E44582.9020100@gmail.com>

On 07/15/2013 01:57 PM, V Wong wrote:
> I tried adding an Alignment2 track in the format of the example to the
> browser with Maker tracks (those get viewed fine), but I am getting the
> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
> though the specified file is in that location.

If you visit that URL in your browser, is the bai file really there?

If so, is the BAI file on a different server from the one you're running 
JBrowse on?  If so, you'll need to enable CORS on the server for the BAI 
and BAM files.

Rob



From Michael.Li3 at AGR.GC.CA  Thu Jul 18 13:06:38 2013
From: Michael.Li3 at AGR.GC.CA (Li, Michael)
Date: Thu, 18 Jul 2013 19:06:38 +0000
Subject: [maker-devel] InterProScan v5
Message-ID: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for users. However, I noticed that maker's iprscan_batch, iprscan_wrap, ipr_update_gff and iprscan2gff3 are not compatible with this new version of IPR. Is there a workaround available or is the script easy to modify to suit the new version?
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From carsonhh at gmail.com  Thu Jul 18 13:18:20 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 18 Jul 2013 15:18:20 -0400
Subject: [maker-devel] InterProScan v5
In-Reply-To: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>
Message-ID: <CE0DB539.77E1%carsonhh@gmail.com>

All those tools were written for InterProScan 4.  We have plans to update
everything for InterProScan 5 sometime in the near future. Some will have to
be dropped or rewritten completely, while other like  ipr_update_gff and
iprscan2gff3 are both relatively simple and I could probably have those
included with the next MAKER release (current release is 2.28).  That would
be about 3 weeks from now.

--Carson



From:  "Li, Michael" <Michael.Li3 at AGR.GC.CA>
Date:  Thursday, July 18, 2013 3:06 PM
To:  "'maker-devel at yandell-lab.org'" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] InterProScan v5

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for
users. However, I noticed that maker?s iprscan_batch, iprscan_wrap,
ipr_update_gff and iprscan2gff3 are not compatible with this new version of
IPR. Is there a workaround available or is the script easy to modify to suit
the new version?
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From vwong at umn.edu  Fri Jul 19 15:36:03 2013
From: vwong at umn.edu (V Wong)
Date: Fri, 19 Jul 2013 17:36:03 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51E44582.9020100@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
	<51E44582.9020100@gmail.com>
Message-ID: <CAEi2voasDqTHLEe00+JDUgWgav-BYJuM+fPSAbK5ysZCKj6VTw@mail.gmail.com>

Ah, I just had some syntax inconsistencies between the file locations on
the server and the path for the web browser.  Thank you Rob!

Best,
Val


On Mon, Jul 15, 2013 at 2:54 PM, Robert Buels <rbuels at gmail.com> wrote:

> On 07/15/2013 01:57 PM, V Wong wrote:
>
>> I tried adding an Alignment2 track in the format of the example to the
>> browser with Maker tracks (those get viewed fine), but I am getting the
>> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
>> though the specified file is in that location.
>>
>
> If you visit that URL in your browser, is the bai file really there?
>
> If so, is the BAI file on a different server from the one you're running
> JBrowse on?  If so, you'll need to enable CORS on the server for the BAI
> and BAM files.
>
> Rob
>
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From jmdoyle at purdue.edu  Sun Jul 21 07:44:26 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Sun, 21 Jul 2013 09:44:26 -0400 (EDT)
Subject: [maker-devel] altest without MPI?
In-Reply-To: <1806377131.45449.1371745335968.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>

I just wanted to check in and say that this strategy worked really nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with protein2genome and my contigs greater than 1200000 bases.  Each of the training runs took less than 4 hours.  My final run with all my contigs (and altest) took about 5 and 1/2 days.  Not bad!   

----- Original Message -----
From: Carson Holt <carsonhh at gmail.com>
To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
Subject: Re: [maker-devel] altest without MPI?

The throughput is based on contig length, so long contigs will take longer
than short contigs.  Any contig less than 10kb is mostly useless for
annotation purposes (so you can filter those from your 800,000 right
away). Take your contigs that finish, and sum up their length to get a
better estimate of how long it will take to complete running.  Most
genomes can complete in a few days an a multi-core machine.  Bigger
genomes or bigger datasets take longer.  (note that altest evidence takes
3-4x longer to align than proteins).

The advantage of proteins is that the species do not have to be closely
related.  Nucleotide sequence diverges quickly and proteins slowly (that's
why proteins are used for phylogenetic trees).

A good strategy would be to get ~10Mb of sequence (use your longest
contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
protein2genome option to generate annotations.  Those annotations should
now be sufficient to train SNAP and Augustus.  Then you can finish by
running all your contigs with the same dataset (protein2genome now turned
off), use the newly trained snap and augustus files along with any altest
files you want to use. Note that the size of the dataset will determine
the total run time.

To get things to run faster, you can also run on your university's
computer cluster (then you will have hundreds of cpus available to you).
The purdue cluster supports MPI and with 30-50 cpus you could annotate
even large genomes in a reasonable time.  Alternatively you can request a
startup account at XSEDE, an NFS funded computer resource open to all US
institutions.  A startup allocation with 50,000 cpu hours only takes 2
weeks to approve. You should request an allocation on the Lonestar cluster
if you go that route, it has 64,000 cpus. I was able to annotate the Maize
genome (which is a very large genome at over 2 gigabases).  I used an
abnormally large EST and protein datasets (~4 gigabases of evidence which
is much more than a normal annotation job), and it completed in under 3
hours on 2,100 cpus.

--Carson


On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hi Carson (and whoever else might be reading this!)
>
>Thanks so much, I think splitting the files up using fasta_tool will
>definitely move things along.  I did a trial version with altest this
>weekend, and seemed to be averaging about an hour a scaffold (with 1
>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>seem like a reasonable estimate of the time it should take to annotate
>one sequence?  Could I be missing something in my maker_opts file?
>
>Let me back up for just a minute and describe the project a little more
>generally.  As I mentioned before, we have no protein sequences or ESTs
>for our species of interest, which is an avian species.  I could
>potentially use proteins from chicken or turkey, but neither is closely
>related to our species.  Time is a bit of an issue... do you have any
>thoughts on how much time per scaffold it should take to annotate using
>protein2genome?  If chicken and turkey are not closely related, is it
>worth the time investment?
>
>Let me finish by saying I think MAKER is wonderful, and I really
>appreciate the discussions on this group.
>
>Best wishes, Jackie 






From carsonhh at gmail.com  Sun Jul 21 15:09:12 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 21 Jul 2013 17:09:12 -0400
Subject: [maker-devel] altest without MPI?
In-Reply-To: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE11C4D7.7990%carsonhh@gmail.com>

Glad I could help. If you come across anything else, just let us know.

Thanks,
Carson



On 7/21/13 9:44 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>I just wanted to check in and say that this strategy worked really
>nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with
>protein2genome and my contigs greater than 1200000 bases.  Each of the
>training runs took less than 4 hours.  My final run with all my contigs
>(and altest) took about 5 and 1/2 days.  Not bad!
>
>----- Original Message -----
>From: Carson Holt <carsonhh at gmail.com>
>To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
>Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
>Subject: Re: [maker-devel] altest without MPI?
>
>The throughput is based on contig length, so long contigs will take longer
>than short contigs.  Any contig less than 10kb is mostly useless for
>annotation purposes (so you can filter those from your 800,000 right
>away). Take your contigs that finish, and sum up their length to get a
>better estimate of how long it will take to complete running.  Most
>genomes can complete in a few days an a multi-core machine.  Bigger
>genomes or bigger datasets take longer.  (note that altest evidence takes
>3-4x longer to align than proteins).
>
>The advantage of proteins is that the species do not have to be closely
>related.  Nucleotide sequence diverges quickly and proteins slowly (that's
>why proteins are used for phylogenetic trees).
>
>A good strategy would be to get ~10Mb of sequence (use your longest
>contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
>protein2genome option to generate annotations.  Those annotations should
>now be sufficient to train SNAP and Augustus.  Then you can finish by
>running all your contigs with the same dataset (protein2genome now turned
>off), use the newly trained snap and augustus files along with any altest
>files you want to use. Note that the size of the dataset will determine
>the total run time.
>
>To get things to run faster, you can also run on your university's
>computer cluster (then you will have hundreds of cpus available to you).
>The purdue cluster supports MPI and with 30-50 cpus you could annotate
>even large genomes in a reasonable time.  Alternatively you can request a
>startup account at XSEDE, an NFS funded computer resource open to all US
>institutions.  A startup allocation with 50,000 cpu hours only takes 2
>weeks to approve. You should request an allocation on the Lonestar cluster
>if you go that route, it has 64,000 cpus. I was able to annotate the Maize
>genome (which is a very large genome at over 2 gigabases).  I used an
>abnormally large EST and protein datasets (~4 gigabases of evidence which
>is much more than a normal annotation job), and it completed in under 3
>hours on 2,100 cpus.
>
>--Carson
>
>
>On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:
>
>>Hi Carson (and whoever else might be reading this!)
>>
>>Thanks so much, I think splitting the files up using fasta_tool will
>>definitely move things along.  I did a trial version with altest this
>>weekend, and seemed to be averaging about an hour a scaffold (with 1
>>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>>seem like a reasonable estimate of the time it should take to annotate
>>one sequence?  Could I be missing something in my maker_opts file?
>>
>>Let me back up for just a minute and describe the project a little more
>>generally.  As I mentioned before, we have no protein sequences or ESTs
>>for our species of interest, which is an avian species.  I could
>>potentially use proteins from chicken or turkey, but neither is closely
>>related to our species.  Time is a bit of an issue... do you have any
>>thoughts on how much time per scaffold it should take to annotate using
>>protein2genome?  If chicken and turkey are not closely related, is it
>>worth the time investment?
>>
>>Let me finish by saying I think MAKER is wonderful, and I really
>>appreciate the discussions on this group.
>>
>>Best wishes, Jackie
>
>
>





From Carson.Holt at oicr.on.ca  Tue Jul 23 13:00:27 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 23 Jul 2013 19:00:27 +0000
Subject: [maker-devel] Fwd: about running MAKER
In-Reply-To: <CAMNfi+gSdTtfBHD7ipTFJ08jvL3UtpbH3q+gCG-N-J-vV+Vpow@mail.gmail.com>
Message-ID: <CE143780.7AD6%carson.holt@oicr.on.ca>

If the log is growing then it is still working.  The time it takes is a function of the evidence dataset, genome size, and gene density.  Is there any way, you could try starting a second maker process in the same directory with additional CPUs to get it to complete sooner (each process will detect each other and avoid overlapping on their work, so it will still get divided up efficiently).  Also if you combine the length of all finished contigs, you will get a better idea of how much run time is remaining (i.e. See if contigs remaining are short or long compared to most contigs in the assembly).

Thanks,
Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 23, 2013 1:12 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Thanks Carson,

gephy.transcripts.fa is 64406072
geph_AS_masked.fa is 296693827

The log is growing. It finished 21700 scaffolds. I think we have nearly 38149 scaffolds. Is that means the program running good?

Sincerely,
Yunxi



2013/7/22 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Nothing looks out of the ordinary.  How big is this file --> gephy.transcripts.fa
How big is this file --> geph_AS_masked.fa

Also is the STDERR log growing or is it frozen?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, July 22, 2013 12:24 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Sorry to bother you again. I ran the MAKER for like around two weeks, but it is still running now. I attached my control files. Can you help me to see if I set something wrong? I used the masked genome as my input, so I skipped the repeatmasker in maker. I think it should be faster. I ran this mpiexec -n 8 maker

I'm running another maker using unmasked data in 16 threads, so I ran this in 8. I already got 34G data for this. Because the time cost in running already out of schedule. I'm worry about something wrong in the setting.

Thank you.
Yunxi


2013/7/14 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson.


2013/7/14 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
I would use the same data to train both.

More information here --> https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J

--Carson

From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Friday, July 12, 2013 9:04 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

One more is when I train the SNAP and Augustus, should I do them in the same time with the est2genome and protein2genome, or do them separately? Thank you.


2013/7/12 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Hi Carson

The MAKER is running fine right now. I'm confusing about using the CEGMA with MAKER to train the SNAP and Augustus.

I'm running the MAKER from est2genome with protein2genome without using the result from CEGMA. I think the data I already enough for generating the hmm.

And I got the zff from the result of CEGMA, and I followed the link last time you gave me to generate the file for SNAP and Augustus.

I'm not that clear how to combine the hmm model from CEGMA and MAKER.

Thank you for your help.

Sincerely,
Yunxi


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I think I should better to use the default, in case it occurs an error after several days' running.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Some operations are not NFS safe (NFS behaves different than normal file systems).  So maker performs those operations in the temporary directory.  If you redirect those files to an NFS location, you may get errors (basically MAKER just dies).  It won't necessarily happen, but the warning lets you know that, if it fails then you should set TMP= somewhere else before trying again.

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 3:22 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got an error message about this:
ERROR: Temporary directory set to an NFS location.
TMP=/home/lin11/tmp
The temporary directory in MAKER is specifically for
operations that are not NFS-safe. You must set TMP
to a locally mounted directory such as /tmp or add
--ignore_nfs_tmp to the maker command line to
override this error message.

Does the MAKER need a big temporary file? Because our system temporary directory may not have that much space. If it does not need that big tmp file, I can set it back to default. Or I just ignore the error message?

Thank you.


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Anything from maker under the ~/perl5/ should be deleted.  MAKER should be self contained in its own directory.  Do 'rm ~/perl5/bin/*maker*'.  If you see anything else that is maker related there delete it as well.

Example:
.../maker/bin/
.../maker/lib/
.../maker/exe/

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 1:40 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I installed the new version of MAKER. But right now have a problem of running it. Because I was missing perl dependencies, I installed the perl local library. And then I tried to run maker, it will automatically go to the one in local library called ~/perl5/bin/maker. Do you know how to get rid of this path? I found this path in .bashrc : export PATH="/home/lin11/perl5/bin:$PATH". If that ok to delete it?

Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It's been stable enough that I could remove the beta tag (no major updates in 2 months).  In fact I'll go ahead and do that.

--Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:21 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Is that the 2.28 only have the beta version?


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I'll try then let you know.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You could just install it in a new directory (I.e. maker_2.28 rather than maker).  The 2.1 version more than 2 years old (lots of changes and improvements since then).

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:11 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson
I think I may need to update MAKER too. My version is 2.1. Is the new version of MAKER changed a lot? Because someone running MAKER on the server now, can I just update it instead of delete the old one then reinstall the new version?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
If you are using MAKER 2.28, and let it do the install for you it will install mpich2 from this location --> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz

The installation will be in the .../maker/exe/mpich2 directory.

Alternatively, if you do the installation yourself, all you have to do set a few flags during install configuration.
--> ./configure --prefix=$path --enable-shared
Set $path to the location where you want MPICH2 to be installed.
Then run 'make install'

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:59 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I think it installed the 1.3.1 version. Can I update it?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It should be installed under .../maker/exe/mpich2.  Having it under ~/perl5/exe/mpich2 is odd as maker should do that.

Type 'which mpiexec' to see if there is another mpiexec installed somewhere.  Also run 'mpiexec --version'.  What does it give?  I ask because the error message you got before is the same as a bug in an old version of MPICH2 (version 1.3).  MAKER will install version 1.5.

Also run 'mpiexec -n 16 hostname'
What happens?

Thanks,
Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:17 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

How's the trip?

I did it followed your instruction. I ran ./build mpich2 first
It installed it into ~/perl5/exe/mpich2 directory.
And then i go back to maker/src ran perl build.pl<http://build.pl> and type Y to accept the MPI.
Then I ran ./build install
After that, I went to ~/.bash_profile to add the ~/perl5/exe/mpich2/bin into the PATH.
I used mpiexec -n 16 maker as the command.
Do I need to set some special variable in that three control file first?

Thank you.

Yunxi Lin

On Jul 2, 2013, at 7:44 AM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

Sorry for not responding sooner (it was a long holiday weekend in Canada).  Did you have maker install MPICH2 or did you install it yourself?  Also what is the exact command line you used to launch?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sunday, June 30, 2013 2:09 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got the errors like:
[mpiexec at bioinfo1] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file hydra_pmi_proxy (No such file or directory)
[mpiexec at bioinfo1] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:315): assert (!closed) failed
[mpiexec at bioinfo1] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec at bioinfo1] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event
[mpiexec at bioinfo1] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion

Is that means our server only has one cpu so I cannot use mpi?

Thank you.



2013/6/25 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.

When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only).  It will be in ?/maker/exe/mpich2.  This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having to get upgraded privileges.  So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.

--Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, 25 June, 2013 11:40 AM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>

Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu?  Because my school own the server, I only have the limit authorization.

Yunxi Lin

On Jun 24, 2013, at 5:39 PM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

You are most likely only getting 1 cpu of performance.

You should just install MPICH2.  It's easy just to let MAKER do it for you:
Go to the ?/maker/src/ directory
Run './Build mpich2'
Once it finishes installing, it will be in the ?/maker/exe/mpich2/bin/ directory.

Setup MAKER again to use MPICH2:
Go to the ?/maker/src/ directory
Run 'perl Build.PL'
Say yes to the "use MPI": question
Run './Build install'

Now run MAKER via 'mpiexec'.
Example --> ?/maker/exe/mpich2/bin/mpiexec -n 16 maker

The ?n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines.  You will get much better performance.

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, 24 June, 2013 7:11 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank your for your help.

My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER.

I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus.

Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way.

Sincerely,
Yunxi



2013/6/24 Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use.  If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time.  This is especially true if you use the alt_est option for evidence as these are aligned via tblastx  which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.

Also you do not need results from the entire genome to train SNAP.  If you get results from ~10Mb of the genome that is usually sufficient.  Also make sure you are taking advantage of parallelization.  Launch via MPI to get maximum performance.  I commonly launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.

--Carson


From: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Date: Sunday, 23 June, 2013 10:15 PM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Cc: <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Subject: [maker-devel] Fwd: about running MAKER

>From the GMOD helpdesk; please cc Lin, lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>.

---------- Forwarded message ----------
From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sun, Jun 23, 2013 at 4:14 PM
Subject: about running MAKER
To: "gmod-help at gmod.org<mailto:gmod-help at gmod.org>" <help at gmod.org<mailto:help at gmod.org>>


Hi

I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server.

Thank you.

Sincerely,
Lin



--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org















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From grburke at uga.edu  Tue Jul 30 13:14:02 2013
From: grburke at uga.edu (Gaelen Burke)
Date: Tue, 30 Jul 2013 19:14:02 -0000
Subject: [maker-devel] unknown error
Message-ID: <602FA505-8A78-4006-8D8F-D3EC81A73FEC@uga.edu>

Hello,
I have an error that occurs in my MAKER run for 52 of several thousand scaffolds. The annotation of these scaffolds fails, even after 3 re-tries. I also pulled out the failed sequences and started a run from scratch, with the same result. Could anyone tell me what this error means and how I could possibly fix it?
Thanks,
Gaelen Burke

Here is the message that occurs:

Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
:411
STACK: PhatHit_utils::_adjust /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit_utils.pm:
880
STACK: PhatHit_utils::adjust_start_stop /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit
_utils.pm:776
STACK: maker::auto_annotator::load_transcript_struct /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/.
./lib/maker/auto_annotator.pm:1808
STACK: maker::auto_annotator::group_transcripts /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib
/maker/auto_annotator.pm:2163
STACK: maker::auto_annotator::annotate_genes /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/ma
ker/auto_annotator.pm:877
STACK: Process::MpiChunk::_go /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:2159
STACK: Process::MpiChunk::run /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:257
STACK: Process::MpiTiers::run_all /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiTi
ers.pm:193
STACK: /usr/local/maker/latest/bin/maker:276
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while clustering transcripts into genes for annotations!!

ERROR: Chunk failed at level 20
!!
FAILED CONTIG:scaffold_0040



From vwong at umn.edu  Tue Jul  2 09:38:26 2013
From: vwong at umn.edu (V Wong)
Date: Tue, 2 Jul 2013 10:38:26 -0500
Subject: [maker-devel] maker2jbrowse implementation
Message-ID: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
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From carsonhh at gmail.com  Tue Jul  2 10:27:19 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 12:27:19 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voaffennDzBxAQhmTocoVSOcqKNZkSMTzgy9MnC2--ODrQ@mail.gmail.com>
Message-ID: <CDF873FE.65B7%carsonhh@gmail.com>

The Jbrowse codebase tends to undergo very rapid alteration (much of which
is not backwards compatible with other Jbrowse versions), as a result the
script maker2jbrowse has had to evolve with Jbrowse (and will not work with
all versions).  I'm not sure if the script is currently behind or ahead of
Jbrowse version 1.9.3 (I'm guessing behind). I can have it working with
whatever the most current repository is if you were to give me a week, or
you can try loading the GFF3's using Jbrowse's own loader (tutorial here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012).  Of course this tutorial is
also likely to be somewhat out of date :-( But the 2013 version is supposed
to be up and running as part of this years GMOD summer school in ~3 weeks.
They use MAKER generated data for the tutorial, so it should be relevant to
what you are doing.

Thanks,
Carson



From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Tuesday, July 2, 2013 11:38 AM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] maker2jbrowse implementation

Hi Maker team,

I'm trying to get Maker output into JBrowse (version 1.9.3) on our server,
using the -d option for the index.log file.  However, I am getting this
error for each contig:

ERROR: No track information for source
'AK_assembly_datastore/22/D4/AK_contig_1/'

Looking at the perl script, the file locations are getting read, but then
the tracks aren't getting found in the hash of commands.

Any advice for getting past this will be most appreciated.  Thank you!

Best,
Val
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From rbuels at gmail.com  Tue Jul  2 11:32:40 2013
From: rbuels at gmail.com (Robert Buels)
Date: Tue, 02 Jul 2013 13:32:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D30EB8.5090002@gmail.com>

One of my objectives has been maintaining complete backward 
compatibility with data formatted from JBrowse 1.2.1 onward.  I add 
capabilities, and the look and feel of the browser improves, but you can 
still view data in it that was formatted with JBrowse 1.2.1 (released 
March 17, 2011).

I would try to have a look at the maker2jbrowse implementation to 
troubleshoot further, but your source code doesn't seem to be public. 
Or at least the link to the source browser on the GMOD wiki page 
(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't 
find any kind of source code links under 
http://www.yandell-lab.org/software/maker.html.  Is the MAKER source 
code actually open?

Regarding the 2012 tutorial, the directions in the 2012 tutorial should 
still work, since I have been keeping backward compatibility with the 
scripts also.

Val, Carson, could you elaborate with details on the backward 
compatibility problems you're seeing?  Or could you give me access to 
the maker2jbrowse source code?


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Tue Jul  2 13:19:40 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 02 Jul 2013 15:19:40 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D30EB8.5090002@gmail.com>
Message-ID: <CDF89913.661B%carsonhh@gmail.com>

Good to know the tutorial is up to date.  I had to make several
consecutive updates to my script about a year ago with Jbrowse updates, so
I'm glad to know I can likely just fix whatever is wrong now and that will
be good for most previous and upcoming Jbrowse version :-)

It has more to do with converting data from GFF3.  maker2jbrowse is just a
script that wraps the flatfile-to-json.pl calls together with some css
files (all included in maker tar ball - it's open source).  So if anything
changes in flatfile-to-json.pl or the expected tags in css files then
maker2jbrowse won't work (the css files are where I usually get into
trouble). I just have to figure out what the changes are and then fix
them.  I know I had to do some updates for colors in Web Apollo recently
and I imagine I can just use that as a template.

Thanks,
Carson




On 7/2/13 1:32 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>One of my objectives has been maintaining complete backward
>compatibility with data formatted from JBrowse 1.2.1 onward.  I add
>capabilities, and the look and feel of the browser improves, but you can
>still view data in it that was formatted with JBrowse 1.2.1 (released
>March 17, 2011).
>
>I would try to have a look at the maker2jbrowse implementation to
>troubleshoot further, but your source code doesn't seem to be public.
>Or at least the link to the source browser on the GMOD wiki page
>(http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't
>find any kind of source code links under
>http://www.yandell-lab.org/software/maker.html.  Is the MAKER source
>code actually open?
>
>Regarding the 2012 tutorial, the directions in the 2012 tutorial should
>still work, since I have been keeping backward compatibility with the
>scripts also.
>
>Val, Carson, could you elaborate with details on the backward
>compatibility problems you're seeing?  Or could you give me access to
>the maker2jbrowse source code?
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From barry.moore at genetics.utah.edu  Tue Jul  2 13:24:43 2013
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Tue, 2 Jul 2013 13:24:43 -0600
Subject: [maker-devel] maker2jbrowse
References: <mailman.69.1372786364.6126.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <E031B282-253C-4DFE-9D08-ECC02501CCAD@genetics.utah.edu>

Hi Robert,

Yes, the MAKER source code is open under either the Artistic or GNU GPL for academic use.  You can download the code here:

http://yandell.topaz.genetics.utah.edu/cgi-bin/maker_license.cgi.

Registration allows us to track unique user downloads and create cool geocoded maps for funding purposes :)

B

> From: Robert Buels <rbuels at gmail.com>
> Subject: Re: [maker-devel] maker2jbrowse implementation
> Date: July 2, 2013 11:32:40 AM MDT
> To: <maker-devel at yandell-lab.org>
> 
> 
> One of my objectives has been maintaining complete backward compatibility with data formatted from JBrowse 1.2.1 onward.  I add capabilities, and the look and feel of the browser improves, but you can still view data in it that was formatted with JBrowse 1.2.1 (released March 17, 2011).
> 
> I would try to have a look at the maker2jbrowse implementation to troubleshoot further, but your source code doesn't seem to be public. Or at least the link to the source browser on the GMOD wiki page (http://gmod.org/wiki/MAKER#MAKER_Development) doesn't work, and I can't find any kind of source code links under http://www.yandell-lab.org/software/maker.html.  Is the MAKER source code actually open?
> 
> Regarding the 2012 tutorial, the directions in the 2012 tutorial should still work, since I have been keeping backward compatibility with the scripts also.
> 
> Val, Carson, could you elaborate with details on the backward compatibility problems you're seeing?  Or could you give me access to the maker2jbrowse source code?
> 
> 
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
> 
> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>  Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>> 
>> Hi Maker team,
>> 
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>> 
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> 
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>> 
>> Any advice for getting past this will be most appreciated.  Thank you!
>> 
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
> 
> 
> 
> 
> From: <maker-devel-request at yandell-lab.org>
> Subject: confirm 25a5d094a80beae62e51d1f0ee53d38a5d0bfacc
> Date: July 2, 2013 11:32:44 AM MDT
> 
> 
> If you reply to this message, keeping the Subject: header intact,
> Mailman will discard the held message.  Do this if the message is
> spam.  If you reply to this message and include an Approved: header
> with the list password in it, the message will be approved for posting
> to the list.  The Approved: header can also appear in the first line
> of the body of the reply.
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> 

Barry Moore
Research Scientist
Dept. of Human Genetics
University of Utah
Salt Lake City, UT 84112
--------------------------------------------
(801) 585-3543




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From rbuels at gmail.com  Wed Jul  3 09:45:53 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 11:45:53 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF873FE.65B7%carsonhh@gmail.com>
References: <CDF873FE.65B7%carsonhh@gmail.com>
Message-ID: <51D44731.6060308@gmail.com>

After looking at the maker2jbrowse source (thanks for giving me access), 
there seems to be some kind of problem with the way maker2jbrowse is 
parsing the MAKER datastore index, leading to the script complaining of 
'no track information'.

This would probably be easier for a MAKER developer to look into.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/02/2013 12:27 PM, Carson Holt wrote:
> The Jbrowse codebase tends to undergo very rapid alteration (much of
> which is not backwards compatible with other Jbrowse versions), as a
> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> not work with all versions).  I'm not sure if the script is currently
> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> have it working with whatever the most current repository is if you were
> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>   Of course this tutorial is also likely to be somewhat out of date
> :-( But the 2013 version is supposed to be up and running as part of
> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> data for the tutorial, so it should be relevant to what you are doing.
>
> Thanks,
> Carson
>
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Tuesday, July 2, 2013 11:38 AM
> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> Subject: [maker-devel] maker2jbrowse implementation
>
> Hi Maker team,
>
> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> server, using the -d option for the index.log file.  However, I am
> getting this error for each contig:
>
> ERROR: No track information for source
> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>
> Looking at the perl script, the file locations are getting read, but
> then the tracks aren't getting found in the hash of commands.
>
> Any advice for getting past this will be most appreciated.  Thank you!
>
> Best,
> Val
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



From carsonhh at gmail.com  Wed Jul  3 10:02:23 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 12:02:23 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D44731.6060308@gmail.com>
Message-ID: <CDF9C28B.66AF%carsonhh@gmail.com>

I think you may not have it set up right.  If you run the example data,
you can then use that.  For me it populates the JSON data tracks
information, but nothing displays.  I think the problem is with the maker
genome.css.  It is very out of date.  I'll do some work on it and then get
your feedback.

Thanks,
Carson



On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:

>After looking at the maker2jbrowse source (thanks for giving me access),
>there seems to be some kind of problem with the way maker2jbrowse is
>parsing the MAKER datastore index, leading to the script complaining of
>'no track information'.
>
>This would probably be easier for a MAKER developer to look into.
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/02/2013 12:27 PM, Carson Holt wrote:
>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> which is not backwards compatible with other Jbrowse versions), as a
>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>> not work with all versions).  I'm not sure if the script is currently
>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>> have it working with whatever the most current repository is if you were
>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>   Of course this tutorial is also likely to be somewhat out of date
>> :-( But the 2013 version is supposed to be up and running as part of
>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> data for the tutorial, so it should be relevant to what you are doing.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Tuesday, July 2, 2013 11:38 AM
>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>> Subject: [maker-devel] maker2jbrowse implementation
>>
>> Hi Maker team,
>>
>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> server, using the -d option for the index.log file.  However, I am
>> getting this error for each contig:
>>
>> ERROR: No track information for source
>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>
>> Looking at the perl script, the file locations are getting read, but
>> then the tracks aren't getting found in the hash of commands.
>>
>> Any advice for getting past this will be most appreciated.  Thank you!
>>
>> Best,
>> Val
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>





From rbuels at gmail.com  Wed Jul  3 10:14:49 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:14:49 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D44DF9.9050908@gmail.com>

How does this have anything to do with CSS?  The errors Val is talking 
about are coming from the maker2jbrowse script:

ERROR: No track information for source
 >>> 'AK_assembly_datastore/22/D4/AK_contig_1/'


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From vwong at umn.edu  Wed Jul  3 10:15:38 2013
From: vwong at umn.edu (V Wong)
Date: Wed, 3 Jul 2013 11:15:38 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <51D44731.6060308@gmail.com>
	<CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <CAEi2voZNLhwS=u2FvTukC6HoxMuF7_3p8K2y1VCy7RAFsw_xgw@mail.gmail.com>

Hi Carson and Robert,

Thank you for your feedback on this!  Carson, could you describe the set up
a little more?  For instance, are you running the script in a specific
location in the JBrowse directory?  I seem to be running into the same
problem as Robert.

Best,
Val


On Wed, Jul 3, 2013 at 11:02 AM, Carson Holt <carsonhh at gmail.com> wrote:

> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
> >After looking at the maker2jbrowse source (thanks for giving me access),
> >there seems to be some kind of problem with the way maker2jbrowse is
> >parsing the MAKER datastore index, leading to the script complaining of
> >'no track information'.
> >
> >This would probably be easier for a MAKER developer to look into.
> >
> >
> >Robert Buels
> >Lead Developer
> >JBrowse - http://jbrowse.org
> >
> >On 07/02/2013 12:27 PM, Carson Holt wrote:
> >> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >> which is not backwards compatible with other Jbrowse versions), as a
> >> result the script maker2jbrowse has had to evolve with Jbrowse (and will
> >> not work with all versions).  I'm not sure if the script is currently
> >> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >> have it working with whatever the most current repository is if you were
> >> to give me a week, or you can try loading the GFF3's using Jbrowse's own
> >> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>   Of course this tutorial is also likely to be somewhat out of date
> >> :-( But the 2013 version is supposed to be up and running as part of
> >> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >> data for the tutorial, so it should be relevant to what you are doing.
> >>
> >> Thanks,
> >> Carson
> >>
> >>
> >>
> >> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >> Date: Tuesday, July 2, 2013 11:38 AM
> >> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
> >> Subject: [maker-devel] maker2jbrowse implementation
> >>
> >> Hi Maker team,
> >>
> >> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >> server, using the -d option for the index.log file.  However, I am
> >> getting this error for each contig:
> >>
> >> ERROR: No track information for source
> >> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>
> >> Looking at the perl script, the file locations are getting read, but
> >> then the tracks aren't getting found in the hash of commands.
> >>
> >> Any advice for getting past this will be most appreciated.  Thank you!
> >>
> >> Best,
> >> Val
> >> _______________________________________________ maker-devel mailing list
> >> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com
> >
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
> >>
> >> _______________________________________________
> >> maker-devel mailing list
> >> maker-devel at box290.bluehost.com
> >> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> >>
>
>
>
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From rbuels at gmail.com  Wed Jul  3 10:39:51 2013
From: rbuels at gmail.com (Robert Buels)
Date: Wed, 03 Jul 2013 12:39:51 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9C28B.66AF%carsonhh@gmail.com>
References: <CDF9C28B.66AF%carsonhh@gmail.com>
Message-ID: <51D453D7.4070801@gmail.com>

Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what 
you're doing with that, but it appears to be a fork of a very old 
JBrowse main css file.  If that's overriding or being copied over the 
JBrowse released CSS, it will break pretty much everything.  It would be 
like me randomly replacing one of MAKER's Perl modules with my own old 
forked copy.

If what you're trying to accomplish is to add some custom styles, the 
best way to do that would be to do one of:

* add just your custom feature styles on the flatfile-to-json.pl command 
line
* add a "css": { "url": "http://url/of/your/custom.css" } to the
   JBrowse trackList.json someplace in the workflow (easy to add
   things to JSON files with JSON.pm) that loads your custom CSS
   (containing only your custom feature styles!)
* add all of the custom styles to the trackList.json as a
   string: "css": "string { of: lots and lots of; css: properties; }"


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/03/2013 12:02 PM, Carson Holt wrote:
> I think you may not have it set up right.  If you run the example data,
> you can then use that.  For me it populates the JSON data tracks
> information, but nothing displays.  I think the problem is with the maker
> genome.css.  It is very out of date.  I'll do some work on it and then get
> your feedback.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>> After looking at the maker2jbrowse source (thanks for giving me access),
>> there seems to be some kind of problem with the way maker2jbrowse is
>> parsing the MAKER datastore index, leading to the script complaining of
>> 'no track information'.
>>
>> This would probably be easier for a MAKER developer to look into.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>> which is not backwards compatible with other Jbrowse versions), as a
>>> result the script maker2jbrowse has had to evolve with Jbrowse (and will
>>> not work with all versions).  I'm not sure if the script is currently
>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>> have it working with whatever the most current repository is if you were
>>> to give me a week, or you can try loading the GFF3's using Jbrowse's own
>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>    Of course this tutorial is also likely to be somewhat out of date
>>> :-( But the 2013 version is supposed to be up and running as part of
>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>> data for the tutorial, so it should be relevant to what you are doing.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>> Date: Tuesday, July 2, 2013 11:38 AM
>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>> Subject: [maker-devel] maker2jbrowse implementation
>>>
>>> Hi Maker team,
>>>
>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>> server, using the -d option for the index.log file.  However, I am
>>> getting this error for each contig:
>>>
>>> ERROR: No track information for source
>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>
>>> Looking at the perl script, the file locations are getting read, but
>>> then the tracks aren't getting found in the hash of commands.
>>>
>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>
>>> Best,
>>> Val
>>> _______________________________________________ maker-devel mailing list
>>> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>
>
>



From carsonhh at gmail.com  Wed Jul  3 13:26:32 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 03 Jul 2013 15:26:32 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51D453D7.4070801@gmail.com>
Message-ID: <CDF9E0AE.6703%carsonhh@gmail.com>

Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
documentation had you modify the genome.css file to create your own
tracks.  Version 1.2.1 looks like it is the last version where the
genome.css file that maker provided works. I can still get simple test
GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
But I need to fix some things, because they are all indistinguishable from
each other (so it is not the desired behavior).

Indepent of that issue though, to regenerate the original error, I do the
following -->
    maker2jbrowse  
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 
    ERROR: No track information for source
'dpp_contig_datastore/05/1F/contig-dpp-500-500/'

Basically you are missing the '-d' flag (whiteout that the script is
expecting a list of GFF3 files).

So this works -->
    maker2jbrowse -d
~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_data
store_index.log 


Of course all tracks look the same though per the original issue I
mentioned.

Thanks,
Carson



Some versions of Jbrowse still load fine with the script as is Jbrowse
1.3, 

On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:

>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>you're doing with that, but it appears to be a fork of a very old
>JBrowse main css file.  If that's overriding or being copied over the
>JBrowse released CSS, it will break pretty much everything.  It would be
>like me randomly replacing one of MAKER's Perl modules with my own old
>forked copy.
>
>If what you're trying to accomplish is to add some custom styles, the
>best way to do that would be to do one of:
>
>* add just your custom feature styles on the flatfile-to-json.pl command
>line
>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>   JBrowse trackList.json someplace in the workflow (easy to add
>   things to JSON files with JSON.pm) that loads your custom CSS
>   (containing only your custom feature styles!)
>* add all of the custom styles to the trackList.json as a
>   string: "css": "string { of: lots and lots of; css: properties; }"
>
>
>Robert Buels
>Lead Developer
>JBrowse - http://jbrowse.org
>
>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> I think you may not have it set up right.  If you run the example data,
>> you can then use that.  For me it populates the JSON data tracks
>> information, but nothing displays.  I think the problem is with the
>>maker
>> genome.css.  It is very out of date.  I'll do some work on it and then
>>get
>> your feedback.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>
>>> After looking at the maker2jbrowse source (thanks for giving me
>>>access),
>>> there seems to be some kind of problem with the way maker2jbrowse is
>>> parsing the MAKER datastore index, leading to the script complaining of
>>> 'no track information'.
>>>
>>> This would probably be easier for a MAKER developer to look into.
>>>
>>>
>>> Robert Buels
>>> Lead Developer
>>> JBrowse - http://jbrowse.org
>>>
>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>will
>>>> not work with all versions).  I'm not sure if the script is currently
>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>> have it working with whatever the most current repository is if you
>>>>were
>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>own
>>>> loader (tutorial here --> http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>> data for the tutorial, so it should be relevant to what you are doing.
>>>>
>>>> Thanks,
>>>> Carson
>>>>
>>>>
>>>>
>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>
>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>
>>>> Hi Maker team,
>>>>
>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>> server, using the -d option for the index.log file.  However, I am
>>>> getting this error for each contig:
>>>>
>>>> ERROR: No track information for source
>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>
>>>> Looking at the perl script, the file locations are getting read, but
>>>> then the tracks aren't getting found in the hash of commands.
>>>>
>>>> Any advice for getting past this will be most appreciated.  Thank you!
>>>>
>>>> Best,
>>>> Val
>>>> _______________________________________________ maker-devel mailing
>>>>list
>>>> maker-devel at box290.bluehost.com
>>>><mailto:maker-devel at box290.bluehost.com>
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>>>
>>>> _______________________________________________
>>>> maker-devel mailing list
>>>> maker-devel at box290.bluehost.com
>>>> 
>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>>
>>
>>
>>





From benayoun at stanford.edu  Fri Jul  5 15:35:44 2013
From: benayoun at stanford.edu (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:35:44 -0700
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
References: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>
Message-ID: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
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From carsonhh at gmail.com  Mon Jul  8 08:20:53 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 10:20:53 -0400
Subject: [maker-devel] FAILED contigs
In-Reply-To: <CACczxvB6Sw=QH1kW6WbfyhRnteA85j3SD4ov6jgZkCy6Fy2C9A@mail.gmail.com>
Message-ID: <CE00422F.6A5C%carsonhh@gmail.com>

In your MAKER STDERR (printed to screen or captured as part of run), search
for the word ERROR.  That will give a more specific explanation as to why it
is failing.  If you did not capture this on your first run, you may need to
redirect it to a file on a retry.

Example --> maker 2> error.log

Thanks,
Carson

From:  B?r?nice Benayoun <benayoun at stanford.edu>
Date:  Friday, July 5, 2013 5:35 PM
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] FAILED contigs

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice


-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
BRUNET Laboratory, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120 
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/ <http://www.stanford.edu/group/brunet/>
<http://www.stanford.edu/group/brunet/>
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From berenice.benayoun at gmail.com  Fri Jul  5 15:33:35 2013
From: berenice.benayoun at gmail.com (=?ISO-8859-1?Q?B=E9r=E9nice_Benayoun?=)
Date: Fri, 5 Jul 2013 14:33:35 -0700
Subject: [maker-devel] FAILED contigs
Message-ID: <CACczxvAY4GBKsR3MYN_sFsyuHMGJR0THuEvvWtuA_mXS8_zCJQ@mail.gmail.com>

Hi maker development team,

sorry to bother you again.

I was going through the results, and it seems I have a number of contigs
that are consistently failing during the annotation of my genome
(eg, in the log, I find something like "GapFilledScaffold_3308
maker_folder_June27_datastore/0E/FF/GapFilledScaffold_3308/ FAILED", and no
annotation gets outputted).

No matter how many times I retry their annotation, they start then fail
during. Most of the contigs in my assembly still make it through the
pipeline.

Do you have any idea on why some contigs fails for annotation or any advice
on what to do to force maker to produce an output on these ? Is there
anything I can do to bypass this issue?

Thanks so much in advance for your insights on this issue!

Best,

Berenice

-- 
B?r?nice A. BENAYOUN, Ph.D.
Stanford University/Genetics Department
*BRUNET Laboratory*, 'Molecular Basis of Longevity and Age Related Diseases'
M312 Alway Building
300, Pasteur Drive
MC 5120
Stanford, CA 94305-5120
USA
Email: benayoun at stanford.edu
Web: www.stanford.edu/group/brunet/
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From onson001 at umn.edu  Mon Jul  8 16:12:06 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Mon, 8 Jul 2013 17:12:06 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
Message-ID: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>

Maker Developers,

I am testing Maker on a well annotated contig from the encode project and
in one of the genes, maker does not output an exon despite HSPs supporting
it. I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question.

I even set the parameters est2genome and protein2genome to 1 but still
Maker did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks,
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From carsonhh at gmail.com  Mon Jul  8 19:55:15 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 08 Jul 2013 21:55:15 -0400
Subject: [maker-devel] Maker not outputting exons with EST and Protein
 Evidence
In-Reply-To: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
Message-ID: <CE00DF97.6C2A%carsonhh@gmail.com>

This is because augustus never calls it either without hints or after being
given hints by MAKER.  This may be because even though the exon has support
from ESTs and protein alignments, it breaks the open reading frame (you can
check using apollo ? just click and drag them into the annotation tier).  I
did this individually for each of the polished proteins and ESTs, and none
have proper open reading frame.

Perhaps the official annotation contains a frame shift or something to make
it work (augustus can't do that).  Such a thing is not all that uncommon.
There are many instances of RefSeq annotations for example where if you cut
out the exons and try and translate them, they won't translate.  This can
happen because the reference sequence changed or is incorrect, and if the
annotation was generated from a different assembly, then it just gets mapped
as best as possible to the current assembly and the correct protein
translation is saved elsewhere in the database (even though manual
translation won't directly reproduce it).  Genes where this happens make up
just under 1% of the human genome (but they can drive you nuts especially if
your analysis expects protein sequence to match the nucleotide sequence
translation).  It's really just an artifacts of the process used to move
annotations forward on the humans genome every time they update the
assembly.

Thanks,
Carson


From:  Innocent Onsongo <onson001 at umn.edu>
Date:  Monday, July 8, 2013 6:12 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Maker not outputting exons with EST and Protein
Evidence

Maker Developers, 

I am testing Maker on a well annotated contig from the encode project and in
one of the genes, maker does not output an exon despite HSPs supporting it.
I have attached a compressed folder with

ENr122_genes.gff: The validated genes as per encode
ENr122.gff: Makers output
maker_opts.ctl: The control file I used
ENr122_98669-134249.pptx: A power point visually illustrated the exon in
question. 

I even set the parameters est2genome and protein2genome to 1 but still Maker
did not output this exon.

Is there a good reason Maker does no have this exon in its final model
despite the HSPs supporting it?

Thanks, 
Getiria

-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From carsonhh at gmail.com  Tue Jul  9 09:57:09 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 09 Jul 2013 11:57:09 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CDF9E0AE.6703%carsonhh@gmail.com>
Message-ID: <CE01A884.6C92%carsonhh@gmail.com>

Hi Val,

I've attached new files for you to test.  These will be bundled in the
next maker release pending successful tests (~ 1 week).

Instructions:
1. Place maker2jbrowse in your .../maker/bin/ directory and
.../maker/src/bin/ directory (this is just to ensure you don't
accidentally overwrite it if you reinstall at any time).
2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
3. You must be in the jbrowse installation directory when running
maker2jbrowse.  Run the script with the -d flag and the datastore index
file.

This new version will assign colors by copying maker.css to the jbrowse
installation as apposed to replacing the genome.css file, and it will also
edit the genome.css file to add the import call for maker.css.  In
addition I have updated command line flags in the wrapper to do what is
currently expected by flatfile-to-json.pl.

Could you test it out and let me know how it goes.

Thanks,
Carson



On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:

>Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>documentation had you modify the genome.css file to create your own
>tracks.  Version 1.2.1 looks like it is the last version where the
>genome.css file that maker provided works. I can still get simple test
>GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>But I need to fix some things, because they are all indistinguishable from
>each other (so it is not the desired behavior).
>
>Indepent of that issue though, to regenerate the original error, I do the
>following -->
>    maker2jbrowse 
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>    ERROR: No track information for source
>'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>
>Basically you are missing the '-d' flag (whiteout that the script is
>expecting a list of GFF3 files).
>
>So this works -->
>    maker2jbrowse -d
>~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>a
>store_index.log 
>
>
>Of course all tracks look the same though per the original issue I
>mentioned.
>
>Thanks,
>Carson
>
>
>
>Some versions of Jbrowse still load fine with the script as is Jbrowse
>1.3, 
>
>On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>
>>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>you're doing with that, but it appears to be a fork of a very old
>>JBrowse main css file.  If that's overriding or being copied over the
>>JBrowse released CSS, it will break pretty much everything.  It would be
>>like me randomly replacing one of MAKER's Perl modules with my own old
>>forked copy.
>>
>>If what you're trying to accomplish is to add some custom styles, the
>>best way to do that would be to do one of:
>>
>>* add just your custom feature styles on the flatfile-to-json.pl command
>>line
>>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>   JBrowse trackList.json someplace in the workflow (easy to add
>>   things to JSON files with JSON.pm) that loads your custom CSS
>>   (containing only your custom feature styles!)
>>* add all of the custom styles to the trackList.json as a
>>   string: "css": "string { of: lots and lots of; css: properties; }"
>>
>>
>>Robert Buels
>>Lead Developer
>>JBrowse - http://jbrowse.org
>>
>>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>> I think you may not have it set up right.  If you run the example data,
>>> you can then use that.  For me it populates the JSON data tracks
>>> information, but nothing displays.  I think the problem is with the
>>>maker
>>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>get
>>> your feedback.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>
>>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>access),
>>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>> parsing the MAKER datastore index, leading to the script complaining
>>>>of
>>>> 'no track information'.
>>>>
>>>> This would probably be easier for a MAKER developer to look into.
>>>>
>>>>
>>>> Robert Buels
>>>> Lead Developer
>>>> JBrowse - http://jbrowse.org
>>>>
>>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>>>>> which is not backwards compatible with other Jbrowse versions), as a
>>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>will
>>>>> not work with all versions).  I'm not sure if the script is currently
>>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>>>>> have it working with whatever the most current repository is if you
>>>>>were
>>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>>>>>own
>>>>> loader (tutorial here -->
>>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>    Of course this tutorial is also likely to be somewhat out of date
>>>>> :-( But the 2013 version is supposed to be up and running as part of
>>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>>>>> data for the tutorial, so it should be relevant to what you are
>>>>>doing.
>>>>>
>>>>> Thanks,
>>>>> Carson
>>>>>
>>>>>
>>>>>
>>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>> To: <maker-devel at yandell-lab.org
>>>>><mailto:maker-devel at yandell-lab.org>>
>>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>
>>>>> Hi Maker team,
>>>>>
>>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>> server, using the -d option for the index.log file.  However, I am
>>>>> getting this error for each contig:
>>>>>
>>>>> ERROR: No track information for source
>>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>
>>>>> Looking at the perl script, the file locations are getting read, but
>>>>> then the tracks aren't getting found in the hash of commands.
>>>>>
>>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>you!
>>>>>
>>>>> Best,
>>>>> Val
>>>>> _______________________________________________ maker-devel mailing
>>>>>list
>>>>> maker-devel at box290.bluehost.com
>>>>><mailto:maker-devel at box290.bluehost.com>
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> maker-devel mailing list
>>>>> maker-devel at box290.bluehost.com
>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>g
>>>>>
>>>
>>>
>>>
>
>

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From Carson.Holt at oicr.on.ca  Tue Jul  9 13:19:14 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 9 Jul 2013 19:19:14 +0000
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE01D9F3.6CF4%carson.holt@oicr.on.ca>

It's perfectly safe to kill.

If you are constantly getting FAIL in the datastore index, then something
is wrong.  If you are capturing the jobs STDERR, try looking for the term
ERROR or FATAL for a better explanation as to why it's failing and send
the error to me.

Thanks,
Carson


On 7/9/13 2:47 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hello Maker Developers!
>
>I have a quick question... I've been using MAKER to annotate a genome (it
>has been running for about 6 days with 48 cpus).  Many of my contigs have
>failed, surely because most of them are smaller than the 10 kb limit I
>set, which is fine.  My concern is that although I've set tries = 2, the
>index log seems to indicate that MAKER is on its fourth try for some of
>the contigs (see attached).  Is is safe to shut MAKER down, or are there
>clean-up steps at the end of the annotation process that need to be
>allowed to occur?  Oh, and I'm using MAKER 2.28.
>
>Best, Jacqueline
>
>




From onson001 at umn.edu  Tue Jul  9 15:29:21 2013
From: onson001 at umn.edu (Innocent Onsongo)
Date: Tue, 9 Jul 2013 16:29:21 -0500
Subject: [maker-devel] Maker not outputting exons with EST and Protein
	Evidence
In-Reply-To: <CE00DF97.6C2A%carsonhh@gmail.com>
References: <CACFwDdLxrr3ubgf3D8bE4bCZk2dx3+9D+wD_ienPjyiRVa0g4g@mail.gmail.com>
	<CE00DF97.6C2A%carsonhh@gmail.com>
Message-ID: <CACFwDdLkUR3A-j8dzFj=GujNz6oKmL0RpXjpH6bZhr53Tr1rcg@mail.gmail.com>

Thanks for the insight.


On Mon, Jul 8, 2013 at 8:55 PM, Carson Holt <carsonhh at gmail.com> wrote:

> This is because augustus never calls it either without hints or after
> being given hints by MAKER.  This may be because even though the exon has
> support from ESTs and protein alignments, it breaks the open reading frame
> (you can check using apollo ? just click and drag them into the annotation
> tier).  I did this individually for each of the polished proteins and ESTs,
> and none have proper open reading frame.
>
> Perhaps the official annotation contains a frame shift or something to
> make it work (augustus can't do that).  Such a thing is not all that
> uncommon.  There are many instances of RefSeq annotations for example where
> if you cut out the exons and try and translate them, they won't translate.
>  This can happen because the reference sequence changed or is incorrect,
> and if the annotation was generated from a different assembly, then it just
> gets mapped as best as possible to the current assembly and the correct
> protein translation is saved elsewhere in the database (even though manual
> translation won't directly reproduce it).  Genes where this happens make up
> just under 1% of the human genome (but they can drive you nuts especially
> if your analysis expects protein sequence to match the nucleotide sequence
> translation).  It's really just an artifacts of the process used to move
> annotations forward on the humans genome every time they update the
> assembly.
>
> Thanks,
> Carson
>
>
> From: Innocent Onsongo <onson001 at umn.edu>
> Date: Monday, July 8, 2013 6:12 PM
> To: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Maker not outputting exons with EST and Protein
> Evidence
>
> Maker Developers,
>
> I am testing Maker on a well annotated contig from the encode project and
> in one of the genes, maker does not output an exon despite HSPs supporting
> it. I have attached a compressed folder with
>
> ENr122_genes.gff: The validated genes as per encode
> ENr122.gff: Makers output
> maker_opts.ctl: The control file I used
> ENr122_98669-134249.pptx: A power point visually illustrated the exon in
> question.
>
> I even set the parameters est2genome and protein2genome to 1 but still
> Maker did not output this exon.
>
> Is there a good reason Maker does no have this exon in its final model
> despite the HSPs supporting it?
>
> Thanks,
> Getiria
>
> --
> Getiria Onsongo, Ph.D.
> Informatics Analyst, Research Informatics Support System
> Minnesota Supercomputing Institute for Advanced Computational Research
> University of Minnesota
> Minneapolis, MN 55455
> Phone: 612-624-0532
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Getiria Onsongo, Ph.D.
Informatics Analyst, Research Informatics Support System
Minnesota Supercomputing Institute for Advanced Computational Research
University of Minnesota
Minneapolis, MN 55455
Phone: 612-624-0532
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From jmdoyle at purdue.edu  Tue Jul  9 12:47:46 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Tue, 9 Jul 2013 14:47:46 -0400 (EDT)
Subject: [maker-devel] MAKER just won't quit?
In-Reply-To: <53458481.77205.1373395049899.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <847425992.77263.1373395666911.JavaMail.root@mailhub042.itcs.purdue.edu>

Hello Maker Developers!

I have a quick question... I've been using MAKER to annotate a genome (it has been running for about 6 days with 48 cpus).  Many of my contigs have failed, surely because most of them are smaller than the 10 kb limit I set, which is fine.  My concern is that although I've set tries = 2, the index log seems to indicate that MAKER is on its fourth try for some of the contigs (see attached).  Is is safe to shut MAKER down, or are there clean-up steps at the end of the annotation process that need to be allowed to occur?  Oh, and I'm using MAKER 2.28.

Best, Jacqueline


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From yuharas at takara-bio.co.jp  Wed Jul 10 20:27:12 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 11:27:12 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>

Dear developers

I'm considering using MAKER2 to annotate plant genome (~1Gb) I've assembled using illumina HiSeq data.
And I'm planning to obtain mRNA-seq data by using HiSeq.
Do you have any recommendation of sequencing depth of RNA-seq data for using MAKER2 annotation pipeline?

Thanks,
Satoshi




From carsonhh at gmail.com  Wed Jul 10 20:40:52 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 10 Jul 2013 22:40:52 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
Message-ID: <CE039117.6E22%carsonhh@gmail.com>

As far as total depth I don't know, but I'd recommend using something like
trinity to assemble the reads and supply them to the est= option in fasta
format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From yuharas at takara-bio.co.jp  Wed Jul 10 22:47:10 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Thu, 11 Jul 2013 13:47:10 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE039117.6E22%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F3445@TKREXMB3.central.takara.co.jp>
	<CE039117.6E22%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>

Dear Carson

Thank you for your quick reply.
Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
although the tutorial contains information about Tophat and Cufflinks?

Satoshi


-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 11:41 AM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

As far as total depth I don't know, but I'd recommend using something like trinity to assemble the reads and supply them to the est= option in fasta format.

--Carson



On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear developers
>
>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>assembled using illumina HiSeq data.
>And I'm planning to obtain mRNA-seq data by using HiSeq.
>Do you have any recommendation of sequencing depth of RNA-seq data for 
>using MAKER2 annotation pipeline?
>
>Thanks,
>Satoshi
>
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From vwong at umn.edu  Wed Jul 10 23:10:52 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 00:10:52 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE01A884.6C92%carsonhh@gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
Message-ID: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser,
but that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:

> Hi Val,
>
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
>
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
>
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl.
>
> Could you test it out and let me know how it goes.
>
> Thanks,
> Carson
>
>
>
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
> >documentation had you modify the genome.css file to create your own
> >tracks.  Version 1.2.1 looks like it is the last version where the
> >genome.css file that maker provided works. I can still get simple test
> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
> >But I need to fix some things, because they are all indistinguishable from
> >each other (so it is not the desired behavior).
> >
> >Indepent of that issue though, to regenerate the original error, I do the
> >following -->
> >    maker2jbrowse
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >    ERROR: No track information for source
> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
> >
> >Basically you are missing the '-d' flag (whiteout that the script is
> >expecting a list of GFF3 files).
> >
> >So this works -->
> >    maker2jbrowse -d
> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
> >a
> >store_index.log
> >
> >
> >Of course all tracks look the same though per the original issue I
> >mentioned.
> >
> >Thanks,
> >Carson
> >
> >
> >
> >Some versions of Jbrowse still load fine with the script as is Jbrowse
> >1.3,
> >
> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
> >
> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
> >>you're doing with that, but it appears to be a fork of a very old
> >>JBrowse main css file.  If that's overriding or being copied over the
> >>JBrowse released CSS, it will break pretty much everything.  It would be
> >>like me randomly replacing one of MAKER's Perl modules with my own old
> >>forked copy.
> >>
> >>If what you're trying to accomplish is to add some custom styles, the
> >>best way to do that would be to do one of:
> >>
> >>* add just your custom feature styles on the flatfile-to-json.pl command
> >>line
> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
> >>   JBrowse trackList.json someplace in the workflow (easy to add
> >>   things to JSON files with JSON.pm) that loads your custom CSS
> >>   (containing only your custom feature styles!)
> >>* add all of the custom styles to the trackList.json as a
> >>   string: "css": "string { of: lots and lots of; css: properties; }"
> >>
> >>
> >>Robert Buels
> >>Lead Developer
> >>JBrowse - http://jbrowse.org
> >>
> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
> >>> I think you may not have it set up right.  If you run the example data,
> >>> you can then use that.  For me it populates the JSON data tracks
> >>> information, but nothing displays.  I think the problem is with the
> >>>maker
> >>> genome.css.  It is very out of date.  I'll do some work on it and then
> >>>get
> >>> your feedback.
> >>>
> >>> Thanks,
> >>> Carson
> >>>
> >>>
> >>>
> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
> >>>
> >>>> After looking at the maker2jbrowse source (thanks for giving me
> >>>>access),
> >>>> there seems to be some kind of problem with the way maker2jbrowse is
> >>>> parsing the MAKER datastore index, leading to the script complaining
> >>>>of
> >>>> 'no track information'.
> >>>>
> >>>> This would probably be easier for a MAKER developer to look into.
> >>>>
> >>>>
> >>>> Robert Buels
> >>>> Lead Developer
> >>>> JBrowse - http://jbrowse.org
> >>>>
> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
> >>>>> which is not backwards compatible with other Jbrowse versions), as a
> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
> >>>>>will
> >>>>> not work with all versions).  I'm not sure if the script is currently
> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
> >>>>> have it working with whatever the most current repository is if you
> >>>>>were
> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
> >>>>>own
> >>>>> loader (tutorial here -->
> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
> >>>>>    Of course this tutorial is also likely to be somewhat out of date
> >>>>> :-( But the 2013 version is supposed to be up and running as part of
> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
> >>>>> data for the tutorial, so it should be relevant to what you are
> >>>>>doing.
> >>>>>
> >>>>> Thanks,
> >>>>> Carson
> >>>>>
> >>>>>
> >>>>>
> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
> >>>>> To: <maker-devel at yandell-lab.org
> >>>>><mailto:maker-devel at yandell-lab.org>>
> >>>>> Subject: [maker-devel] maker2jbrowse implementation
> >>>>>
> >>>>> Hi Maker team,
> >>>>>
> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
> >>>>> server, using the -d option for the index.log file.  However, I am
> >>>>> getting this error for each contig:
> >>>>>
> >>>>> ERROR: No track information for source
> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
> >>>>>
> >>>>> Looking at the perl script, the file locations are getting read, but
> >>>>> then the tracks aren't getting found in the hash of commands.
> >>>>>
> >>>>> Any advice for getting past this will be most appreciated.  Thank
> >>>>>you!
> >>>>>
> >>>>> Best,
> >>>>> Val
> >>>>> _______________________________________________ maker-devel mailing
> >>>>>list
> >>>>> maker-devel at box290.bluehost.com
> >>>>><mailto:maker-devel at box290.bluehost.com>
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> maker-devel mailing list
> >>>>> maker-devel at box290.bluehost.com
> >>>>>
> >>>>>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
> >>>>>g
> >>>>>
> >>>
> >>>
> >>>
> >
> >
>
>
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From carsonhh at gmail.com  Thu Jul 11 05:37:13 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:37:13 -0400
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
Message-ID: <CE0410D8.6E4A%carsonhh@gmail.com>

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to
cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks,
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something
>like trinity to assemble the reads and supply them to the est= option in
>fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>





From carsonhh at gmail.com  Thu Jul 11 05:44:07 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 07:44:07 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <CE04120C.6E55%carsonhh@gmail.com>

You next put the entire JBrowse directory into the /var/www/html/ directory
or wherever you have apache set up to load from (if it's not already there).
Then it will be accessible as a webpage (browser is inside the JBrowse
directory).

Example /var/www/html/Jbrowse/
Webpage --> http://localhost/Jbrowse/

--Carson

From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:10 AM
To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Thanks!  I followed your instructions, and maker2jbrowse, and it
successfully populated the ../JBrowse/data/tracks directory with
RepeatMasker, Augustus, and GeneMark predictions.

I'm not entirely sure how to get these numerous tracks into the browser, but
that may be something to work out with JBrowse rather than Maker.

Best,
Val


On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
> Hi Val,
> 
> I've attached new files for you to test.  These will be bundled in the
> next maker release pending successful tests (~ 1 week).
> 
> Instructions:
> 1. Place maker2jbrowse in your .../maker/bin/ directory and
> .../maker/src/bin/ directory (this is just to ensure you don't
> accidentally overwrite it if you reinstall at any time).
> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
> 3. You must be in the jbrowse installation directory when running
> maker2jbrowse.  Run the script with the -d flag and the datastore index
> file.
> 
> This new version will assign colors by copying maker.css to the jbrowse
> installation as apposed to replacing the genome.css file, and it will also
> edit the genome.css file to add the import call for maker.css.  In
> addition I have updated command line flags in the wrapper to do what is
> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
> 
> Could you test it out and let me know how it goes.
> 
> Thanks,
> Carson
> 
> 
> 
> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
> 
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>> >>you're doing with that, but it appears to be a fork of a very old
>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>> >>forked copy.
>>> >>
>>> >>If what you're trying to accomplish is to add some custom styles, the
>>> >>best way to do that would be to do one of:
>>> >>
>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>> <http://flatfile-to-json.pl>  command
>>> >>line
>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>> >>   (containing only your custom feature styles!)
>>> >>* add all of the custom styles to the trackList.json as a
>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>> >>
>>> >>
>>> >>Robert Buels
>>> >>Lead Developer
>>> >>JBrowse - http://jbrowse.org
>>> >>
>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>> >>> I think you may not have it set up right.  If you run the example data,
>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>> >>> information, but nothing displays.  I think the problem is with the
>>>> >>>maker
>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>> >>>get
>>>> >>> your feedback.
>>>> >>>
>>>> >>> Thanks,
>>>> >>> Carson
>>>> >>>
>>>> >>>
>>>> >>>
>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>> >>>
>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>> >>>>access),
>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>> >>>>of
>>>>> >>>> 'no track information'.
>>>>> >>>>
>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>> >>>>
>>>>> >>>>
>>>>> >>>> Robert Buels
>>>>> >>>> Lead Developer
>>>>> >>>> JBrowse - http://jbrowse.org
>>>>> >>>>
>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>>>>>> >>>>>will
>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>> currently
>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>> >>>>> have it working with whatever the most current repository is if you
>>>>>> >>>>>were
>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>> Jbrowse's
>>>>>> >>>>>own
>>>>>> >>>>> loader (tutorial here -->
>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>> generated
>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>> >>>>>doing.
>>>>>> >>>>>
>>>>>> >>>>> Thanks,
>>>>>> >>>>> Carson
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>> >>>>>
>>>>>> >>>>> Hi Maker team,
>>>>>> >>>>>
>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>> >>>>> getting this error for each contig:
>>>>>> >>>>>
>>>>>> >>>>> ERROR: No track information for source
>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>> >>>>>
>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>> >>>>>
>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>> >>>>>you!
>>>>>> >>>>>
>>>>>> >>>>> Best,
>>>>>> >>>>> Val
>>>>>> >>>>> _______________________________________________ maker-devel mailing
>>>>>> >>>>>list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>>>> >>>>>
>>>>>> >>>>> _______________________________________________
>>>>>> >>>>> maker-devel mailing list
>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>> >>>>>
>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>> >>>>>g
>>>>>> >>>>>
>>>> >>>
>>>> >>>
>>>> >>>
>> >
>> >
> 



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From vwong at umn.edu  Thu Jul 11 11:58:42 2013
From: vwong at umn.edu (V Wong)
Date: Thu, 11 Jul 2013 12:58:42 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE04120C.6E55%carsonhh@gmail.com>
References: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
	<CE04120C.6E55%carsonhh@gmail.com>
Message-ID: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl is doing the job.  Is it possible to merge these tracks
into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:

> You next put the entire JBrowse directory into the /var/www/html/
> directory or wherever you have apache set up to load from (if it's not
> already there).  Then it will be accessible as a webpage (browser is inside
> the JBrowse directory).
>
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
>
> --Carson
>
> From: V Wong <vwong at umn.edu>
> Reply-To: <vwong at umn.edu>
> Date: Thursday, July 11, 2013 1:10 AM
> To: Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc: <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Thanks!  I followed your instructions, and maker2jbrowse, and it
> successfully populated the ../JBrowse/data/tracks directory with
> RepeatMasker, Augustus, and GeneMark predictions.
>
> I'm not entirely sure how to get these numerous tracks into the browser,
> but that may be something to work out with JBrowse rather than Maker.
>
> Best,
> Val
>
>
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Hi Val,
>>
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>>
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>>
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl.
>>
>> Could you test it out and let me know how it goes.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>>
>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>> >documentation had you modify the genome.css file to create your own
>> >tracks.  Version 1.2.1 looks like it is the last version where the
>> >genome.css file that maker provided works. I can still get simple test
>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>> >But I need to fix some things, because they are all indistinguishable
>> from
>> >each other (so it is not the desired behavior).
>> >
>> >Indepent of that issue though, to regenerate the original error, I do the
>> >following -->
>> >    maker2jbrowse
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >    ERROR: No track information for source
>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>> >
>> >Basically you are missing the '-d' flag (whiteout that the script is
>> >expecting a list of GFF3 files).
>> >
>> >So this works -->
>> >    maker2jbrowse -d
>>
>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>> >a
>> >store_index.log
>> >
>> >
>> >Of course all tracks look the same though per the original issue I
>> >mentioned.
>> >
>> >Thanks,
>> >Carson
>> >
>> >
>> >
>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>> >1.3,
>> >
>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >
>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>> >>you're doing with that, but it appears to be a fork of a very old
>> >>JBrowse main css file.  If that's overriding or being copied over the
>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>> >>forked copy.
>> >>
>> >>If what you're trying to accomplish is to add some custom styles, the
>> >>best way to do that would be to do one of:
>> >>
>> >>* add just your custom feature styles on the flatfile-to-json.plcommand
>> >>line
>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>> >>   (containing only your custom feature styles!)
>> >>* add all of the custom styles to the trackList.json as a
>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>> >>
>> >>
>> >>Robert Buels
>> >>Lead Developer
>> >>JBrowse - http://jbrowse.org
>> >>
>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>> >>> I think you may not have it set up right.  If you run the example
>> data,
>> >>> you can then use that.  For me it populates the JSON data tracks
>> >>> information, but nothing displays.  I think the problem is with the
>> >>>maker
>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>> >>>get
>> >>> your feedback.
>> >>>
>> >>> Thanks,
>> >>> Carson
>> >>>
>> >>>
>> >>>
>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>> >>>
>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>> >>>>access),
>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>> >>>> parsing the MAKER datastore index, leading to the script complaining
>> >>>>of
>> >>>> 'no track information'.
>> >>>>
>> >>>> This would probably be easier for a MAKER developer to look into.
>> >>>>
>> >>>>
>> >>>> Robert Buels
>> >>>> Lead Developer
>> >>>> JBrowse - http://jbrowse.org
>> >>>>
>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>> >>>>> which is not backwards compatible with other Jbrowse versions), as a
>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>> >>>>>will
>> >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
>> can
>> >>>>> have it working with whatever the most current repository is if you
>> >>>>>were
>> >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>> >>>>>own
>> >>>>> loader (tutorial here -->
>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>> >>>>>    Of course this tutorial is also likely to be somewhat out of date
>> >>>>> :-( But the 2013 version is supposed to be up and running as part of
>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>> >>>>> data for the tutorial, so it should be relevant to what you are
>> >>>>>doing.
>> >>>>>
>> >>>>> Thanks,
>> >>>>> Carson
>> >>>>>
>> >>>>>
>> >>>>>
>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>> >>>>> To: <maker-devel at yandell-lab.org
>> >>>>><mailto:maker-devel at yandell-lab.org>>
>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>> >>>>>
>> >>>>> Hi Maker team,
>> >>>>>
>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>> >>>>> server, using the -d option for the index.log file.  However, I am
>> >>>>> getting this error for each contig:
>> >>>>>
>> >>>>> ERROR: No track information for source
>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>> >>>>>
>> >>>>> Looking at the perl script, the file locations are getting read, but
>> >>>>> then the tracks aren't getting found in the hash of commands.
>> >>>>>
>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>> >>>>>you!
>> >>>>>
>> >>>>> Best,
>> >>>>> Val
>> >>>>> _______________________________________________ maker-devel mailing
>> >>>>>list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>><mailto:maker-devel at box290.bluehost.com>
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>>>
>> >>>>> _______________________________________________
>> >>>>> maker-devel mailing list
>> >>>>> maker-devel at box290.bluehost.com
>> >>>>>
>> >>>>>
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>> >>>>>g
>> >>>>>
>> >>>
>> >>>
>> >>>
>> >
>> >
>>
>>
>
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From carsonhh at gmail.com  Thu Jul 11 12:23:04 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 11 Jul 2013 14:23:04 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2vobbR3f8-q6U+JU+1wC02GYoL8ZQM9Wi6=S=Hdz_LkEuag@mail.gmail.com>
Message-ID: <CE046E99.6E7F%carsonhh@gmail.com>

If you have a previous Jbrowse with already populated tracks you can just,
run maker2jbrowse in that directory instead of the new Jbrowse directory,
then the maker features will be added there.  Make a backup copy of the
directory before you do this of course incase you need to roll back the
changes.

Alternatively you will have to add those to the new Jbrowse directory using
bin/bam-to-json.pl and following the instructions here -->
http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data

I guess Robert can chime in here as well, since we have now moved outside of
MAKER scripts and fully into JBrowse.

--Carson


From:  V Wong <vwong at umn.edu>
Reply-To:  <vwong at umn.edu>
Date:  Thursday, July 11, 2013 1:58 PM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Ignazio Carbone <icarbon at ncsu.edu>, <maker-devel at yandell-lab.org>,
Robert Buels <rbuels at gmail.com>
Subject:  Re: [maker-devel] maker2jbrowse implementation

Hi Carson,

Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
directory, the Maker tracks are now on view.

However, I'm having some trouble getting our older tracks (bam alignments
and coverage tracks) into the same browser.  Neither 1. copying and pasting
the tracks from the previous trackList.json to the new one nor 2. running
add-track-json.pl <http://add-track-json.pl>  is doing the job.  Is it
possible to merge these tracks into one browser?

Best,
Val


On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com> wrote:
> You next put the entire JBrowse directory into the /var/www/html/ directory or
> wherever you have apache set up to load from (if it's not already there).
> Then it will be accessible as a webpage (browser is inside the JBrowse
> directory).
> 
> Example /var/www/html/Jbrowse/
> Webpage --> http://localhost/Jbrowse/
> 
> --Carson
> 
> From:  V Wong <vwong at umn.edu>
> Reply-To:  <vwong at umn.edu>
> Date:  Thursday, July 11, 2013 1:10 AM
> To:  Carson Holt <carsonhh at gmail.com>, Ignazio Carbone <icarbon at ncsu.edu>
> Cc:  <maker-devel at yandell-lab.org>, Robert Buels <rbuels at gmail.com>
> 
> Subject:  Re: [maker-devel] maker2jbrowse implementation
> 
> Hi Carson,
> 
> Thanks!  I followed your instructions, and maker2jbrowse, and it successfully
> populated the ../JBrowse/data/tracks directory with RepeatMasker, Augustus,
> and GeneMark predictions.
> 
> I'm not entirely sure how to get these numerous tracks into the browser, but
> that may be something to work out with JBrowse rather than Maker.
> 
> Best,
> Val
> 
> 
> On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com> wrote:
>> Hi Val,
>> 
>> I've attached new files for you to test.  These will be bundled in the
>> next maker release pending successful tests (~ 1 week).
>> 
>> Instructions:
>> 1. Place maker2jbrowse in your .../maker/bin/ directory and
>> .../maker/src/bin/ directory (this is just to ensure you don't
>> accidentally overwrite it if you reinstall at any time).
>> 2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>> 3. You must be in the jbrowse installation directory when running
>> maker2jbrowse.  Run the script with the -d flag and the datastore index
>> file.
>> 
>> This new version will assign colors by copying maker.css to the jbrowse
>> installation as apposed to replacing the genome.css file, and it will also
>> edit the genome.css file to add the import call for maker.css.  In
>> addition I have updated command line flags in the wrapper to do what is
>> currently expected by flatfile-to-json.pl <http://flatfile-to-json.pl> .
>> 
>> Could you test it out and let me know how it goes.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com> wrote:
>> 
>>> >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>>> >documentation had you modify the genome.css file to create your own
>>> >tracks.  Version 1.2.1 looks like it is the last version where the
>>> >genome.css file that maker provided works. I can still get simple test
>>> >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>>> >But I need to fix some things, because they are all indistinguishable from
>>> >each other (so it is not the desired behavior).
>>> >
>>> >Indepent of that issue though, to regenerate the original error, I do the
>>> >following -->
>>> >    maker2jbrowse
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >    ERROR: No track information for source
>>> >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>>> >
>>> >Basically you are missing the '-d' flag (whiteout that the script is
>>> >expecting a list of GFF3 files).
>>> >
>>> >So this works -->
>>> >    maker2jbrowse -d
>>> >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>>> >a
>>> >store_index.log
>>> >
>>> >
>>> >Of course all tracks look the same though per the original issue I
>>> >mentioned.
>>> >
>>> >Thanks,
>>> >Carson
>>> >
>>> >
>>> >
>>> >Some versions of Jbrowse still load fine with the script as is Jbrowse
>>> >1.3,
>>> >
>>> >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com> wrote:
>>> >
>>>> >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>>>> >>you're doing with that, but it appears to be a fork of a very old
>>>> >>JBrowse main css file.  If that's overriding or being copied over the
>>>> >>JBrowse released CSS, it will break pretty much everything.  It would be
>>>> >>like me randomly replacing one of MAKER's Perl modules with my own old
>>>> >>forked copy.
>>>> >>
>>>> >>If what you're trying to accomplish is to add some custom styles, the
>>>> >>best way to do that would be to do one of:
>>>> >>
>>>> >>* add just your custom feature styles on the flatfile-to-json.pl
>>>> <http://flatfile-to-json.pl>  command
>>>> >>line
>>>> >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>>>> >>   JBrowse trackList.json someplace in the workflow (easy to add
>>>> >>   things to JSON files with JSON.pm) that loads your custom CSS
>>>> >>   (containing only your custom feature styles!)
>>>> >>* add all of the custom styles to the trackList.json as a
>>>> >>   string: "css": "string { of: lots and lots of; css: properties; }"
>>>> >>
>>>> >>
>>>> >>Robert Buels
>>>> >>Lead Developer
>>>> >>JBrowse - http://jbrowse.org
>>>> >>
>>>> >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>>>> >>> I think you may not have it set up right.  If you run the example
>>>>> data,
>>>>> >>> you can then use that.  For me it populates the JSON data tracks
>>>>> >>> information, but nothing displays.  I think the problem is with the
>>>>> >>>maker
>>>>> >>> genome.css.  It is very out of date.  I'll do some work on it and then
>>>>> >>>get
>>>>> >>> your feedback.
>>>>> >>>
>>>>> >>> Thanks,
>>>>> >>> Carson
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>>>> >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com> wrote:
>>>>> >>>
>>>>>> >>>> After looking at the maker2jbrowse source (thanks for giving me
>>>>>> >>>>access),
>>>>>> >>>> there seems to be some kind of problem with the way maker2jbrowse is
>>>>>> >>>> parsing the MAKER datastore index, leading to the script complaining
>>>>>> >>>>of
>>>>>> >>>> 'no track information'.
>>>>>> >>>>
>>>>>> >>>> This would probably be easier for a MAKER developer to look into.
>>>>>> >>>>
>>>>>> >>>>
>>>>>> >>>> Robert Buels
>>>>>> >>>> Lead Developer
>>>>>> >>>> JBrowse - http://jbrowse.org
>>>>>> >>>>
>>>>>> >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>>>>>> >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much
of
>>>>>>> >>>>> which is not backwards compatible with other Jbrowse versions), as
a
>>>>>>> >>>>> result the script maker2jbrowse has had to evolve with Jbrowse
(and
>>>>>>> >>>>>will
>>>>>>> >>>>> not work with all versions).  I'm not sure if the script is
>>>>>>> currently
>>>>>>> >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I
can
>>>>>>> >>>>> have it working with whatever the most current repository is if
you
>>>>>>> >>>>>were
>>>>>>> >>>>> to give me a week, or you can try loading the GFF3's using
>>>>>>> Jbrowse's
>>>>>>> >>>>>own
>>>>>>> >>>>> loader (tutorial here -->
>>>>>>> >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>>>>>>> >>>>>    Of course this tutorial is also likely to be somewhat out of
date
>>>>>>> >>>>> :-( But the 2013 version is supposed to be up and running as part
of
>>>>>>> >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>>>>>>> generated
>>>>>>> >>>>> data for the tutorial, so it should be relevant to what you are
>>>>>>> >>>>>doing.
>>>>>>> >>>>>
>>>>>>> >>>>> Thanks,
>>>>>>> >>>>> Carson
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>>>>>> >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>>>>>> >>>>> To: <maker-devel at yandell-lab.org
>>>>>>> >>>>><mailto:maker-devel at yandell-lab.org>>
>>>>>>> >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>>>>>> >>>>>
>>>>>>> >>>>> Hi Maker team,
>>>>>>> >>>>>
>>>>>>> >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>>>>>>> >>>>> server, using the -d option for the index.log file.  However, I am
>>>>>>> >>>>> getting this error for each contig:
>>>>>>> >>>>>
>>>>>>> >>>>> ERROR: No track information for source
>>>>>>> >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>>>>>>> >>>>>
>>>>>>> >>>>> Looking at the perl script, the file locations are getting read,
but
>>>>>>> >>>>> then the tracks aren't getting found in the hash of commands.
>>>>>>> >>>>>
>>>>>>> >>>>> Any advice for getting past this will be most appreciated.  Thank
>>>>>>> >>>>>you!
>>>>>>> >>>>>
>>>>>>> >>>>> Best,
>>>>>>> >>>>> Val
>>>>>>> >>>>> _______________________________________________ maker-devel
>>>>>>> mailing
>>>>>>> >>>>>list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>><mailto:maker-devel at box290.bluehost.com>
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>>>> >>>>>
>>>>>>> >>>>> _______________________________________________
>>>>>>> >>>>> maker-devel mailing list
>>>>>>> >>>>> maker-devel at box290.bluehost.com
>>>>>>> >>>>>
>>>>>>> 
>>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>>>>>> >>>>>g
>>>>>>> >>>>>
>>>>> >>>
>>>>> >>>
>>>>> >>>
>>> >
>>> >
>> 
> 



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From rbuels at gmail.com  Thu Jul 11 12:27:10 2013
From: rbuels at gmail.com (Robert Buels)
Date: Thu, 11 Jul 2013 14:27:10 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CE046E99.6E7F%carsonhh@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
Message-ID: <51DEF8FE.2000907@gmail.com>

These days, it's better to use direct BAM access.  bam-to-json.pl still 
works, but the direct BAM access is much better.

See 
http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 07/11/2013 02:23 PM, Carson Holt wrote:
> If you have a previous Jbrowse with already populated tracks you can
> just, run maker2jbrowse in that directory instead of the new Jbrowse
> directory, then the maker features will be added there.  Make a backup
> copy of the directory before you do this of course incase you need to
> roll back the changes.
>
> Alternatively you will have to add those to the new Jbrowse directory
> using bin/bam-to-json.pl and following the instructions here -->
> http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data
>
> I guess Robert can chime in here as well, since we have now moved
> outside of MAKER scripts and fully into JBrowse.
>
> --Carson
>
>
> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
> Date: Thursday, July 11, 2013 1:58 PM
> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>,
> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
> Subject: Re: [maker-devel] maker2jbrowse implementation
>
> Hi Carson,
>
> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
> directory, the Maker tracks are now on view.
>
> However, I'm having some trouble getting our older tracks (bam
> alignments and coverage tracks) into the same browser.  Neither 1.
> copying and pasting the tracks from the previous trackList.json to the
> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
> doing the job.  Is it possible to merge these tracks into one browser?
>
> Best,
> Val
>
>
> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
> <mailto:carsonhh at gmail.com>> wrote:
>
>     You next put the entire JBrowse directory into the /var/www/html/
>     directory or wherever you have apache set up to load from (if it's
>     not already there).  Then it will be accessible as a webpage
>     (browser is inside the JBrowse directory).
>
>     Example /var/www/html/Jbrowse/
>     Webpage --> http://localhost/Jbrowse/
>
>     --Carson
>
>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>     Date: Thursday, July 11, 2013 1:10 AM
>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>     Cc: <maker-devel at yandell-lab.org
>     <mailto:maker-devel at yandell-lab.org>>, Robert Buels
>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>
>     Subject: Re: [maker-devel] maker2jbrowse implementation
>
>     Hi Carson,
>
>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>     successfully populated the ../JBrowse/data/tracks directory with
>     RepeatMasker, Augustus, and GeneMark predictions.
>
>     I'm not entirely sure how to get these numerous tracks into the
>     browser, but that may be something to work out with JBrowse rather
>     than Maker.
>
>     Best,
>     Val
>
>
>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>     <mailto:carsonhh at gmail.com>> wrote:
>
>         Hi Val,
>
>         I've attached new files for you to test.  These will be bundled
>         in the
>         next maker release pending successful tests (~ 1 week).
>
>         Instructions:
>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>         .../maker/src/bin/ directory (this is just to ensure you don't
>         accidentally overwrite it if you reinstall at any time).
>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>         3. You must be in the jbrowse installation directory when running
>         maker2jbrowse.  Run the script with the -d flag and the
>         datastore index
>         file.
>
>         This new version will assign colors by copying maker.css to the
>         jbrowse
>         installation as apposed to replacing the genome.css file, and it
>         will also
>         edit the genome.css file to add the import call for maker.css.  In
>         addition I have updated command line flags in the wrapper to do
>         what is
>         currently expected by flatfile-to-json.pl
>         <http://flatfile-to-json.pl>.
>
>         Could you test it out and let me know how it goes.
>
>         Thanks,
>         Carson
>
>
>
>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>         <mailto:carsonhh at gmail.com>> wrote:
>
>         >Like I said that css file is ~1 year old.  Once upon a time the Jbrowse
>         >documentation had you modify the genome.css file to create your own
>         >tracks.  Version 1.2.1 looks like it is the last version where the
>         >genome.css file that maker provided works. I can still get simple test
>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse script.
>         >But I need to fix some things, because they are all indistinguishable from
>         >each other (so it is not the desired behavior).
>         >
>         >Indepent of that issue though, to regenerate the original error, I do the
>         >following -->
>         >    maker2jbrowse
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >    ERROR: No track information for source
>         >'dpp_contig_datastore/05/1F/contig-dpp-500-500/'
>         >
>         >Basically you are missing the '-d' flag (whiteout that the script is
>         >expecting a list of GFF3 files).
>         >
>         >So this works -->
>         >    maker2jbrowse -d
>         >~/Developer/maker/trunk/data/dpp_contig.maker.output/dpp_contig_master_dat
>         >a
>         >store_index.log
>         >
>         >
>         >Of course all tracks look the same though per the original issue I
>         >mentioned.
>         >
>         >Thanks,
>         >Carson
>         >
>         >
>         >
>         >Some versions of Jbrowse still load fine with the script as is Jbrowse
>         >1.3,
>         >
>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >
>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not sure what
>         >>you're doing with that, but it appears to be a fork of a very old
>         >>JBrowse main css file.  If that's overriding or being copied over the
>         >>JBrowse released CSS, it will break pretty much everything.  It would be
>         >>like me randomly replacing one of MAKER's Perl modules with my own old
>         >>forked copy.
>         >>
>         >>If what you're trying to accomplish is to add some custom styles, the
>         >>best way to do that would be to do one of:
>         >>
>         >>* add just your custom feature styles on theflatfile-to-json.pl <http://flatfile-to-json.pl> command
>         >>line
>         >>* add a "css": { "url": "http://url/of/your/custom.css" } to the
>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>         >>   (containing only your custom feature styles!)
>         >>* add all of the custom styles to the trackList.json as a
>         >>   string: "css": "string { of: lots and lots of; css: properties; }"
>         >>
>         >>
>         >>Robert Buels
>         >>Lead Developer
>         >>JBrowse -http://jbrowse.org
>         >>
>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>         >>> I think you may not have it set up right.  If you run the example data,
>         >>> you can then use that.  For me it populates the JSON data tracks
>         >>> information, but nothing displays.  I think the problem is with the
>         >>>maker
>         >>> genome.css.  It is very out of date.  I'll do some work on it and then
>         >>>get
>         >>> your feedback.
>         >>>
>         >>> Thanks,
>         >>> Carson
>         >>>
>         >>>
>         >>>
>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:rbuels at gmail.com>> wrote:
>         >>>
>         >>>> After looking at the maker2jbrowse source (thanks for giving me
>         >>>>access),
>         >>>> there seems to be some kind of problem with the way maker2jbrowse is
>         >>>> parsing the MAKER datastore index, leading to the script complaining
>         >>>>of
>         >>>> 'no track information'.
>         >>>>
>         >>>> This would probably be easier for a MAKER developer to look into.
>         >>>>
>         >>>>
>         >>>> Robert Buels
>         >>>> Lead Developer
>         >>>> JBrowse -http://jbrowse.org
>         >>>>
>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration (much of
>         >>>>> which is not backwards compatible with other Jbrowse versions), as a
>         >>>>> result the script maker2jbrowse has had to evolve with Jbrowse (and
>         >>>>>will
>         >>>>> not work with all versions).  I'm not sure if the script is currently
>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing behind). I can
>         >>>>> have it working with whatever the most current repository is if you
>         >>>>>were
>         >>>>> to give me a week, or you can try loading the GFF3's using Jbrowse's
>         >>>>>own
>         >>>>> loader (tutorial here -->
>         >>>>>http://gmod.org/wiki/JBrowse_Tutorial_2012).
>         >>>>>    Of course this tutorial is also likely to be somewhat out of date
>         >>>>> :-( But the 2013 version is supposed to be up and running as part of
>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER generated
>         >>>>> data for the tutorial, so it should be relevant to what you are
>         >>>>>doing.
>         >>>>>
>         >>>>> Thanks,
>         >>>>> Carson
>         >>>>>
>         >>>>>
>         >>>>>
>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:vwong at umn.edu
>         <mailto:vwong at umn.edu>>>
>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>         >>>>> To: <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>         >>>>><mailto:maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>>>
>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>         >>>>>
>         >>>>> Hi Maker team,
>         >>>>>
>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3) on our
>         >>>>> server, using the -d option for the index.log file.  However, I am
>         >>>>> getting this error for each contig:
>         >>>>>
>         >>>>> ERROR: No track information for source
>         >>>>> 'AK_assembly_datastore/22/D4/AK_contig_1/'
>         >>>>>
>         >>>>> Looking at the perl script, the file locations are getting read, but
>         >>>>> then the tracks aren't getting found in the hash of commands.
>         >>>>>
>         >>>>> Any advice for getting past this will be most appreciated.  Thank
>         >>>>>you!
>         >>>>>
>         >>>>> Best,
>         >>>>> Val
>         >>>>> _______________________________________________ maker-devel mailing
>         >>>>>list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>><mailto:maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>>>
>         >>>>> _______________________________________________
>         >>>>> maker-devel mailing list
>         >>>>>maker-devel at box290.bluehost.com
>         <mailto:maker-devel at box290.bluehost.com>
>         >>>>>
>         >>>>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>         >>>>>g
>         >>>>>
>         >>>
>         >>>
>         >>>
>         >
>         >
>
>
>



From yuharas at takara-bio.co.jp  Fri Jul 12 00:19:39 2013
From: yuharas at takara-bio.co.jp (yuharas at takara-bio.co.jp)
Date: Fri, 12 Jul 2013 15:19:39 +0900
Subject: [maker-devel] RNA-seq data for MAKER2
In-Reply-To: <CE0410D8.6E4A%carsonhh@gmail.com>
References: <D4FB1041559FB3418665A7FA30940B7B025F35C6@TKREXMB3.central.takara.co.jp>
	<CE0410D8.6E4A%carsonhh@gmail.com>
Message-ID: <D4FB1041559FB3418665A7FA30940B7B025F3F37@TKREXMB3.central.takara.co.jp>

I understand?
Thank you for your useful information.

Satoshi

-----Original Message-----
From: Carson Holt [mailto:carsonhh at gmail.com] 
Sent: Thursday, July 11, 2013 8:37 PM
To: ?????; maker-devel at yandell-lab.org
Subject: Re: [maker-devel] RNA-seq data for MAKER2

Trinity didn't exist when I first made the tutorial, soI used cufflinks.
But more people seem to prefer the results of trinity/maker to cufflinks/maker.

--Carson


On 7/11/13 12:47 AM, "yuharas at takara-bio.co.jp" <yuharas at takara-bio.co.jp>
wrote:

>Dear Carson
>
>Thank you for your quick reply.
>Do you mean that we should use Trinity instead of Tophat and Cufflinks, 
>although the tutorial contains information about Tophat and Cufflinks?
>
>Satoshi
>
>
>-----Original Message-----
>From: Carson Holt [mailto:carsonhh at gmail.com]
>Sent: Thursday, July 11, 2013 11:41 AM
>To: ?????; maker-devel at yandell-lab.org
>Subject: Re: [maker-devel] RNA-seq data for MAKER2
>
>As far as total depth I don't know, but I'd recommend using something 
>like trinity to assemble the reads and supply them to the est= option 
>in fasta format.
>
>--Carson
>
>
>
>On 7/10/13 10:27 PM, "yuharas at takara-bio.co.jp" 
><yuharas at takara-bio.co.jp>
>wrote:
>
>>Dear developers
>>
>>I'm considering using MAKER2 to annotate plant genome (~1Gb) I've 
>>assembled using illumina HiSeq data.
>>And I'm planning to obtain mRNA-seq data by using HiSeq.
>>Do you have any recommendation of sequencing depth of RNA-seq data for 
>>using MAKER2 annotation pipeline?
>>
>>Thanks,
>>Satoshi
>>
>>
>>_______________________________________________
>>maker-devel mailing list
>>maker-devel at box290.bluehost.com
>>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or
>>g
>
>





From Carson.Holt at oicr.on.ca  Fri Jul 12 07:34:06 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Fri, 12 Jul 2013 13:34:06 +0000
Subject: [maker-devel] failed contigs error report
In-Reply-To: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>
Message-ID: <CE05726A.6EBE%carson.holt@oicr.on.ca>

Could you pack up and send me this directory (use dropbox if they are too
big) -->
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.m
aker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_co
ntig_12295/

And this file -->
AG1-IA_China_Prot.fasta

--Carson


On 7/12/13 6:47 AM, "Ian Misner" <ianmisner at my.uri.edu> wrote:

>Hello,
>
>I have collected my failed contigs and I have rerun them in Maker v. 2.28
>but they have failed again. I don't know what the error codes mean but I
>have attached the run log for your review. Any help would be appreciated.
>
>Cheers
>Ian
>
>
>




From ianmisner at my.uri.edu  Fri Jul 12 04:47:39 2013
From: ianmisner at my.uri.edu (Ian Misner)
Date: Fri, 12 Jul 2013 06:47:39 -0400
Subject: [maker-devel] failed contigs error report
In-Reply-To: <CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
References: <CDF9E0AE.6703%carsonhh@gmail.com>
	<CE01A884.6C92%carsonhh@gmail.com>
	<CAEi2vobXfiQd=RRMd4xaqeua3YbjEbt7AhEPSLgsj85OJaUkhg@mail.gmail.com>
Message-ID: <DFF7FC2B-7CCA-4D2C-8852-AE27D568B040@my.uri.edu>

Hello,

I have collected my failed contigs and I have rerun them in Maker v. 2.28 but they have failed again. I don't know what the error codes mean but I have attached the run log for your review. Any help would be appreciated. 

Cheers
Ian

-------------- next part --------------
STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore

To access files for individual sequences use the datastore index:
/home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.all.rb
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/te_proteins%2Efasta.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_593.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.0
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.1
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.2
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.3
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.4
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.5
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.6
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.7
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.8
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype prot -in /tmp/maker_h0nzdY/0/blastprep/AG1-IA_China_Prot%2Efasta.mpi.10.9
#-------------------------------#
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/0/AG2-2IIIB_contig_593.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917043%7Cgb%7CELU37906%2E1%7C.for.650-2882.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_593.650-2882.gi%7C443917043%7Cgb%7CELU37906%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	173	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_1981.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/0/AG2-2IIIB_contig_1981.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926460%7Cgb%7CELU45116%2E1%7C.for.1-1765.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1-1765.gi%7C443926460%7Cgb%7CELU45116%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926461%7Cgb%7CELU45117%2E1%7C.for.1462-7346.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-7346.gi%7C443926461%7Cgb%7CELU45117%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912614%7Cgb%7CELU35926%2E1%7C.for.4446-5532.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.4446-5532.gi%7C443912614%7Cgb%7CELU35926%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916327%7Cgb%7CELU37443%2E1%7C.for.1450-6472.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1450-6472.gi%7C443916327%7Cgb%7CELU37443%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912636%7Cgb%7CELU35932%2E1%7C.for.1832-6106.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1832-6106.gi%7C443912636%7Cgb%7CELU35932%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916324%7Cgb%7CELU37441%2E1%7C.for.1618-7085.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1618-7085.gi%7C443916324%7Cgb%7CELU37441%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926454%7Cgb%7CELU45111%2E1%7C.for.3156-7343.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.3156-7343.gi%7C443926454%7Cgb%7CELU45111%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912965%7Cgb%7CELU36010%2E1%7C.for.1462-5499.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.1462-5499.gi%7C443912965%7Cgb%7CELU36010%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926455%7Cgb%7CELU45112%2E1%7C.for.7818-9781.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_1981.7818-9781.gi%7C443926455%7Cgb%7CELU45112%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
total clusters:8 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 14
 ...processing 1 of 14
 ...processing 2 of 14
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
 ...processing 9 of 14
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	109	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3516.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/0/AG2-2IIIB_contig_3516.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924210%7Cgb%7CELU43269%2E1%7C.for.1-1171.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1171.gi%7C443924210%7Cgb%7CELU43269%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926803%7Cgb%7CELU45366%2E1%7C.for.1-1446.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1-1446.gi%7C443926803%7Cgb%7CELU45366%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926802%7Cgb%7CELU45365%2E1%7C.for.1965-3272.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3516.1965-3272.gi%7C443926802%7Cgb%7CELU45365%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	216	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_3821
Length: 7594
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_3821.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/D7/AG2-2IIIB_contig_3821//theVoid.AG2-2IIIB_contig_3821/0/AG2-2IIIB_contig_3821.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922723%7Cgb%7CELU42120%2E1%7C.for.2325-6375.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_3821.2325-6375.gi%7C443922723%7Cgb%7CELU42120%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:7 now processing 0
total clusters:7 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1478-6315.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4802
Length: 7225
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4802.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C6/94/AG2-2IIIB_contig_4802//theVoid.AG2-2IIIB_contig_4802/0/AG2-2IIIB_contig_4802.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914461%7Cgb%7CELU36415%2E1%7C.for.5310-7225.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4802.5310-7225.gi%7C443914461%7Cgb%7CELU36415%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.5497-7225.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_4885
Length: 2762
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_4885.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CB/1E/AG2-2IIIB_contig_4885//theVoid.AG2-2IIIB_contig_4885/0/AG2-2IIIB_contig_4885.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925371%7Cgb%7CELU44224%2E1%7C.for.1-1052.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_4885.1-1052.gi%7C443925371%7Cgb%7CELU44224%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.559-1302.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.2274-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.548-1284.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.2265-2762.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6364.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:3 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/0/AG2-2IIIB_contig_6364.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:2 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:3   current j:0
 j_size:3   current j:1
 j_size:3   current j:2
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925319%7Cgb%7CELU44178%2E1%7C.for.1-1315.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1315.gi%7C443925319%7Cgb%7CELU44178%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923087%7Cgb%7CELU42401%2E1%7C.for.1-1712.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1712.gi%7C443923087%7Cgb%7CELU42401%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916516%7Cgb%7CELU37570%2E1%7C.for.1-1705.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1-1705.gi%7C443916516%7Cgb%7CELU37570%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916517%7Cgb%7CELU37571%2E1%7C.for.1422-2768.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.1422-2768.gi%7C443916517%7Cgb%7CELU37571%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916518%7Cgb%7CELU37572%2E1%7C.for.2243-6168.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6364.2243-6168.gi%7C443916518%7Cgb%7CELU37572%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:3 now processing 0
total clusters:3 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	313	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_6661.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8D/79/AG2-2IIIB_contig_6661//theVoid.AG2-2IIIB_contig_6661/0/AG2-2IIIB_contig_6661.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919777%7Cgb%7CELU39849%2E1%7C.for.1-1825.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.1-1825.gi%7C443919777%7Cgb%7CELU39849%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919779%7Cgb%7CELU39851%2E1%7C.for.4180-5237.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_6661.4180-5237.gi%7C443919779%7Cgb%7CELU39851%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7259.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/0/AG2-2IIIB_contig_7259.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919366%7Cgb%7CELU39560%2E1%7C.for.701-2706.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7259.701-2706.gi%7C443919366%7Cgb%7CELU39560%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	93	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7484.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/0/AG2-2IIIB_contig_7484.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925858%7Cgb%7CELU44619%2E1%7C.for.3225-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3225-4350.gi%7C443925858%7Cgb%7CELU44619%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926070%7Cgb%7CELU44813%2E1%7C.for.1-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.1-4350.gi%7C443926070%7Cgb%7CELU44813%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918793%7Cgb%7CELU39161%2E1%7C.for.3207-4350.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7484.3207-4350.gi%7C443918793%7Cgb%7CELU39161%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	195	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_7871
Length: 3828
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_7871.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4A/28/AG2-2IIIB_contig_7871//theVoid.AG2-2IIIB_contig_7871/0/AG2-2IIIB_contig_7871.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915640%7Cgb%7CELU37016%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443915640%7Cgb%7CELU37016%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925409%7Cgb%7CELU44250%2E1%7C.for.1-719.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_7871.1-719.gi%7C443925409%7Cgb%7CELU44250%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:5 now processing 0
total clusters:5 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
total clusters:5 now processing 0
total clusters:5 now processing 0
total clusters:5 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-920.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-942.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1513-3828.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12295.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/0/AG2-2IIIB_contig_12295.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-2576.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12295.1-2576.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	194	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_12395.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/0/AG2-2IIIB_contig_12395.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915594%7Cgb%7CELU36979%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915594%7Cgb%7CELU36979%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915591%7Cgb%7CELU36976%2E1%7C.for.1-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1-2252.gi%7C443915591%7Cgb%7CELU36976%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926575%7Cgb%7CELU45191%2E1%7C.for.1373-2252.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_12395.1373-2252.gi%7C443926575%7Cgb%7CELU45191%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	494	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_13247.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/0/AG2-2IIIB_contig_13247.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926761%7Cgb%7CELU45333%2E1%7C.for.1-1216.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_13247.1-1216.gi%7C443926761%7Cgb%7CELU45333%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	782	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_14991.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/0/AG2-2IIIB_contig_14991.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926230%7Cgb%7CELU44941%2E1%7C.for.1-813.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.1-813.gi%7C443926230%7Cgb%7CELU44941%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926228%7Cgb%7CELU44939%2E1%7C.for.5427-6593.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_14991.5427-6593.gi%7C443926228%7Cgb%7CELU44939%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
total clusters:6 now processing 0
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:6 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	201	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_17930.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/0/AG2-2IIIB_contig_17930.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918707%7Cgb%7CELU39101%2E1%7C.for.1-1581.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_17930.1-1581.gi%7C443918707%7Cgb%7CELU39101%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	967	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18181.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/0/AG2-2IIIB_contig_18181.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920490%7Cgb%7CELU40399%2E1%7C.for.1-933.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18181.1-933.gi%7C443920490%7Cgb%7CELU40399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-6	166	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_18734
Length: 1555
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_18734.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:4 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:7 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:6 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:6 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:5 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5C/2F/AG2-2IIIB_contig_18734//theVoid.AG2-2IIIB_contig_18734/0/AG2-2IIIB_contig_18734.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915003%7Cgb%7CELU36646%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915003%7Cgb%7CELU36646%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921070%7Cgb%7CELU40845%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443921070%7Cgb%7CELU40845%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915001%7Cgb%7CELU36644%2E1%7C.for.1-1507.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1507.gi%7C443915001%7Cgb%7CELU36644%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923632%7Cgb%7CELU42812%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443923632%7Cgb%7CELU42812%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915695%7Cgb%7CELU37052%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443915695%7Cgb%7CELU37052%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924765%7Cgb%7CELU43732%2E1%7C.for.1-976.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-976.gi%7C443924765%7Cgb%7CELU43732%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917077%7Cgb%7CELU37931%2E1%7C.for.1-838.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-838.gi%7C443917077%7Cgb%7CELU37931%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916648%7Cgb%7CELU37640%2E1%7C.for.1-1555.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_18734.1-1555.gi%7C443916648%7Cgb%7CELU37640%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 6
 ...processing 1 of 6
 ...processing 2 of 6
 ...processing 3 of 6
 ...processing 4 of 6
 ...processing 5 of 6
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 8
 ...processing 1 of 8
 ...processing 2 of 8
 ...processing 3 of 8
 ...processing 4 of 8
 ...processing 5 of 8
 ...processing 6 of 8
 ...processing 7 of 8
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1555.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19042
Length: 1697
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19042.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/CC/AG2-2IIIB_contig_19042//theVoid.AG2-2IIIB_contig_19042/0/AG2-2IIIB_contig_19042.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926334%7Cgb%7CELU45026%2E1%7C.for.1-1697.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19042.1-1697.gi%7C443926334%7Cgb%7CELU45026%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1697.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19068.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/0/AG2-2IIIB_contig_19068.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443920586%7Cgb%7CELU40485%2E1%7C.for.1-1079.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19068.1-1079.gi%7C443920586%7Cgb%7CELU40485%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-4	179	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_19560
Length: 1347
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_19560.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_19560.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/65/42/AG2-2IIIB_contig_19560//theVoid.AG2-2IIIB_contig_19560/0/AG2-2IIIB_contig_19560.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1347.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20762.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/0/AG2-2IIIB_contig_20762.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924504%7Cgb%7CELU43508%2E1%7C.for.1-982.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20762.1-982.gi%7C443924504%7Cgb%7CELU43508%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	154	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_20773.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/0/AG2-2IIIB_contig_20773.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923085%7Cgb%7CELU42399%2E1%7C.for.76-1596.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_20773.76-1596.gi%7C443923085%7Cgb%7CELU42399%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	228	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21166
Length: 2541
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21166.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AB/70/AG2-2IIIB_contig_21166//theVoid.AG2-2IIIB_contig_21166/0/AG2-2IIIB_contig_21166.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912610%7Cgb%7CELU35925%2E1%7C.for.1700-2541.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21166.1700-2541.gi%7C443912610%7Cgb%7CELU35925%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.1569-2541.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21504.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/0/AG2-2IIIB_contig_21504.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917001%7Cgb%7CELU37876%2E1%7C.for.1-1497.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21504.1-1497.gi%7C443917001%7Cgb%7CELU37876%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	1025	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_21572.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/0/AG2-2IIIB_contig_21572.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918865%7Cgb%7CELU39212%2E1%7C.for.1-1139.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_21572.1-1139.gi%7C443918865%7Cgb%7CELU39212%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	760	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_22153.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_22153.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/0/AG2-2IIIB_contig_22153.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	295	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153

examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23198
Length: 2379
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23198.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BE/BB/AG2-2IIIB_contig_23198//theVoid.AG2-2IIIB_contig_23198/0/AG2-2IIIB_contig_23198.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915448%7Cgb%7CELU36902%2E1%7C.for.1-2379.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23198.1-2379.gi%7C443915448%7Cgb%7CELU36902%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2379.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_23332
Length: 1024
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_23332.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7E/A3/AG2-2IIIB_contig_23332//theVoid.AG2-2IIIB_contig_23332/0/AG2-2IIIB_contig_23332.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924676%7Cgb%7CELU43665%2E1%7C.for.1-1024.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_23332.1-1024.gi%7C443924676%7Cgb%7CELU43665%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1024.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_24240
Length: 1060
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_24240.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_24240.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/4A/AG2-2IIIB_contig_24240//theVoid.AG2-2IIIB_contig_24240/0/AG2-2IIIB_contig_24240.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1060.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26300
Length: 1034
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26300.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26300.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/8F/A2/AG2-2IIIB_contig_26300//theVoid.AG2-2IIIB_contig_26300/0/AG2-2IIIB_contig_26300.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_26955
Length: 1407
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_26955.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/06/29/AG2-2IIIB_contig_26955//theVoid.AG2-2IIIB_contig_26955/0/AG2-2IIIB_contig_26955.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917806%7Cgb%7CELU38443%2E1%7C.for.379-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.379-1407.gi%7C443917806%7Cgb%7CELU38443%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917814%7Cgb%7CELU38450%2E1%7C.for.442-1407.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_26955.442-1407.gi%7C443917814%7Cgb%7CELU38450%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27128
Length: 2040
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27128.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/6B/AG2-2IIIB_contig_27128//theVoid.AG2-2IIIB_contig_27128/0/AG2-2IIIB_contig_27128.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443919020%7Cgb%7CELU39318%2E1%7C.for.1-941.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-941.gi%7C443919020%7Cgb%7CELU39318%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923430%7Cgb%7CELU42674%2E1%7C.for.1-1055.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1-1055.gi%7C443923430%7Cgb%7CELU42674%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443927136%7Cgb%7CELU45660%2E1%7C.for.1096-2040.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27128.1096-2040.gi%7C443927136%7Cgb%7CELU45660%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-2040.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27180
Length: 1087
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27180.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/0C/EB/AG2-2IIIB_contig_27180//theVoid.AG2-2IIIB_contig_27180/0/AG2-2IIIB_contig_27180.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915961%7Cgb%7CELU37227%2E1%7C.for.1-1087.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27180.1-1087.gi%7C443915961%7Cgb%7CELU37227%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_27507
Length: 2741
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_27507.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:2 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/FC/AG2-2IIIB_contig_27507//theVoid.AG2-2IIIB_contig_27507/0/AG2-2IIIB_contig_27507.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914358%7Cgb%7CELU36379%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443914358%7Cgb%7CELU36379%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912830%7Cgb%7CELU35979%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443912830%7Cgb%7CELU35979%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918905%7Cgb%7CELU39238%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443918905%7Cgb%7CELU39238%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916513%7Cgb%7CELU37568%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916513%7Cgb%7CELU37568%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915770%7Cgb%7CELU37108%2E1%7C.for.1-787.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-787.gi%7C443915770%7Cgb%7CELU37108%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913539%7Cgb%7CELU36157%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443913539%7Cgb%7CELU36157%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913039%7Cgb%7CELU36027%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443913039%7Cgb%7CELU36027%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443911450%7Cgb%7CELU35667%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443911450%7Cgb%7CELU35667%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915845%7Cgb%7CELU37156%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443915845%7Cgb%7CELU37156%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915742%7Cgb%7CELU37086%2E1%7C.for.890-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.890-2741.gi%7C443915742%7Cgb%7CELU37086%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924323%7Cgb%7CELU43365%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443924323%7Cgb%7CELU43365%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914832%7Cgb%7CELU36565%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914832%7Cgb%7CELU36565%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913337%7Cgb%7CELU36105%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443913337%7Cgb%7CELU36105%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443916857%7Cgb%7CELU37794%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443916857%7Cgb%7CELU37794%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915502%7Cgb%7CELU36924%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443915502%7Cgb%7CELU36924%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921084%7Cgb%7CELU40854%2E1%7C.for.1-799.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-799.gi%7C443921084%7Cgb%7CELU40854%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443915712%7Cgb%7CELU37064%2E1%7C.for.2201-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2201-2741.gi%7C443915712%7Cgb%7CELU37064%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922842%7Cgb%7CELU42213%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922842%7Cgb%7CELU42213%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443918751%7Cgb%7CELU39123%2E1%7C.for.1-793.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-793.gi%7C443918751%7Cgb%7CELU39123%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443912860%7Cgb%7CELU35983%2E1%7C.for.869-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.869-2741.gi%7C443912860%7Cgb%7CELU35983%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443922901%7Cgb%7CELU42252%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443922901%7Cgb%7CELU42252%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443913566%7Cgb%7CELU36162%2E1%7C.for.1157-2601.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1157-2601.gi%7C443913566%7Cgb%7CELU36162%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443914292%7Cgb%7CELU36361%2E1%7C.for.893-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.893-2741.gi%7C443914292%7Cgb%7CELU36361%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443917664%7Cgb%7CELU38330%2E1%7C.for.1-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.1-2741.gi%7C443917664%7Cgb%7CELU38330%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921379%7Cgb%7CELU41050%2E1%7C.for.2069-2741.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_27507.2069-2741.gi%7C443921379%7Cgb%7CELU41050%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 14
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total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
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 ...processing 21 of 38
 ...trimming the rest
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
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 ...trimming the rest
 ...processing 0 of 12
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cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
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running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2741.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-599.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 20
 ...processing 1 of 20
 ...processing 2 of 20
 ...processing 3 of 20
 ...processing 4 of 20
 ...processing 5 of 20
 ...processing 6 of 20
 ...processing 7 of 20
 ...processing 8 of 20
 ...processing 9 of 20
 ...processing 10 of 20
 ...processing 11 of 20
 ...processing 12 of 20
 ...processing 13 of 20
 ...processing 14 of 20
 ...processing 15 of 20
 ...processing 16 of 20
 ...processing 17 of 20
 ...processing 18 of 20
 ...processing 19 of 20
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_28349
Length: 1535
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_28349.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/3C/28/AG2-2IIIB_contig_28349//theVoid.AG2-2IIIB_contig_28349/0/AG2-2IIIB_contig_28349.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:1 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443926253%7Cgb%7CELU44961%2E1%7C.for.535-1535.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.535-1535.gi%7C443926253%7Cgb%7CELU44961%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443921201%7Cgb%7CELU40930%2E1%7C.for.1-1427.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_28349.1-1427.gi%7C443921201%7Cgb%7CELU40930%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1535.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:2   current j:0
 j_size:2   current j:1
...finished clustering.
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
 ...processing 0 of 2
 ...processing 1 of 2
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29160
Length: 1830
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29160.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/BA/90/AG2-2IIIB_contig_29160//theVoid.AG2-2IIIB_contig_29160/0/AG2-2IIIB_contig_29160.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
in cluster::shadow_cluster...
 sorting hits in shadow cluster...
 j_size:1   current j:0
...finished clustering.
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924283%7Cgb%7CELU43333%2E1%7C.for.652-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.652-1830.gi%7C443924283%7Cgb%7CELU43333%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924238%7Cgb%7CELU43291%2E1%7C.for.589-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.589-1830.gi%7C443924238%7Cgb%7CELU43291%2E1%7C.p.exonerate
#-------------------------------#
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443924237%7Cgb%7CELU43290%2E1%7C.for.547-1830.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29160.547-1830.gi%7C443924237%7Cgb%7CELU43290%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.743-1830.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29352
Length: 1073
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29352.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/59/33/AG2-2IIIB_contig_29352//theVoid.AG2-2IIIB_contig_29352/0/AG2-2IIIB_contig_29352.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443925337%7Cgb%7CELU44194%2E1%7C.for.1-1073.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29352.1-1073.gi%7C443925337%7Cgb%7CELU44194%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_29511
Length: 1330
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_29511.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/49/4C/AG2-2IIIB_contig_29511//theVoid.AG2-2IIIB_contig_29511/0/AG2-2IIIB_contig_29511.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
polishing proteins
running  exonerate search.
#--------- command -------------#
Widget::exonerate::protein2genome:
/home/ian_usda/Programs/exonerate-2.2.0-x86_64/bin/exonerate -q /tmp/maker_h0nzdY/0/gi%7C443923460%7Cgb%7CELU42699%2E1%7C.for.1-1229.0.fasta -t /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.0.fasta -Q protein -T dna -m protein2genome --softmasktarget  --percent 20 --showcigar  > /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_29511.1-1229.gi%7C443923460%7Cgb%7CELU42699%2E1%7C.p.exonerate
#-------------------------------#
cleaning blastx...
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: AG2-2IIIB_contig_32665
Length: 1132
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
running  repeat masker.
#--------- command -------------#
Widget::RepeatMasker:
cd /tmp/maker_h0nzdY; /home/ian_usda/Programs/RepeatMasker/RepeatMasker /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb -species all -dir /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0 -pa 6
#-------------------------------#



No repetitive sequences were detected in /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.all.rb
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.0.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.1.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.2.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.3.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.4.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.5.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.6.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.7.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.8.repeatrunner
#-------------------------------#
deleted:0 hits
doing blastx repeats
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/te_proteins%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.te_proteins%2Efasta.repeatrunner.temp_dir/te_proteins%2Efasta.mpi.10.9.repeatrunner
#-------------------------------#
deleted:0 hits
collecting blastx repeatmasking
processing all repeats
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap AG2-2IIIB.hmm /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.AG2-2IIIB%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --UTR=off /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0 > /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_masked.0.laccaria_bicolor.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/usr/bin/perl /home/ian_usda/Programs/maker_v2.28/bin/../lib/Widget/genemark/gmhmm_wrap -m AG2-2IIIB.mod -g /home/ian_usda/Programs/gmes/gmhmme3 -p /home/ian_usda/Programs/gmes/probuild -o /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0.AG2-2IIIB%2Emod.genemark /tmp/maker_h0nzdY/AG2-2IIIB_contig_32665.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.0 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.0.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.1 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.1.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.2 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.2.blastx
#-------------------------------#
deleted:1 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.3 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.3.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.4 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.4.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.5 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.5.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.6 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.6.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.7 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.7.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.8 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.8.blastx
#-------------------------------#
deleted:0 hits
doing blastx of proteins
running  blast search.
#--------- command -------------#
Widget::blastx:
/usr/bin/blastx -db /tmp/maker_h0nzdY/AG1-IA_China_Prot%2Efasta.mpi.10.9 -query /tmp/maker_h0nzdY/0/AG2-2IIIB_contig_32665.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-06 -dbsize 300 -searchsp 500000000 -num_threads 6 -seg yes -soft_masking true -lcase_masking -show_gis -out /home/ian_usda/Desktop/AG2-2IIIB_Maker/AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/95/DC/AG2-2IIIB_contig_32665//theVoid.AG2-2IIIB_contig_32665/0/AG2-2IIIB_contig_32665.0.AG1-IA_China_Prot%2Efasta.blastx.temp_dir/AG1-IA_China_Prot%2Efasta.mpi.10.9.blastx
#-------------------------------#
deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
Gathering GFF3 input into hits - chunk:0
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
annotating transcripts
Making transcripts
clustering transcripts into genes for annotations
Processing transcripts into genes
adding statistics to annotations
Calculating annotation quality statistics
choosing best annotation set
Choosing best annotations
processing chunk output
processing contig output
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_593
Length: 2882
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	173	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_593

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_593

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_1981
Length: 10563
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
total clusters:4 now processing 0
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
 ...processing 0 of 7
 ...processing 1 of 7
 ...processing 2 of 7
 ...processing 3 of 7
 ...processing 4 of 7
 ...processing 5 of 7
 ...processing 6 of 7
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/9_0.852-1622.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/10_0.5290-6220.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/11_0.8017-9584.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 14
 ...processing 1 of 14
 ...processing 2 of 14
 ...processing 3 of 14
 ...processing 4 of 14
 ...processing 5 of 14
 ...processing 6 of 14
 ...processing 7 of 14
 ...processing 8 of 14
 ...processing 9 of 14
 ...processing 10 of 14
 ...processing 11 of 14
 ...processing 12 of 14
 ...processing 13 of 14
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/12_0.0-7386.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/13_0.8583-9424.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	109	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_1981

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_1981

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_3516
Length: 3272
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	216	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_3516

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_3516

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6364
Length: 6168
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:4 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:4 now processing 0
total clusters:4 now processing 0
total clusters:4 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 5
 ...processing 1 of 5
 ...processing 2 of 5
 ...processing 3 of 5
 ...processing 4 of 5
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-1530.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	313	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6364

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6364

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_6661
Length: 5237
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.4281-5237.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/7_0.0-1662.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
clustering transcripts into genes for annotations
Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/share/perl5/Bio/Tools/CodonTable.pm:411
STACK: PhatHit_utils::_adjust /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:838
STACK: PhatHit_utils::adjust_start_stop /home/ian_usda/Programs/maker_v2.28/bin/../lib/PhatHit_utils.pm:786
STACK: maker::auto_annotator::load_transcript_struct /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2086
STACK: maker::auto_annotator::group_transcripts /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:2495
STACK: maker::auto_annotator::annotate_genes /home/ian_usda/Programs/maker_v2.28/bin/../lib/maker/auto_annotator.pm:925
STACK: Process::MpiChunk::_go /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:3798
STACK: Process::MpiChunk::run /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: Process::MpiTiers::run_all /home/ian_usda/Programs/maker_v2.28/bin/../lib/Process/MpiTiers.pm:286
STACK: /home/ian_usda/Programs/maker_v2.28/bin/maker_v2.28:667
-----------------------------------------------------------
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while clustering transcripts into genes for annotations
ERROR: Chunk failed at level:2, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_6661

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_6661

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7259
Length: 2706
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	93	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7259

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7259

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_7484
Length: 4350
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 4
 ...processing 1 of 4
 ...processing 2 of 4
 ...processing 3 of 4
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.1394-2233.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	195	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_7484

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_7484

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12295
Length: 2576
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	194	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12295

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12295

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_12395
Length: 2252
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 3
 ...processing 1 of 3
 ...processing 2 of 3
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	494	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_12395

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_12395

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_13247
Length: 1216
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.34-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	782	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_13247

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_13247

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_14991
Length: 6593
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:3 now processing 0
total clusters:3 now processing 0
 ...processing 0 of 2
 ...processing 1 of 2
total clusters:3 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/5_0.0-653.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding10.20.30.40.50.60.70.80.90100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-2	201	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_14991

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_14991

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_17930
Length: 1764
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	...	967	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_17930

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_17930

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_18181
Length: 1918
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-6	166	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_18181

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_18181

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_19068
Length: 1079
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-4	179	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_19068

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_19068

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20762
Length: 1062
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 2
 ...processing 1 of 2
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=forward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -plus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
deleted:0 genes
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	154	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20762

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20762

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_20773
Length: 1596
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:2 now processing 0
total clusters:2 now processing 0
in cluster::shadow_cluster...
...finished clustering.
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-5	228	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_20773

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_20773

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21504
Length: 1823
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
in cluster::shadow_cluster...
...finished clustering.
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 2
 ...processing 1 of 2
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	1025	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21504

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21504

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_21572
Length: 1139
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: undefined coordinates
Coding	0	760	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_21572

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_21572

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
#---------------------------------------------------------------------
Now retrying the contig!!
SeqID: AG2-2IIIB_contig_22153
Length: 1068
Tries: 2!!
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
 ...processing 0 of 1
running  augustus.
#--------- command -------------#
Widget::augustus:
/home/ian_usda/Programs/augustus/bin/augustus --species=laccaria_bicolor --strand=backward --UTR=off --hintsfile=/tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.xdef.augustus --extrinsicCfgFile=/home/ian_usda/Programs/augustus/config//extrinsic/extrinsic.MPE.cfg /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.laccaria_bicolor.auto_annotator.augustus
#-------------------------------#
deleted:0 genes
 ...processing 0 of 1
running  snap.
#--------- command -------------#
Widget::snap:
/home/ian_usda/Programs/snap/snap -minus AG2-2IIIB.hmm -xdef /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.xdef.snap  /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap.fasta > /tmp/maker_h0nzdY/0/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
#-------------------------------#
ZOE WARNING (from /home/ian_usda/Programs/snap/snap): zoeVerifyFeature: coordinate not positive
Coding	-7	295	+	0.200	.	.	.	ADJ
ZOE ERROR (from /home/ian_usda/Programs/snap/snap): zoeNewFeature illegal feature
ZOE library version 2006-07-28
ERROR: Snap failed
--> rank=NA, hostname=LakshmanLinux
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:AG2-2IIIB_contig_22153

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:AG2-2IIIB_contig_22153

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/64/E3/AG2-2IIIB_contig_593//theVoid.AG2-2IIIB_contig_593/3_0.849-2882.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/1C/86/AG2-2IIIB_contig_1981//theVoid.AG2-2IIIB_contig_1981/14_0.9504-10563.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/C0/BB/AG2-2IIIB_contig_3516//theVoid.AG2-2IIIB_contig_3516/4_0.2052-3272.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/16/69/AG2-2IIIB_contig_6364//theVoid.AG2-2IIIB_contig_6364/5_0.1618-6168.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/2D/08/AG2-2IIIB_contig_7259//theVoid.AG2-2IIIB_contig_7259/2_0.897-2706.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/F3/02/AG2-2IIIB_contig_7484//theVoid.AG2-2IIIB_contig_7484/6_0.0-4350.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/4B/6F/AG2-2IIIB_contig_12295//theVoid.AG2-2IIIB_contig_12295/2_0.0-2576.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/7C/1F/AG2-2IIIB_contig_12395//theVoid.AG2-2IIIB_contig_12395/4_0.0-2252.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/24/7E/AG2-2IIIB_contig_13247//theVoid.AG2-2IIIB_contig_13247/3_0.0-1216.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A3/29/AG2-2IIIB_contig_14991//theVoid.AG2-2IIIB_contig_14991/6_0.5581-6593.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/53/38/AG2-2IIIB_contig_17930//theVoid.AG2-2IIIB_contig_17930/2_0.106-1764.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/B2/D1/AG2-2IIIB_contig_18181//theVoid.AG2-2IIIB_contig_18181/4_0.965-1918.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/CD/41/AG2-2IIIB_contig_19068//theVoid.AG2-2IIIB_contig_19068/2_0.0-1079.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/6E/F8/AG2-2IIIB_contig_20762//theVoid.AG2-2IIIB_contig_20762/3_0.504-1062.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/A8/90/AG2-2IIIB_contig_20773//theVoid.AG2-2IIIB_contig_20773/2_0.269-1596.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/5A/74/AG2-2IIIB_contig_21504//theVoid.AG2-2IIIB_contig_21504/2_0.0-1823.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/AC/69/AG2-2IIIB_contig_21572//theVoid.AG2-2IIIB_contig_21572/2_0.0-1139.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased
examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...
MAKER WARNING: The file AG2-2IIIB_Failed_contigs_July_2013.maker.output/AG2-2IIIB_Failed_contigs_July_2013_datastore/83/34/AG2-2IIIB_contig_22153//theVoid.AG2-2IIIB_contig_22153/2_0.0-1068.AG2-2IIIB.hmm.auto_annotator.snap
did not finish on the last run and must be erased


Maker is now finished!!!

-------------- next part --------------



From vwong at umn.edu  Mon Jul 15 11:57:30 2013
From: vwong at umn.edu (V Wong)
Date: Mon, 15 Jul 2013 12:57:30 -0500
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51DEF8FE.2000907@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com>
	<51DEF8FE.2000907@gmail.com>
Message-ID: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>

Hi Carson,

I tried running maker2jbrowse in the browser directory with existing
tracks, but the script expects to be run in the JBrowse directory and
printed this error:

FATAL: Can not find ./bin/flatfile-to-json.pl

Make sure you are running inside the JBrowse directory


Hi Robert,

I tried adding an Alignment2 track in the format of the example to the
browser with Maker tracks (those get viewed fine), but I am getting the
error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
though the specified file is in that location.


Thank you both for your continued aid.

Since this is departing Maker for strictly JBrowse territory, would it be
more appropriate to move to the JBrowse list?

Best,

Val


On Thu, Jul 11, 2013 at 1:27 PM, Robert Buels <rbuels at gmail.com> wrote:

> These days, it's better to use direct BAM access.  bam-to-json.pl still
> works, but the direct BAM access is much better.
>
> See http://gmod.org/wiki/JBrowse_**Configuration_Guide#Alignment_**
> Tracks_.28BAM.29<http://gmod.org/wiki/JBrowse_Configuration_Guide#Alignment_Tracks_.28BAM.29>
>
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
> On 07/11/2013 02:23 PM, Carson Holt wrote:
>
>> If you have a previous Jbrowse with already populated tracks you can
>> just, run maker2jbrowse in that directory instead of the new Jbrowse
>> directory, then the maker features will be added there.  Make a backup
>> copy of the directory before you do this of course incase you need to
>> roll back the changes.
>>
>> Alternatively you will have to add those to the new Jbrowse directory
>> using bin/bam-to-json.pl and following the instructions here -->
>> http://gmod.org/wiki/JBrowse_**Tutorial_2012#BAM_data<http://gmod.org/wiki/JBrowse_Tutorial_2012#BAM_data>
>>
>> I guess Robert can chime in here as well, since we have now moved
>> outside of MAKER scripts and fully into JBrowse.
>>
>> --Carson
>>
>>
>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>> Date: Thursday, July 11, 2013 1:58 PM
>> To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>
>> Cc: Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>,
>> <maker-devel at yandell-lab.org <mailto:maker-devel at yandell-**lab.org<maker-devel at yandell-lab.org>
>> >>,
>> Robert Buels <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>> Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>> Hi Carson,
>>
>> Ah, great!  After moving the contents of ../JBrowse/data/ to our browser
>> directory, the Maker tracks are now on view.
>>
>> However, I'm having some trouble getting our older tracks (bam
>> alignments and coverage tracks) into the same browser.  Neither 1.
>> copying and pasting the tracks from the previous trackList.json to the
>> new one nor 2. running add-track-json.pl <http://add-track-json.pl> is
>>
>> doing the job.  Is it possible to merge these tracks into one browser?
>>
>> Best,
>> Val
>>
>>
>> On Thu, Jul 11, 2013 at 6:44 AM, Carson Holt <carsonhh at gmail.com
>> <mailto:carsonhh at gmail.com>> wrote:
>>
>>     You next put the entire JBrowse directory into the /var/www/html/
>>     directory or wherever you have apache set up to load from (if it's
>>     not already there).  Then it will be accessible as a webpage
>>     (browser is inside the JBrowse directory).
>>
>>     Example /var/www/html/Jbrowse/
>>     Webpage --> http://localhost/Jbrowse/
>>
>>     --Carson
>>
>>     From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu>>
>>     Date: Thursday, July 11, 2013 1:10 AM
>>     To: Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>>,
>>     Ignazio Carbone <icarbon at ncsu.edu <mailto:icarbon at ncsu.edu>>
>>     Cc: <maker-devel at yandell-lab.org
>>     <mailto:maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>,
>> Robert Buels
>>     <rbuels at gmail.com <mailto:rbuels at gmail.com>>
>>
>>
>>     Subject: Re: [maker-devel] maker2jbrowse implementation
>>
>>     Hi Carson,
>>
>>     Thanks!  I followed your instructions, and maker2jbrowse, and it
>>     successfully populated the ../JBrowse/data/tracks directory with
>>     RepeatMasker, Augustus, and GeneMark predictions.
>>
>>     I'm not entirely sure how to get these numerous tracks into the
>>     browser, but that may be something to work out with JBrowse rather
>>     than Maker.
>>
>>     Best,
>>     Val
>>
>>
>>     On Tue, Jul 9, 2013 at 10:57 AM, Carson Holt <carsonhh at gmail.com
>>     <mailto:carsonhh at gmail.com>> wrote:
>>
>>         Hi Val,
>>
>>         I've attached new files for you to test.  These will be bundled
>>         in the
>>         next maker release pending successful tests (~ 1 week).
>>
>>         Instructions:
>>         1. Place maker2jbrowse in your .../maker/bin/ directory and
>>         .../maker/src/bin/ directory (this is just to ensure you don't
>>         accidentally overwrite it if you reinstall at any time).
>>         2. Place maker.css in the .../maker/GMOD/Jbrowse/ directory.
>>         3. You must be in the jbrowse installation directory when running
>>         maker2jbrowse.  Run the script with the -d flag and the
>>         datastore index
>>         file.
>>
>>         This new version will assign colors by copying maker.css to the
>>         jbrowse
>>         installation as apposed to replacing the genome.css file, and it
>>         will also
>>         edit the genome.css file to add the import call for maker.css.  In
>>         addition I have updated command line flags in the wrapper to do
>>         what is
>>         currently expected by flatfile-to-json.pl
>>         <http://flatfile-to-json.pl>.
>>
>>
>>         Could you test it out and let me know how it goes.
>>
>>         Thanks,
>>         Carson
>>
>>
>>
>>         On 7/3/13 3:26 PM, "Carson Holt" <carsonhh at gmail.com
>>         <mailto:carsonhh at gmail.com>> wrote:
>>
>>         >Like I said that css file is ~1 year old.  Once upon a time the
>> Jbrowse
>>         >documentation had you modify the genome.css file to create your
>> own
>>         >tracks.  Version 1.2.1 looks like it is the last version where
>> the
>>         >genome.css file that maker provided works. I can still get
>> simple test
>>         >GFF3 tracks to load with current Jbrowse and the maker2jbrowse
>> script.
>>         >But I need to fix some things, because they are all
>> indistinguishable from
>>         >each other (so it is not the desired behavior).
>>         >
>>         >Indepent of that issue though, to regenerate the original error,
>> I do the
>>         >following -->
>>         >    maker2jbrowse
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >    ERROR: No track information for source
>>         >'dpp_contig_datastore/05/1F/**contig-dpp-500-500/'
>>         >
>>         >Basically you are missing the '-d' flag (whiteout that the
>> script is
>>         >expecting a list of GFF3 files).
>>         >
>>         >So this works -->
>>         >    maker2jbrowse -d
>>         >~/Developer/maker/trunk/data/**dpp_contig.maker.output/dpp_**
>> contig_master_dat
>>         >a
>>         >store_index.log
>>         >
>>         >
>>         >Of course all tracks look the same though per the original issue
>> I
>>         >mentioned.
>>         >
>>         >Thanks,
>>         >Carson
>>         >
>>         >
>>         >
>>         >Some versions of Jbrowse still load fine with the script as is
>> Jbrowse
>>         >1.3,
>>         >
>>         >On 7/3/13 12:39 PM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >
>>         >>Regarding the genome.css file that's in GMOD/JBrowse, I'm not
>> sure what
>>         >>you're doing with that, but it appears to be a fork of a very
>> old
>>         >>JBrowse main css file.  If that's overriding or being copied
>> over the
>>         >>JBrowse released CSS, it will break pretty much everything.  It
>> would be
>>         >>like me randomly replacing one of MAKER's Perl modules with my
>> own old
>>         >>forked copy.
>>         >>
>>         >>If what you're trying to accomplish is to add some custom
>> styles, the
>>         >>best way to do that would be to do one of:
>>         >>
>>         >>* add just your custom feature styles on theflatfile-to-json.pl<
>> http://flatfile-to-json.pl> command
>>
>>         >>line
>>         >>* add a "css": { "url": "http://url/of/your/custom.css**" } to
>> the
>>         >>   JBrowse trackList.json someplace in the workflow (easy to add
>>         >>   things to JSON files with JSON.pm) that loads your custom CSS
>>         >>   (containing only your custom feature styles!)
>>         >>* add all of the custom styles to the trackList.json as a
>>         >>   string: "css": "string { of: lots and lots of; css:
>> properties; }"
>>         >>
>>         >>
>>         >>Robert Buels
>>         >>Lead Developer
>>         >>JBrowse -http://jbrowse.org
>>
>>         >>
>>         >>On 07/03/2013 12:02 PM, Carson Holt wrote:
>>         >>> I think you may not have it set up right.  If you run the
>> example data,
>>         >>> you can then use that.  For me it populates the JSON data
>> tracks
>>         >>> information, but nothing displays.  I think the problem is
>> with the
>>         >>>maker
>>         >>> genome.css.  It is very out of date.  I'll do some work on it
>> and then
>>         >>>get
>>         >>> your feedback.
>>         >>>
>>         >>> Thanks,
>>         >>> Carson
>>         >>>
>>         >>>
>>         >>>
>>         >>> On 7/3/13 11:45 AM, "Robert Buels" <rbuels at gmail.com <mailto:
>> rbuels at gmail.com>> wrote:
>>         >>>
>>         >>>> After looking at the maker2jbrowse source (thanks for giving
>> me
>>         >>>>access),
>>         >>>> there seems to be some kind of problem with the way
>> maker2jbrowse is
>>         >>>> parsing the MAKER datastore index, leading to the script
>> complaining
>>         >>>>of
>>         >>>> 'no track information'.
>>         >>>>
>>         >>>> This would probably be easier for a MAKER developer to look
>> into.
>>         >>>>
>>         >>>>
>>         >>>> Robert Buels
>>         >>>> Lead Developer
>>         >>>> JBrowse -http://jbrowse.org
>>
>>         >>>>
>>         >>>> On 07/02/2013 12:27 PM, Carson Holt wrote:
>>         >>>>> The Jbrowse codebase tends to undergo very rapid alteration
>> (much of
>>         >>>>> which is not backwards compatible with other Jbrowse
>> versions), as a
>>         >>>>> result the script maker2jbrowse has had to evolve with
>> Jbrowse (and
>>         >>>>>will
>>         >>>>> not work with all versions).  I'm not sure if the script is
>> currently
>>         >>>>> behind or ahead of Jbrowse version 1.9.3 (I'm guessing
>> behind). I can
>>         >>>>> have it working with whatever the most current repository
>> is if you
>>         >>>>>were
>>         >>>>> to give me a week, or you can try loading the GFF3's using
>> Jbrowse's
>>         >>>>>own
>>         >>>>> loader (tutorial here -->
>>         >>>>>http://gmod.org/wiki/**JBrowse_Tutorial_2012<http://gmod.org/wiki/JBrowse_Tutorial_2012>
>> ).
>>         >>>>>    Of course this tutorial is also likely to be somewhat
>> out of date
>>         >>>>> :-( But the 2013 version is supposed to be up and running
>> as part of
>>         >>>>> this years GMOD summer school in ~3 weeks.  They use MAKER
>> generated
>>         >>>>> data for the tutorial, so it should be relevant to what you
>> are
>>         >>>>>doing.
>>         >>>>>
>>         >>>>> Thanks,
>>         >>>>> Carson
>>         >>>>>
>>         >>>>>
>>         >>>>>
>>         >>>>> From: V Wong <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Reply-To: <vwong at umn.edu <mailto:vwong at umn.edu> <mailto:
>> vwong at umn.edu
>>
>>         <mailto:vwong at umn.edu>>>
>>         >>>>> Date: Tuesday, July 2, 2013 11:38 AM
>>         >>>>> To: <maker-devel at yandell-lab.org <mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>
>>         >>>>><mailto:maker-devel@**yandell-lab.org<maker-devel at yandell-lab.org><mailto:
>> maker-devel at yandell-**lab.org <maker-devel at yandell-lab.org>>>>
>>
>>         >>>>> Subject: [maker-devel] maker2jbrowse implementation
>>         >>>>>
>>         >>>>> Hi Maker team,
>>         >>>>>
>>         >>>>> I'm trying to get Maker output into JBrowse (version 1.9.3)
>> on our
>>         >>>>> server, using the -d option for the index.log file.
>>  However, I am
>>         >>>>> getting this error for each contig:
>>         >>>>>
>>         >>>>> ERROR: No track information for source
>>         >>>>> 'AK_assembly_datastore/22/D4/**AK_contig_1/'
>>         >>>>>
>>         >>>>> Looking at the perl script, the file locations are getting
>> read, but
>>         >>>>> then the tracks aren't getting found in the hash of
>> commands.
>>         >>>>>
>>         >>>>> Any advice for getting past this will be most appreciated.
>>  Thank
>>         >>>>>you!
>>         >>>>>
>>         >>>>> Best,
>>         >>>>> Val
>>         >>>>> ______________________________**_________________
>> maker-devel mailing
>>         >>>>>list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>><mailto:maker-devel@**box290.bluehost.com<maker-devel at box290.bluehost.com>
>>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >>
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>>>
>>         >>>>> ______________________________**_________________
>>         >>>>> maker-devel mailing list
>>         >>>>>maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>>         <mailto:maker-devel at box290.**bluehost.com<maker-devel at box290.bluehost.com>
>> >
>>         >>>>>
>>         >>>>>http://box290.bluehost.**com/mailman/listinfo/maker-**
>> devel_yandell-lab.or<http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.or>
>>         >>>>>g
>>         >>>>>
>>         >>>
>>         >>>
>>         >>>
>>         >
>>         >
>>
>>
>>
>>
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From rbuels at gmail.com  Mon Jul 15 12:54:58 2013
From: rbuels at gmail.com (Robert Buels)
Date: Mon, 15 Jul 2013 14:54:58 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
Message-ID: <51E44582.9020100@gmail.com>

On 07/15/2013 01:57 PM, V Wong wrote:
> I tried adding an Alignment2 track in the format of the example to the
> browser with Maker tracks (those get viewed fine), but I am getting the
> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
> though the specified file is in that location.

If you visit that URL in your browser, is the bai file really there?

If so, is the BAI file on a different server from the one you're running 
JBrowse on?  If so, you'll need to enable CORS on the server for the BAI 
and BAM files.

Rob



From Michael.Li3 at AGR.GC.CA  Thu Jul 18 13:06:38 2013
From: Michael.Li3 at AGR.GC.CA (Li, Michael)
Date: Thu, 18 Jul 2013 19:06:38 +0000
Subject: [maker-devel] InterProScan v5
Message-ID: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for users. However, I noticed that maker's iprscan_batch, iprscan_wrap, ipr_update_gff and iprscan2gff3 are not compatible with this new version of IPR. Is there a workaround available or is the script easy to modify to suit the new version?
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From carsonhh at gmail.com  Thu Jul 18 13:18:20 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 18 Jul 2013 15:18:20 -0400
Subject: [maker-devel] InterProScan v5
In-Reply-To: <229AF11430CC544B8987653593A750A92FB333B0@ONOTTAXES3.AGR.GC.CA>
Message-ID: <CE0DB539.77E1%carsonhh@gmail.com>

All those tools were written for InterProScan 4.  We have plans to update
everything for InterProScan 5 sometime in the near future. Some will have to
be dropped or rewritten completely, while other like  ipr_update_gff and
iprscan2gff3 are both relatively simple and I could probably have those
included with the next MAKER release (current release is 2.28).  That would
be about 3 weeks from now.

--Carson



From:  "Li, Michael" <Michael.Li3 at AGR.GC.CA>
Date:  Thursday, July 18, 2013 3:06 PM
To:  "'maker-devel at yandell-lab.org'" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] InterProScan v5

My department has maker.2-10 and InterProScan 5R6 installed on a cluster for
users. However, I noticed that maker?s iprscan_batch, iprscan_wrap,
ipr_update_gff and iprscan2gff3 are not compatible with this new version of
IPR. Is there a workaround available or is the script easy to modify to suit
the new version?
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.com
http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From vwong at umn.edu  Fri Jul 19 15:36:03 2013
From: vwong at umn.edu (V Wong)
Date: Fri, 19 Jul 2013 17:36:03 -0400
Subject: [maker-devel] maker2jbrowse implementation
In-Reply-To: <51E44582.9020100@gmail.com>
References: <CE046E99.6E7F%carsonhh@gmail.com> <51DEF8FE.2000907@gmail.com>
	<CAEi2voYD+de3Knfmpcps6_46VwqZTZ77HgUs6bNX3qPmONJNSA@mail.gmail.com>
	<51E44582.9020100@gmail.com>
Message-ID: <CAEi2voasDqTHLEe00+JDUgWgav-BYJuM+fPSAbK5ysZCKj6VTw@mail.gmail.com>

Ah, I just had some syntax inconsistencies between the file locations on
the server and the path for the web browser.  Thank you Rob!

Best,
Val


On Mon, Jul 15, 2013 at 2:54 PM, Robert Buels <rbuels at gmail.com> wrote:

> On 07/15/2013 01:57 PM, V Wong wrote:
>
>> I tried adding an Alignment2 track in the format of the example to the
>> browser with Maker tracks (those get viewed fine), but I am getting the
>> error "404 (Not found) when attempting to fetch ...[bam.bai file]" even
>> though the specified file is in that location.
>>
>
> If you visit that URL in your browser, is the bai file really there?
>
> If so, is the BAI file on a different server from the one you're running
> JBrowse on?  If so, you'll need to enable CORS on the server for the BAI
> and BAM files.
>
> Rob
>
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From jmdoyle at purdue.edu  Sun Jul 21 07:44:26 2013
From: jmdoyle at purdue.edu (Jacqueline R M Doyle)
Date: Sun, 21 Jul 2013 09:44:26 -0400 (EDT)
Subject: [maker-devel] altest without MPI?
In-Reply-To: <1806377131.45449.1371745335968.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>

I just wanted to check in and say that this strategy worked really nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with protein2genome and my contigs greater than 1200000 bases.  Each of the training runs took less than 4 hours.  My final run with all my contigs (and altest) took about 5 and 1/2 days.  Not bad!   

----- Original Message -----
From: Carson Holt <carsonhh at gmail.com>
To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
Subject: Re: [maker-devel] altest without MPI?

The throughput is based on contig length, so long contigs will take longer
than short contigs.  Any contig less than 10kb is mostly useless for
annotation purposes (so you can filter those from your 800,000 right
away). Take your contigs that finish, and sum up their length to get a
better estimate of how long it will take to complete running.  Most
genomes can complete in a few days an a multi-core machine.  Bigger
genomes or bigger datasets take longer.  (note that altest evidence takes
3-4x longer to align than proteins).

The advantage of proteins is that the species do not have to be closely
related.  Nucleotide sequence diverges quickly and proteins slowly (that's
why proteins are used for phylogenetic trees).

A good strategy would be to get ~10Mb of sequence (use your longest
contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
protein2genome option to generate annotations.  Those annotations should
now be sufficient to train SNAP and Augustus.  Then you can finish by
running all your contigs with the same dataset (protein2genome now turned
off), use the newly trained snap and augustus files along with any altest
files you want to use. Note that the size of the dataset will determine
the total run time.

To get things to run faster, you can also run on your university's
computer cluster (then you will have hundreds of cpus available to you).
The purdue cluster supports MPI and with 30-50 cpus you could annotate
even large genomes in a reasonable time.  Alternatively you can request a
startup account at XSEDE, an NFS funded computer resource open to all US
institutions.  A startup allocation with 50,000 cpu hours only takes 2
weeks to approve. You should request an allocation on the Lonestar cluster
if you go that route, it has 64,000 cpus. I was able to annotate the Maize
genome (which is a very large genome at over 2 gigabases).  I used an
abnormally large EST and protein datasets (~4 gigabases of evidence which
is much more than a normal annotation job), and it completed in under 3
hours on 2,100 cpus.

--Carson


On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>Hi Carson (and whoever else might be reading this!)
>
>Thanks so much, I think splitting the files up using fasta_tool will
>definitely move things along.  I did a trial version with altest this
>weekend, and seemed to be averaging about an hour a scaffold (with 1
>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>seem like a reasonable estimate of the time it should take to annotate
>one sequence?  Could I be missing something in my maker_opts file?
>
>Let me back up for just a minute and describe the project a little more
>generally.  As I mentioned before, we have no protein sequences or ESTs
>for our species of interest, which is an avian species.  I could
>potentially use proteins from chicken or turkey, but neither is closely
>related to our species.  Time is a bit of an issue... do you have any
>thoughts on how much time per scaffold it should take to annotate using
>protein2genome?  If chicken and turkey are not closely related, is it
>worth the time investment?
>
>Let me finish by saying I think MAKER is wonderful, and I really
>appreciate the discussions on this group.
>
>Best wishes, Jackie 






From carsonhh at gmail.com  Sun Jul 21 15:09:12 2013
From: carsonhh at gmail.com (Carson Holt)
Date: Sun, 21 Jul 2013 17:09:12 -0400
Subject: [maker-devel] altest without MPI?
In-Reply-To: <2141521972.100389.1374414266869.JavaMail.root@mailhub042.itcs.purdue.edu>
Message-ID: <CE11C4D7.7990%carsonhh@gmail.com>

Glad I could help. If you come across anything else, just let us know.

Thanks,
Carson



On 7/21/13 9:44 AM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:

>I just wanted to check in and say that this strategy worked really
>nicely.  I ended up using MPI and 48 cpus.  I trained SNAP with
>protein2genome and my contigs greater than 1200000 bases.  Each of the
>training runs took less than 4 hours.  My final run with all my contigs
>(and altest) took about 5 and 1/2 days.  Not bad!
>
>----- Original Message -----
>From: Carson Holt <carsonhh at gmail.com>
>To: Jacqueline R M Doyle <jmdoyle at purdue.edu>, maker-devel at yandell-lab.org
>Sent: Wed, 19 Jun 2013 21:05:49 -0400 (EDT)
>Subject: Re: [maker-devel] altest without MPI?
>
>The throughput is based on contig length, so long contigs will take longer
>than short contigs.  Any contig less than 10kb is mostly useless for
>annotation purposes (so you can filter those from your 800,000 right
>away). Take your contigs that finish, and sum up their length to get a
>better estimate of how long it will take to complete running.  Most
>genomes can complete in a few days an a multi-core machine.  Bigger
>genomes or bigger datasets take longer.  (note that altest evidence takes
>3-4x longer to align than proteins).
>
>The advantage of proteins is that the species do not have to be closely
>related.  Nucleotide sequence diverges quickly and proteins slowly (that's
>why proteins are used for phylogenetic trees).
>
>A good strategy would be to get ~10Mb of sequence (use your longest
>contigs).  Run with Chicken, turkey, and pigeon proteins.  Use the
>protein2genome option to generate annotations.  Those annotations should
>now be sufficient to train SNAP and Augustus.  Then you can finish by
>running all your contigs with the same dataset (protein2genome now turned
>off), use the newly trained snap and augustus files along with any altest
>files you want to use. Note that the size of the dataset will determine
>the total run time.
>
>To get things to run faster, you can also run on your university's
>computer cluster (then you will have hundreds of cpus available to you).
>The purdue cluster supports MPI and with 30-50 cpus you could annotate
>even large genomes in a reasonable time.  Alternatively you can request a
>startup account at XSEDE, an NFS funded computer resource open to all US
>institutions.  A startup allocation with 50,000 cpu hours only takes 2
>weeks to approve. You should request an allocation on the Lonestar cluster
>if you go that route, it has 64,000 cpus. I was able to annotate the Maize
>genome (which is a very large genome at over 2 gigabases).  I used an
>abnormally large EST and protein datasets (~4 gigabases of evidence which
>is much more than a normal annotation job), and it completed in under 3
>hours on 2,100 cpus.
>
>--Carson
>
>
>On 13-06-19 5:12 PM, "Jacqueline R M Doyle" <jmdoyle at purdue.edu> wrote:
>
>>Hi Carson (and whoever else might be reading this!)
>>
>>Thanks so much, I think splitting the files up using fasta_tool will
>>definitely move things along.  I did a trial version with altest this
>>weekend, and seemed to be averaging about an hour a scaffold (with 1
>>cpu).  I'm a little concerned, as we have ~800,000 scaffolds.  Does this
>>seem like a reasonable estimate of the time it should take to annotate
>>one sequence?  Could I be missing something in my maker_opts file?
>>
>>Let me back up for just a minute and describe the project a little more
>>generally.  As I mentioned before, we have no protein sequences or ESTs
>>for our species of interest, which is an avian species.  I could
>>potentially use proteins from chicken or turkey, but neither is closely
>>related to our species.  Time is a bit of an issue... do you have any
>>thoughts on how much time per scaffold it should take to annotate using
>>protein2genome?  If chicken and turkey are not closely related, is it
>>worth the time investment?
>>
>>Let me finish by saying I think MAKER is wonderful, and I really
>>appreciate the discussions on this group.
>>
>>Best wishes, Jackie
>
>
>





From Carson.Holt at oicr.on.ca  Tue Jul 23 13:00:27 2013
From: Carson.Holt at oicr.on.ca (Carson Holt)
Date: Tue, 23 Jul 2013 19:00:27 +0000
Subject: [maker-devel] Fwd: about running MAKER
In-Reply-To: <CAMNfi+gSdTtfBHD7ipTFJ08jvL3UtpbH3q+gCG-N-J-vV+Vpow@mail.gmail.com>
Message-ID: <CE143780.7AD6%carson.holt@oicr.on.ca>

If the log is growing then it is still working.  The time it takes is a function of the evidence dataset, genome size, and gene density.  Is there any way, you could try starting a second maker process in the same directory with additional CPUs to get it to complete sooner (each process will detect each other and avoid overlapping on their work, so it will still get divided up efficiently).  Also if you combine the length of all finished contigs, you will get a better idea of how much run time is remaining (i.e. See if contigs remaining are short or long compared to most contigs in the assembly).

Thanks,
Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 23, 2013 1:12 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Thanks Carson,

gephy.transcripts.fa is 64406072
geph_AS_masked.fa is 296693827

The log is growing. It finished 21700 scaffolds. I think we have nearly 38149 scaffolds. Is that means the program running good?

Sincerely,
Yunxi



2013/7/22 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Nothing looks out of the ordinary.  How big is this file --> gephy.transcripts.fa
How big is this file --> geph_AS_masked.fa

Also is the STDERR log growing or is it frozen?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, July 22, 2013 12:24 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Sorry to bother you again. I ran the MAKER for like around two weeks, but it is still running now. I attached my control files. Can you help me to see if I set something wrong? I used the masked genome as my input, so I skipped the repeatmasker in maker. I think it should be faster. I ran this mpiexec -n 8 maker

I'm running another maker using unmasked data in 16 threads, so I ran this in 8. I already got 34G data for this. Because the time cost in running already out of schedule. I'm worry about something wrong in the setting.

Thank you.
Yunxi


2013/7/14 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson.


2013/7/14 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
I would use the same data to train both.

More information here --> https://groups.google.com/forum/#!msg/maker-devel/Tnkc5RCkgQQ/Qtykuh9hVc8J

--Carson

From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Friday, July 12, 2013 9:04 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

One more is when I train the SNAP and Augustus, should I do them in the same time with the est2genome and protein2genome, or do them separately? Thank you.


2013/7/12 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Hi Carson

The MAKER is running fine right now. I'm confusing about using the CEGMA with MAKER to train the SNAP and Augustus.

I'm running the MAKER from est2genome with protein2genome without using the result from CEGMA. I think the data I already enough for generating the hmm.

And I got the zff from the result of CEGMA, and I followed the link last time you gave me to generate the file for SNAP and Augustus.

I'm not that clear how to combine the hmm model from CEGMA and MAKER.

Thank you for your help.

Sincerely,
Yunxi


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I think I should better to use the default, in case it occurs an error after several days' running.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Some operations are not NFS safe (NFS behaves different than normal file systems).  So maker performs those operations in the temporary directory.  If you redirect those files to an NFS location, you may get errors (basically MAKER just dies).  It won't necessarily happen, but the warning lets you know that, if it fails then you should set TMP= somewhere else before trying again.

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 3:22 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got an error message about this:
ERROR: Temporary directory set to an NFS location.
TMP=/home/lin11/tmp
The temporary directory in MAKER is specifically for
operations that are not NFS-safe. You must set TMP
to a locally mounted directory such as /tmp or add
--ignore_nfs_tmp to the maker command line to
override this error message.

Does the MAKER need a big temporary file? Because our system temporary directory may not have that much space. If it does not need that big tmp file, I can set it back to default. Or I just ignore the error message?

Thank you.


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
Anything from maker under the ~/perl5/ should be deleted.  MAKER should be self contained in its own directory.  Do 'rm ~/perl5/bin/*maker*'.  If you see anything else that is maker related there delete it as well.

Example:
.../maker/bin/
.../maker/lib/
.../maker/exe/

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 1:40 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I installed the new version of MAKER. But right now have a problem of running it. Because I was missing perl dependencies, I installed the perl local library. And then I tried to run maker, it will automatically go to the one in local library called ~/perl5/bin/maker. Do you know how to get rid of this path? I found this path in .bashrc : export PATH="/home/lin11/perl5/bin:$PATH". If that ok to delete it?

Thank you.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It's been stable enough that I could remove the beta tag (no major updates in 2 months).  In fact I'll go ahead and do that.

--Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:21 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Is that the 2.28 only have the beta version?


2013/7/2 Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Thank you Carson. I'll try then let you know.


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You could just install it in a new directory (I.e. maker_2.28 rather than maker).  The 2.1 version more than 2 years old (lots of changes and improvements since then).

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 12:11 PM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson
I think I may need to update MAKER too. My version is 2.1. Is the new version of MAKER changed a lot? Because someone running MAKER on the server now, can I just update it instead of delete the old one then reinstall the new version?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
If you are using MAKER 2.28, and let it do the install for you it will install mpich2 from this location --> http://www.mcs.anl.gov/research/projects/mpich2/downloads/tarballs/1.5/mpich2-1.5.tar.gz

The installation will be in the .../maker/exe/mpich2 directory.

Alternatively, if you do the installation yourself, all you have to do set a few flags during install configuration.
--> ./configure --prefix=$path --enable-shared
Set $path to the location where you want MPICH2 to be installed.
Then run 'make install'

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:59 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I think it installed the 1.3.1 version. Can I update it?


2013/7/2 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
It should be installed under .../maker/exe/mpich2.  Having it under ~/perl5/exe/mpich2 is odd as maker should do that.

Type 'which mpiexec' to see if there is another mpiexec installed somewhere.  Also run 'mpiexec --version'.  What does it give?  I ask because the error message you got before is the same as a bug in an old version of MPICH2 (version 1.3).  MAKER will install version 1.5.

Also run 'mpiexec -n 16 hostname'
What happens?

Thanks,
Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, July 2, 2013 11:17 AM

To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

How's the trip?

I did it followed your instruction. I ran ./build mpich2 first
It installed it into ~/perl5/exe/mpich2 directory.
And then i go back to maker/src ran perl build.pl<http://build.pl> and type Y to accept the MPI.
Then I ran ./build install
After that, I went to ~/.bash_profile to add the ~/perl5/exe/mpich2/bin into the PATH.
I used mpiexec -n 16 maker as the command.
Do I need to set some special variable in that three control file first?

Thank you.

Yunxi Lin

On Jul 2, 2013, at 7:44 AM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

Sorry for not responding sooner (it was a long holiday weekend in Canada).  Did you have maker install MPICH2 or did you install it yourself?  Also what is the exact command line you used to launch?

--Carson


From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sunday, June 30, 2013 2:09 PM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

I got the errors like:
[mpiexec at bioinfo1] HYDU_create_process (./utils/launch/launch.c:69): execvp error on file hydra_pmi_proxy (No such file or directory)
[mpiexec at bioinfo1] HYD_pmcd_pmiserv_proxy_init_cb (./pm/pmiserv/pmiserv_cb.c:315): assert (!closed) failed
[mpiexec at bioinfo1] HYDT_dmxu_poll_wait_for_event (./tools/demux/demux_poll.c:76): callback returned error status
[mpiexec at bioinfo1] HYD_pmci_wait_for_completion (./pm/pmiserv/pmiserv_pmci.c:342): error waiting for event
[mpiexec at bioinfo1] main (./ui/mpich/mpiexec.c:302): process manager error waiting for completion

Is that means our server only has one cpu so I cannot use mpi?

Thank you.



2013/6/25 Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>>
You can get blast to use more than 1 cpu via the cpus= option, but that is still significantly limiting MAKER's performance.

When you let MAKER install MPICH2, it will be local to the MAKER installation (MAKER only).  It will be in ?/maker/exe/mpich2.  This was purposely done for people who have limited access and install MAKER themselves, so they can run via MPI without having to get upgraded privileges.  So I don't know if you installed MAKER yourself, but if you did, then this is an option that will let you run.

--Carson


From: csusm <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Tuesday, 25 June, 2013 11:40 AM
To: Carson Holt <carson.holt at oicr.on.ca<mailto:carson.holt at oicr.on.ca>>

Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank you for your suggestion. Do you mean if I dont use MPI, i could only run it on one cpu?  Because my school own the server, I only have the limit authorization.

Yunxi Lin

On Jun 24, 2013, at 5:39 PM, Carson Holt <Carson.Holt at oicr.on.ca<mailto:Carson.Holt at oicr.on.ca>> wrote:

You are most likely only getting 1 cpu of performance.

You should just install MPICH2.  It's easy just to let MAKER do it for you:
Go to the ?/maker/src/ directory
Run './Build mpich2'
Once it finishes installing, it will be in the ?/maker/exe/mpich2/bin/ directory.

Setup MAKER again to use MPICH2:
Go to the ?/maker/src/ directory
Run 'perl Build.PL'
Say yes to the "use MPI": question
Run './Build install'

Now run MAKER via 'mpiexec'.
Example --> ?/maker/exe/mpich2/bin/mpiexec -n 16 maker

The ?n flag specifies how many CPUS to use. Mpiexec handles process communication either on the same machine or across machines.  You will get much better performance.

Thanks,
Carson



From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Monday, 24 June, 2013 7:11 PM
To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Cc: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>, <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Fwd: about running MAKER

Hi Carson

Thank your for your help.

My genome estimated size is 250M base pairs. I ran it in 16cpu, but we don't have the MPI so I cannot use it. I don't think I'm using the alt_est option. I was following the tutorial to do that. I used TopHat and Cufflinks to generate the ESTs from the assembly sequence based on RNA-seq. I used that ESTs to run the MAKER.

I think I already got more than 10Mb data. The information you mentioned is very helpful. I may go to use them to try to train the SNAP and Augustus.

Because this is my first time using the MAKER, I ran already a month, I was wondering maybe the command I used in a wrong way.

Sincerely,
Yunxi



2013/6/24 Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
Run time is dependent on the size of your evidence dataset, genome size, and number of processors you use.  If you have a large genome (Gb size) and you are running on a single cpu then that could take a long time.  This is especially true if you use the alt_est option for evidence as these are aligned via tblastx  which is 3-4 times slower than protein alignments, and 10-20 time slower than standard EST alignments. 95% of MAKER's runtime is BLAST alignment so your evidence dataset is the major factor.

Also you do not need results from the entire genome to train SNAP.  If you get results from ~10Mb of the genome that is usually sufficient.  Also make sure you are taking advantage of parallelization.  Launch via MPI to get maximum performance.  I commonly launch on 16 and 32 cpu Linux servers which can annotate most fungal genomes in a few hours and larger genomes in a few days.

--Carson


From: Amelia Ireland <amelia.ireland at gmod.org<mailto:amelia.ireland at gmod.org>>
Date: Sunday, 23 June, 2013 10:15 PM
To: <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Cc: <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Subject: [maker-devel] Fwd: about running MAKER

>From the GMOD helpdesk; please cc Lin, lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>.

---------- Forwarded message ----------
From: Yunxi Lin <lin11 at cougars.csusm.edu<mailto:lin11 at cougars.csusm.edu>>
Date: Sun, Jun 23, 2013 at 4:14 PM
Subject: about running MAKER
To: "gmod-help at gmod.org<mailto:gmod-help at gmod.org>" <help at gmod.org<mailto:help at gmod.org>>


Hi

I'm running a eukaryote project on our server. Because our server do not have the GUI, is that still work for MAKER? And our command already ran more than one month to try to generate the model use for the training of SNAP and Augustus. Is that normal? I'm running on a 256G memory 64 Linux server.

Thank you.

Sincerely,
Lin



--
Amelia Ireland
GMOD Community Support
http://gmod.org || @gmodproject

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From grburke at uga.edu  Tue Jul 30 13:14:02 2013
From: grburke at uga.edu (Gaelen Burke)
Date: Tue, 30 Jul 2013 19:14:02 -0000
Subject: [maker-devel] unknown error
Message-ID: <602FA505-8A78-4006-8D8F-D3EC81A73FEC@uga.edu>

Hello,
I have an error that occurs in my MAKER run for 52 of several thousand scaffolds. The annotation of these scaffolds fails, even after 3 re-tries. I also pulled out the failed sequences and started a run from scratch, with the same result. Could anyone tell me what this error means and how I could possibly fix it?
Thanks,
Gaelen Burke

Here is the message that occurs:

Processing transcripts into genes

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Root/Root.pm:472
STACK: Bio::Tools::CodonTable::translate /usr/local/perl/5.14.1/lib/site_perl/5.14.1/Bio/Tools/CodonTable.pm
:411
STACK: PhatHit_utils::_adjust /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit_utils.pm:
880
STACK: PhatHit_utils::adjust_start_stop /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/PhatHit
_utils.pm:776
STACK: maker::auto_annotator::load_transcript_struct /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/.
./lib/maker/auto_annotator.pm:1808
STACK: maker::auto_annotator::group_transcripts /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib
/maker/auto_annotator.pm:2163
STACK: maker::auto_annotator::annotate_genes /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/ma
ker/auto_annotator.pm:877
STACK: Process::MpiChunk::_go /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:2159
STACK: Process::MpiChunk::run /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiChunk.
pm:257
STACK: Process::MpiTiers::run_all /panfs/pstor.storage/rcclocal/zcluster/maker/2.10/bin/../lib/Process/MpiTi
ers.pm:193
STACK: /usr/local/maker/latest/bin/maker:276
-----------------------------------------------------------

FATAL ERROR
ERROR: Failed while clustering transcripts into genes for annotations!!

ERROR: Chunk failed at level 20
!!
FAILED CONTIG:scaffold_0040