From qlian003 at ucr.edu  Wed Jun  1 14:22:29 2016
From: qlian003 at ucr.edu (Qihua Liang)
Date: Wed, 1 Jun 2016 12:22:29 -0700
Subject: [maker-devel] fasta/gff3_merge problem
Message-ID: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>

Hi Maker developers,

I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
Synopsis:

fasta_merge -d maker_datastore_index.log
fasta_merge -o genome.all -i <fasta1> <fasta2> ...
Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 

Is it any explicit reason for this error?

Thanks
Qihua
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From carsonhh at gmail.com  Fri Jun  3 13:01:26 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 3 Jun 2016 12:01:26 -0600
Subject: [maker-devel] fasta/gff3_merge problem
In-Reply-To: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
References: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
Message-ID: <43A96AEB-DC28-4BBC-BDC2-BAEE35CFAAC9@gmail.com>

If it is just printing out the usage statement, then you have something wrong with your command line.

If you are getting no results back, then you have no gene models (you may have failed to provide an HMM for the gene predictors.).

Thanks,
Carson


> On Jun 1, 2016, at 1:22 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi Maker developers,
> 
> I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
> Synopsis:
> 
> fasta_merge -d maker_datastore_index.log
> fasta_merge -o genome.all -i <fasta1> <fasta2> ...
> Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 
> 
> Is it any explicit reason for this error?
> 
> Thanks
> Qihua
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Mon Jun  6 14:51:45 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Mon, 06 Jun 2016 15:51:45 -0400
Subject: [maker-devel] grab your part right now
Message-ID: <5755D451.1000506@yandell-lab.org>

Hello, 
 
Just wanted to know where I should send you the profits you'll be making?
 
My team is all setup and ready to welcome you on board,
so that we can start you on one of the most amazing pesos making journeys you'll ever take.
 
>>
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Let's not waste another minute, click the link below and your first commissions will be coming in as early as in the next 30 minutes.
 
>>
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To your success, Charley Berger
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From maker-devel at yandell-lab.org  Wed Jun  8 03:11:50 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 8 Jun 2016 15:11:50 +0700
Subject: [maker-devel] look for a companion
Message-ID: <393096489.201606081534@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Darlene Carson, I am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun  9 13:23:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 9 Jun 2016 22:23:15 +0400
Subject: [maker-devel] partial occupation
Message-ID: <001c01d1c280$021aeb65$6c7a7bbe$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Alma, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 12 11:57:19 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 12 Jun 2016 20:57:19 +0400
Subject: [maker-devel] partial occupation
Message-ID: <349471532331748141280616@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Dudley, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From willett4 at email.unc.edu  Mon Jun 13 08:01:09 2016
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 13 Jun 2016 13:01:09 +0000
Subject: [maker-devel] integrating results from Augustus
Message-ID: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>

Hi All-

I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs.

The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:

"ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:Contig149

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:Contig149?


Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?

Thanks for any help you can give me,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: Genome Sciences Building 2252
phone: 919-843-8663
fax: 919-962-1625

http://labs.bio.unc.edu/Willett/

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From carsonhh at gmail.com  Mon Jun 13 13:28:33 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 13 Jun 2016 12:28:33 -0600
Subject: [maker-devel] integrating results from Augustus
In-Reply-To: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
References: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
Message-ID: <BAC5552D-4D70-4E0D-9B8D-10593E19F782@gmail.com>

You need to install augustus and place the species parameter files into the ?/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.

?Carson



> On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi All-
> 
> I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs. 
> 
> The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:
> 
> "ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:Contig149
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:Contig149?
> 
>   
> Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?
> 
> Thanks for any help you can give me,
> 
> Best,
> 
> Chris Willett
> 
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: Genome Sciences Building 2252
> phone: 919-843-8663
> fax: 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> 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 bmoore at genetics.utah.edu  Tue Jun 14 00:36:27 2016
From: bmoore at genetics.utah.edu (Barry Moore)
Date: Tue, 14 Jun 2016 05:36:27 +0000
Subject: [maker-devel] Fwd: possible problems in maker
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
Message-ID: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>

Hi Alexander,

I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.

It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:

sudo cpan forks
sudo cpan Time::HiRes

Regards,

Barry

Begin forwarded message:

From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>
Subject: possible problems in maker
Date: June 13, 2016 at 10:33:25 PM MDT
To: "barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>>
Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>>

Dear All

Please excuse me if you are not the right people to address, but there is no clear support stated in your page.

I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel).
My perl is 5.10 and my set up libraries are:

Here is my dialog:

./Build distclean
Cleaning up build files
Cleaning up configuration files
Not in MANIFEST: bin/AED_cdf_generator.pl
Not in MANIFEST: bin/quality_filter.pl
MANIFEST appears to be out of sync with the distribution

?

Next:

The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 3
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK


Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu

Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)

My PERL libraries are:

?.
Characteristics of this binary (from libperl):
  Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
  Built under linux
  Compiled at Nov 22 2013 18:29:21
  %ENV:
    PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
  @INC:
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /usr/local/lib64/perl5
    /usr/local/share/perl5
    /usr/lib64/perl5/vendor_perl
    /usr/share/perl5/vendor_perl
    /usr/lib64/perl5
    /usr/share/perl5


 The  ./Build install pass without errors.

However when I try to start the maker exacutable I got the following error:

./maker
Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
Compilation failed in require at ./maker line 42.
BEGIN failed--compilation aborted at ./maker line 42.
Undefined subroutine &threads::_END called at (eval 6) line 1.
END failed--call queue aborted at ./maker line 42.

Is there any other mising module which I have to install in order to make this software work. Thank you in advance

Alexander Tzanov



________________________________
Take a picture. Write a caption. Win a prize. Where?s Danny the Dolphin today?<http://www.csi.cuny.edu/wheresdanny/>

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From carsonhh at gmail.com  Wed Jun 15 09:50:54 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 15 Jun 2016 08:50:54 -0600
Subject: [maker-devel] possible problems in maker
In-Reply-To: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
	<A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
Message-ID: <7B96A90D-D5E7-4933-A005-334BFA50AC36@gmail.com>

Yes. I agree. The issue is your copy of some perl modules. You will need to install those via CPAN. Perhaps using the force option.

?Carson



> On Jun 13, 2016, at 11:36 PM, Barry Moore <bmoore at genetics.utah.edu> wrote:
> 
> Hi Alexander,
> 
> I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.
> 
> It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:
> 
> sudo cpan forks
> sudo cpan Time::HiRes
> 
> Regards,
> 
> Barry
> 
>> Begin forwarded message:
>> 
>> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>
>> Subject: possible problems in maker
>> Date: June 13, 2016 at 10:33:25 PM MDT
>> To: "barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>>
>> Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>>
>> 
>> Dear All
>> 
>> Please excuse me if you are not the right people to address, but there is no clear support stated in your page. 
>> 
>> I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel). 
>> My perl is 5.10 and my set up libraries are:
>> 
>> Here is my dialog:
>> 
>> ./Build distclean
>> Cleaning up build files
>> Cleaning up configuration files
>> Not in MANIFEST: bin/AED_cdf_generator.pl
>> Not in MANIFEST: bin/quality_filter.pl
>> MANIFEST appears to be out of sync with the distribution
>> 
>> ? 
>> 
>> Next:
>> 
>> The file 'Build' has been created for you to finish installing MAKER.
>> 
>> 
>> ==============================================================================
>> STATUS MAKER 3
>> ==============================================================================
>> PERL Dependencies:
>> VERIFIED
>> External Programs:
>> VERIFIED
>> External C Libraries:
>> VERIFIED
>> MPI SUPPORT:
>> ENABLED
>> MWAS Web Interface:
>> DISABLED
>> MAKER PACKAGE:
>> CONFIGURATION OK
>> 
>> 
>> Important Commands:
>> ./Build installdeps
>> #installs missing PERL dependencies
>> ./Build installexes
>> #installs all missing external programs
>> ./Build install
>> #installs MAKER
>> ./Build status
>> #Shows this status menu
>> 
>> Other Commands:
>> ./Build repeatmasker
>> #installs RepeatMasker (asks for RepBase)
>> ./Build blast
>> #installs BLAST (NCBI BLAST+)
>> ./Build exonerate
>> #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
>> ./Build snap
>> #installs SNAP
>> ./Build augustus
>> #installs Augustus
>> ./Build apollo
>> #installs Apollo
>> ./Build gbrowse
>> #installs GBrowse (must be root)
>> ./Build jbrowse
>> #installs JBrowse (MAKER copy, not web accecible)
>> ./Build webapollo
>> #installs WebApollo (use maker2wap to create DBs)
>> ./Build mpich2
>> #installs MPICH2 (but manual install recommended)
>> 
>> My PERL libraries are: 
>> 
>> ?.
>> Characteristics of this binary (from libperl): 
>>   Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>>                         PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>>                         USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>>                         USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>>   Built under linux
>>   Compiled at Nov 22 2013 18:29:21
>>   %ENV:
>>     PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
>> ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
>>   @INC:
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /usr/local/lib64/perl5
>>     /usr/local/share/perl5
>>     /usr/lib64/perl5/vendor_perl
>>     /usr/share/perl5/vendor_perl
>>     /usr/lib64/perl5
>>     /usr/share/perl5
>> 
>> 
>>  The  ./Build install pass without errors. 
>> 
>> However when I try to start the maker exacutable I got the following error:
>> 
>> ./maker
>> Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
>> Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
>> BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
>> Compilation failed in require at ./maker line 42.
>> BEGIN failed--compilation aborted at ./maker line 42.
>> Undefined subroutine &threads::_END called at (eval 6) line 1.
>> END failed--call queue aborted at ./maker line 42.
>> 
>> Is there any other mising module which I have to install in order to make this software work. Thank you in advance
>> 
>> Alexander Tzanov
>> 
>> 
>> 
>> Take a picture. Write a caption. Win a prize.  <>Where?s Danny the Dolphin today? <http://www.csi.cuny.edu/wheresdanny/>
> _______________________________________________
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> maker-devel at box290.bluehost.com
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From maker-devel at yandell-lab.org  Thu Jun 16 07:28:59 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 16 Jun 2016 16:28:59 +0400
Subject: [maker-devel] Healthy Lifestyle Plan Will Help Your Get Back In
	Shape
Message-ID: <004001d1c7cd$06e48b02$22298c96@jjjwfs>

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From maker-devel at yandell-lab.org  Sun Jun 19 05:49:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 19 Jun 2016 16:49:15 +0600
Subject: [maker-devel] Flexible schedule
Message-ID: <003801d1ca1b$07a06da6$05acaba6$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Wendi, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

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From maker-devel at yandell-lab.org  Mon Jun 20 10:41:04 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 20 Jun 2016 18:41:04 +0300
Subject: [maker-devel] Career growth
Message-ID: <D76325B51291F3823670E047C4A6D763@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Elliott, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From macmanes at gmail.com  Mon Jun 20 07:34:49 2016
From: macmanes at gmail.com (Matthew MacManes)
Date: Mon, 20 Jun 2016 07:34:49 -0500
Subject: [maker-devel] SegFault with MPI
Message-ID: <etPan.5767e2ee.49e7393e.19ff@gmail.com>

Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful.

I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set

export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior.

/openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer

or  

/openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
lots of output
?
choosing best annotation set
Choosing best annotations
deleted:30 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
_46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
#-------------------------------#
processing contig output
examining contents of the fasta file and run log
[davinci:09219] *** Process received signal ***
[davinci:09219] Signal: Segmentation fault (11)
[davinci:09219] Signal code: Address not mapped (1)
[davinci:09219] Failing at address: 0x50c
[davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
[davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 3]


--Next Contig--

/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
[davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
[davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
[davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
[davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
[davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
[davinci:09219] *** End of error message ***
SIGTERM received
SIGTERM received
Perl exited with active threads:
        1 running and unjoined
        0 finished and unjoined
        0 running and detached
SIGTERM received
SIGTERM received
SIGTERM received
Thanks for any advice,

Matt



Matthew MacManes, Ph.D.
University of New Hampshire? I? Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH? 03824
Phone: 603-862-4052? | Twitter:?@macmanes?| Web:?genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
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From carsonhh at gmail.com  Wed Jun 22 09:52:34 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jun 2016 08:52:34 -0600
Subject: [maker-devel] SegFault with MPI
In-Reply-To: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
References: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
Message-ID: <D75DC8C3-00F8-47B3-AFA8-EB67430EC9AB@gmail.com>

You may have more than one MPI flavor. For example, the mpicc used to compile or the mpi.h referred to during maker setup and compile may be from mpich2 but your running with mpiexec from OpenMPI. Or they may be from a different OpenMPI version than the one you are running with. Also make sure LD_PRELOAD gets exported in your bash_profile or each time before running MAKER (not just during install). Finally if all else fails, you can try installing perl without pthread support, and use that version of Perl to run with instead of /usr/bin/perl. Very very rarely needed, but in cases involving /lib/x86_64-linux-gnu/libpthread.so in a seg fault it can be the source of all grief. Usually indicates that something is broken with your package manager for the MPI install, Perl install, or GNU C library install.

?Carson


> On Jun 20, 2016, at 6:34 AM, Matthew MacManes <macmanes at gmail.com> wrote:
> 
> Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful. 
> 
> I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set 
> 
> export LD_PRELOAD=/openmpi/lib/libmpi.so
> export OMPI_MCA_mpi_warn_on_fork=0
> and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior. 
> 
> /openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> 
> or  
> 
> /openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> lots of output
> ?
> choosing best annotation set
> Choosing best annotations
> deleted:30 hits
> doing blastn of ESTs
> formating database...
> #--------- command -------------#
> Widget::formater:
> /usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
> #-------------------------------#
> processing chunk output
> running  blast search.
> #--------- command -------------#
> Widget::blastn:
> /usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
>  -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
> _46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
> #-------------------------------#
> processing contig output
> examining contents of the fasta file and run log
> [davinci:09219] *** Process received signal ***
> [davinci:09219] Signal: Segmentation fault (11)
> [davinci:09219] Signal code: Address not mapped (1)
> [davinci:09219] Failing at address: 0x50c
> [davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
> [davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 3]
> 
> 
> --Next Contig--
> 
> /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
> [davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
> [davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
> [davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
> [davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
> [davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
> [davinci:09219] *** End of error message ***
> SIGTERM received
> SIGTERM received
> Perl exited with active threads:
>         1 running and unjoined
>         0 finished and unjoined
>         0 running and detached
> SIGTERM received
> SIGTERM received
> SIGTERM received
> Thanks for any advice, 
> 
> Matt
> 
> 
> 
> 
> Matthew MacManes, Ph.D.
> University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
> Department of Molecular, Cellular, & Biomedical Sciences
> Durham, NH  03824
> Phone: 603-862-4052 <tel://Phone:%20603-862-4052>  | Twitter: @macmanes <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_macmanes&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=UqTeeQPXM6sdQU60Nu8UgU2jh30ms8LUeLT76lhbY44&e=> | Web: genomebio.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__genomebio.org_&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=xcTCYRLTnvXh7r_eBb-HmHZgaIA-ba7vE62iQnWHFdk&e=>
> Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
> 
> _______________________________________________
> 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 <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>

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From maker-devel at yandell-lab.org  Wed Jun 22 14:51:20 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 22 Jun 2016 20:51:20 +0100
Subject: [maker-devel] Wanted regional manageres
Message-ID: <001601d1ccc4$02290ba7$3a6d21b2$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Adrian, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun 23 18:14:00 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 06:14:00 +0700
Subject: [maker-devel] Wanted regional manageres
Message-ID: <004901d1cda9$04fd272a$3f9f4e93$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Shelia, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Fri Jun 24 03:20:23 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 12:20:23 +0400
Subject: [maker-devel] hi!
Message-ID: <732645530.201606241240@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelsey, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From sullis02 at nyu.edu  Fri Jun 24 11:53:25 2016
From: sullis02 at nyu.edu (Steven Sullivan)
Date: Fri, 24 Jun 2016 12:53:25 -0400
Subject: [maker-devel] what is a 'model file' for the web annotation service?
Message-ID: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>

Sorry if this is a dumb question.

Using the MAKER web service I have the option of adding an AUGUSTUS 'model
file' as input

I generated a  training set of genes from my species through use of online
AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
sequences,and a set of protein sequences from those cDNAs, for the species.
I received these files (folders) back from the AUGUSTUS server (in addition
to log and err files):


*Species parameter archive*:  parameters.tar.gz

*Training genes: * training.gb.gz

*Ab initio predictions*:  ab_initio.tar.gz

*predictions with hints:*  hints_pred.tar.gz



The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
train itself. The format is Genbank.

the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
folders), 1 gff and 1 gtf.

Do you know which file would be correct for input to online MAKER as a
'model' file?


(NB there is no UTR predictions file, as my input cDNAs did not have enough
UTR information in them )
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From jason.stajich at gmail.com  Fri Jun 24 20:22:37 2016
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 25 Jun 2016 01:22:37 +0000
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
Message-ID: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>

the parameters.tar.gz should contain this. - untar in the species folder in
you local Augustus install or set the Augustus config env variable to point
to a personal copy of the Augustus config folder and put this there.
Whatever you name this parameters folder is the species name you put in the
maker config.

On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu> wrote:

> Sorry if this is a dumb question.
>
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model
> file' as input
>
> I generated a  training set of genes from my species through use of online
> AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
> input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
> sequences,and a set of protein sequences from those cDNAs, for the species.
> I received these files (folders) back from the AUGUSTUS server (in addition
> to log and err files):
>
>
> *Species parameter archive*:  parameters.tar.gz
>
> *Training genes: * training.gb.gz
>
> *Ab initio predictions*:  ab_initio.tar.gz
>
> *predictions with hints:*  hints_pred.tar.gz
>
>
>
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
> train itself. The format is Genbank.
>
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
> folders), 1 gff and 1 gtf.
>
> Do you know which file would be correct for input to online MAKER as a
> 'model' file?
>
>
> (NB there is no UTR predictions file, as my input cDNAs did not have
> enough UTR information in them )
>
>
>
>
>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Fri Jun 24 18:13:46 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 15:13:46 -0800
Subject: [maker-devel] We offer new vacancy
Message-ID: <576DC40E.8044.C865E3@maker-devel.yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Ericka, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 27 00:12:27 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 26 Jun 2016 23:12:27 -0600
Subject: [maker-devel] The beautiful work in crisis!
Message-ID: <087723970956431164706690@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelvin, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Mon Jun 27 10:32:15 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 27 Jun 2016 09:32:15 -0600
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
	<CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
Message-ID: <4BE66531-1935-4B08-BD84-EB8118EAFBE9@gmail.com>

Also it?s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.

?Carson



> On Jun 24, 2016, at 7:22 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. 
> 
> On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu <mailto:sullis02 at nyu.edu>> wrote:
> Sorry if this is a dumb question.
> 
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input
> 
> I generated a  training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):
> 
> 
> 
> Species parameter archive:  parameters.tar.gz
> 
> Training genes:  training.gb.gz
> 
> Ab initio predictions:  ab_initio.tar.gz
> 
> predictions with hints:  hints_pred.tar.gz
> 
> 
> 
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.
> 
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.
> 
> Do you know which file would be correct for input to online MAKER as a 'model' file?
> 
> 
> (NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )
> 
> 
> 
> 
> 
> _______________________________________________
> 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 <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
> _______________________________________________
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> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From maker-devel at yandell-lab.org  Mon Jun 27 06:17:39 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 05:17:39 -0600
Subject: [maker-devel] Cooperation with the great company
Message-ID: <3C4249810B378AC3BDB67EF4C8753C42@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Leigh, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Tue Jun 28 02:35:52 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Tue, 28 Jun 2016 14:35:52 +0700
Subject: [maker-devel] DOC9732563123
Message-ID: <4C1EEB87-FE30-392B-9BC3-8BE15A78C15B@yandell-lab.org>

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From maker-devel at yandell-lab.org  Tue Jun 28 04:40:25 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 28 Jun 2016 09:40:25 +0000
Subject: [maker-devel] The crisis has finished! Work with us!
Message-ID: <98168ECD71005532BC2467DBAAFF9816@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Louisa, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 27 22:03:30 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 19:03:30 -0800
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <134877952880848613282257@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Jerrod, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From mmacd at udel.edu  Tue Jun 28 20:24:12 2016
From: mmacd at udel.edu (Madolyn Macdonald)
Date: Tue, 28 Jun 2016 21:24:12 -0400
Subject: [maker-devel] Segmentation Fault
Message-ID: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>

Hi Maker,
I am trying to run Maker and got the following in my stderr.log file for
one of my scaffolds.

sh: line 1: 34865 Segmentation fault      (core dumped)
/usr/local/exonerate-2.2.0/bin/exonerate -q
/tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m
protein2genome --softmasktarget --percent 20 --showcigar >
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
ERROR: Exonerate failed
--> rank=1, hostname=biomix2.dbi.local
ERROR: Failed while polishing proteins
ERROR: Chunk failed at level:10, tier_type:3
FAILED CONTIG:picr50

I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help
with this issue?
Any other thoughts?
Thanks

-- 
Madolyn Stinner (formerly Madolyn MacDonald)
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'
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From maker-devel at yandell-lab.org  Thu Jun 30 15:16:53 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 1 Jul 2016 03:16:53 +0700
Subject: [maker-devel] hi!
Message-ID: <219003668054710392676282@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Gale, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Thu Jun 30 13:11:31 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 30 Jun 2016 12:11:31 -0600
Subject: [maker-devel] Segmentation Fault
In-Reply-To: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
References: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
Message-ID: <659615D9-BDD3-4BE4-8832-C3129D3E4A37@gmail.com>

Seg faults will be the result of one of the programs used by MAKER or MPI itself.

If using OpenMPI, add '-mca btl ^openib? to your command line.
Example: mpiexec -mca btl ^openib -n 20 maker

Also you nY need to do this before running MAKER ?> export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so

Both steps are explained in the ../maker/INSTALL file.

MAKER is not compatible with MVAPICH2 or Intel MPI.


For external programs that segfault. Just reinstall them or pick different versions.


Finally the error from the forks module. See the following from the devel list ?> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA
It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)

?Carson



> On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd at udel.edu> wrote:
> 
> Hi Maker,
> I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.
> 
> sh: line 1: 34865 Segmentation fault      (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> ERROR: Exonerate failed
> --> rank=1, hostname=biomix2.dbi.local
> ERROR: Failed while polishing proteins
> ERROR: Chunk failed at level:10, tier_type:3
> FAILED CONTIG:picr50
> 
> I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help with this issue?
> Any other thoughts?
> Thanks
> 
> -- 
> Madolyn Stinner (formerly Madolyn MacDonald)
> UDel Bioinformatics and Systems Biology, PhD student
> RIT Alumnus 13'
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 30 16:19:02 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 30 Jun 2016 23:19:02 +0200
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <676D6E4F64644C454F4C6D46466E676D@DL0YF88>

Hello!

We are looking for employees working remotely.

My name is Nelson, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From courtney.stairs at icm.uu.se  Wed Jun 29 04:29:48 2016
From: courtney.stairs at icm.uu.se (Courtney Stairs)
Date: Wed, 29 Jun 2016 11:29:48 +0200
Subject: [maker-devel] Alternative genetic code
Message-ID: <5773950C.8030102@icm.uu.se>

Hello there,

I noticed on the google group that someone has asked about using an 
alternative genetic code with Maker.  Has such a function been 
implemented on the newer versions of Maker?  I understand that this is 
not a straight-forward task. I am interested in using Maker on a genome 
that using code 6.

Thank you very much for your time,

Courtney

-- 
------------------------------------
Courtney Stairs, PhD
Post-doctoral fellow
Laboratory of Dr. Thijs Ettema
Institute for Cell and Molecular Biology
Uppsala University
Sweden




From qlian003 at ucr.edu  Wed Jun  1 13:22:29 2016
From: qlian003 at ucr.edu (Qihua Liang)
Date: Wed, 1 Jun 2016 12:22:29 -0700
Subject: [maker-devel] fasta/gff3_merge problem
Message-ID: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>

Hi Maker developers,

I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
Synopsis:

fasta_merge -d maker_datastore_index.log
fasta_merge -o genome.all -i <fasta1> <fasta2> ...
Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 

Is it any explicit reason for this error?

Thanks
Qihua
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From carsonhh at gmail.com  Fri Jun  3 12:01:26 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 3 Jun 2016 12:01:26 -0600
Subject: [maker-devel] fasta/gff3_merge problem
In-Reply-To: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
References: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
Message-ID: <43A96AEB-DC28-4BBC-BDC2-BAEE35CFAAC9@gmail.com>

If it is just printing out the usage statement, then you have something wrong with your command line.

If you are getting no results back, then you have no gene models (you may have failed to provide an HMM for the gene predictors.).

Thanks,
Carson


> On Jun 1, 2016, at 1:22 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi Maker developers,
> 
> I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
> Synopsis:
> 
> fasta_merge -d maker_datastore_index.log
> fasta_merge -o genome.all -i <fasta1> <fasta2> ...
> Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 
> 
> Is it any explicit reason for this error?
> 
> Thanks
> Qihua
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Mon Jun  6 13:51:45 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Mon, 06 Jun 2016 15:51:45 -0400
Subject: [maker-devel] grab your part right now
Message-ID: <5755D451.1000506@yandell-lab.org>

Hello, 
 
Just wanted to know where I should send you the profits you'll be making?
 
My team is all setup and ready to welcome you on board,
so that we can start you on one of the most amazing pesos making journeys you'll ever take.
 
>>
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Let's not waste another minute, click the link below and your first commissions will be coming in as early as in the next 30 minutes.
 
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To your success, Charley Berger
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From maker-devel at yandell-lab.org  Wed Jun  8 02:11:50 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 8 Jun 2016 15:11:50 +0700
Subject: [maker-devel] look for a companion
Message-ID: <393096489.201606081534@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Darlene Carson, I am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun  9 12:23:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 9 Jun 2016 22:23:15 +0400
Subject: [maker-devel] partial occupation
Message-ID: <001c01d1c280$021aeb65$6c7a7bbe$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Alma, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 12 10:57:19 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 12 Jun 2016 20:57:19 +0400
Subject: [maker-devel] partial occupation
Message-ID: <349471532331748141280616@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Dudley, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From willett4 at email.unc.edu  Mon Jun 13 07:01:09 2016
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 13 Jun 2016 13:01:09 +0000
Subject: [maker-devel] integrating results from Augustus
Message-ID: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>

Hi All-

I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs.

The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:

"ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:Contig149

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:Contig149?


Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?

Thanks for any help you can give me,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: Genome Sciences Building 2252
phone: 919-843-8663
fax: 919-962-1625

http://labs.bio.unc.edu/Willett/

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From carsonhh at gmail.com  Mon Jun 13 12:28:33 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 13 Jun 2016 12:28:33 -0600
Subject: [maker-devel] integrating results from Augustus
In-Reply-To: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
References: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
Message-ID: <BAC5552D-4D70-4E0D-9B8D-10593E19F782@gmail.com>

You need to install augustus and place the species parameter files into the ?/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.

?Carson



> On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi All-
> 
> I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs. 
> 
> The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:
> 
> "ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:Contig149
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:Contig149?
> 
>   
> Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?
> 
> Thanks for any help you can give me,
> 
> Best,
> 
> Chris Willett
> 
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: Genome Sciences Building 2252
> phone: 919-843-8663
> fax: 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> 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 bmoore at genetics.utah.edu  Mon Jun 13 23:36:27 2016
From: bmoore at genetics.utah.edu (Barry Moore)
Date: Tue, 14 Jun 2016 05:36:27 +0000
Subject: [maker-devel] Fwd: possible problems in maker
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
Message-ID: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>

Hi Alexander,

I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.

It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:

sudo cpan forks
sudo cpan Time::HiRes

Regards,

Barry

Begin forwarded message:

From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>
Subject: possible problems in maker
Date: June 13, 2016 at 10:33:25 PM MDT
To: "barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>>
Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>>

Dear All

Please excuse me if you are not the right people to address, but there is no clear support stated in your page.

I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel).
My perl is 5.10 and my set up libraries are:

Here is my dialog:

./Build distclean
Cleaning up build files
Cleaning up configuration files
Not in MANIFEST: bin/AED_cdf_generator.pl
Not in MANIFEST: bin/quality_filter.pl
MANIFEST appears to be out of sync with the distribution

?

Next:

The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 3
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK


Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu

Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)

My PERL libraries are:

?.
Characteristics of this binary (from libperl):
  Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
  Built under linux
  Compiled at Nov 22 2013 18:29:21
  %ENV:
    PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
  @INC:
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /usr/local/lib64/perl5
    /usr/local/share/perl5
    /usr/lib64/perl5/vendor_perl
    /usr/share/perl5/vendor_perl
    /usr/lib64/perl5
    /usr/share/perl5


 The  ./Build install pass without errors.

However when I try to start the maker exacutable I got the following error:

./maker
Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
Compilation failed in require at ./maker line 42.
BEGIN failed--compilation aborted at ./maker line 42.
Undefined subroutine &threads::_END called at (eval 6) line 1.
END failed--call queue aborted at ./maker line 42.

Is there any other mising module which I have to install in order to make this software work. Thank you in advance

Alexander Tzanov



________________________________
Take a picture. Write a caption. Win a prize. Where?s Danny the Dolphin today?<http://www.csi.cuny.edu/wheresdanny/>

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From carsonhh at gmail.com  Wed Jun 15 08:50:54 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 15 Jun 2016 08:50:54 -0600
Subject: [maker-devel] possible problems in maker
In-Reply-To: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
	<A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
Message-ID: <7B96A90D-D5E7-4933-A005-334BFA50AC36@gmail.com>

Yes. I agree. The issue is your copy of some perl modules. You will need to install those via CPAN. Perhaps using the force option.

?Carson



> On Jun 13, 2016, at 11:36 PM, Barry Moore <bmoore at genetics.utah.edu> wrote:
> 
> Hi Alexander,
> 
> I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.
> 
> It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:
> 
> sudo cpan forks
> sudo cpan Time::HiRes
> 
> Regards,
> 
> Barry
> 
>> Begin forwarded message:
>> 
>> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>
>> Subject: possible problems in maker
>> Date: June 13, 2016 at 10:33:25 PM MDT
>> To: "barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>>
>> Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>>
>> 
>> Dear All
>> 
>> Please excuse me if you are not the right people to address, but there is no clear support stated in your page. 
>> 
>> I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel). 
>> My perl is 5.10 and my set up libraries are:
>> 
>> Here is my dialog:
>> 
>> ./Build distclean
>> Cleaning up build files
>> Cleaning up configuration files
>> Not in MANIFEST: bin/AED_cdf_generator.pl
>> Not in MANIFEST: bin/quality_filter.pl
>> MANIFEST appears to be out of sync with the distribution
>> 
>> ? 
>> 
>> Next:
>> 
>> The file 'Build' has been created for you to finish installing MAKER.
>> 
>> 
>> ==============================================================================
>> STATUS MAKER 3
>> ==============================================================================
>> PERL Dependencies:
>> VERIFIED
>> External Programs:
>> VERIFIED
>> External C Libraries:
>> VERIFIED
>> MPI SUPPORT:
>> ENABLED
>> MWAS Web Interface:
>> DISABLED
>> MAKER PACKAGE:
>> CONFIGURATION OK
>> 
>> 
>> Important Commands:
>> ./Build installdeps
>> #installs missing PERL dependencies
>> ./Build installexes
>> #installs all missing external programs
>> ./Build install
>> #installs MAKER
>> ./Build status
>> #Shows this status menu
>> 
>> Other Commands:
>> ./Build repeatmasker
>> #installs RepeatMasker (asks for RepBase)
>> ./Build blast
>> #installs BLAST (NCBI BLAST+)
>> ./Build exonerate
>> #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
>> ./Build snap
>> #installs SNAP
>> ./Build augustus
>> #installs Augustus
>> ./Build apollo
>> #installs Apollo
>> ./Build gbrowse
>> #installs GBrowse (must be root)
>> ./Build jbrowse
>> #installs JBrowse (MAKER copy, not web accecible)
>> ./Build webapollo
>> #installs WebApollo (use maker2wap to create DBs)
>> ./Build mpich2
>> #installs MPICH2 (but manual install recommended)
>> 
>> My PERL libraries are: 
>> 
>> ?.
>> Characteristics of this binary (from libperl): 
>>   Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>>                         PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>>                         USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>>                         USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>>   Built under linux
>>   Compiled at Nov 22 2013 18:29:21
>>   %ENV:
>>     PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
>> ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
>>   @INC:
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /usr/local/lib64/perl5
>>     /usr/local/share/perl5
>>     /usr/lib64/perl5/vendor_perl
>>     /usr/share/perl5/vendor_perl
>>     /usr/lib64/perl5
>>     /usr/share/perl5
>> 
>> 
>>  The  ./Build install pass without errors. 
>> 
>> However when I try to start the maker exacutable I got the following error:
>> 
>> ./maker
>> Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
>> Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
>> BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
>> Compilation failed in require at ./maker line 42.
>> BEGIN failed--compilation aborted at ./maker line 42.
>> Undefined subroutine &threads::_END called at (eval 6) line 1.
>> END failed--call queue aborted at ./maker line 42.
>> 
>> Is there any other mising module which I have to install in order to make this software work. Thank you in advance
>> 
>> Alexander Tzanov
>> 
>> 
>> 
>> Take a picture. Write a caption. Win a prize.  <>Where?s Danny the Dolphin today? <http://www.csi.cuny.edu/wheresdanny/>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 16 06:28:59 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 16 Jun 2016 16:28:59 +0400
Subject: [maker-devel] Healthy Lifestyle Plan Will Help Your Get Back In
	Shape
Message-ID: <004001d1c7cd$06e48b02$22298c96@jjjwfs>

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From maker-devel at yandell-lab.org  Sun Jun 19 04:49:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 19 Jun 2016 16:49:15 +0600
Subject: [maker-devel] Flexible schedule
Message-ID: <003801d1ca1b$07a06da6$05acaba6$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Wendi, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 20 09:41:04 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 20 Jun 2016 18:41:04 +0300
Subject: [maker-devel] Career growth
Message-ID: <D76325B51291F3823670E047C4A6D763@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Elliott, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From macmanes at gmail.com  Mon Jun 20 06:34:49 2016
From: macmanes at gmail.com (Matthew MacManes)
Date: Mon, 20 Jun 2016 07:34:49 -0500
Subject: [maker-devel] SegFault with MPI
Message-ID: <etPan.5767e2ee.49e7393e.19ff@gmail.com>

Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful.

I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set

export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior.

/openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer

or  

/openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
lots of output
?
choosing best annotation set
Choosing best annotations
deleted:30 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
_46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
#-------------------------------#
processing contig output
examining contents of the fasta file and run log
[davinci:09219] *** Process received signal ***
[davinci:09219] Signal: Segmentation fault (11)
[davinci:09219] Signal code: Address not mapped (1)
[davinci:09219] Failing at address: 0x50c
[davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
[davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 3]


--Next Contig--

/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
[davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
[davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
[davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
[davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
[davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
[davinci:09219] *** End of error message ***
SIGTERM received
SIGTERM received
Perl exited with active threads:
        1 running and unjoined
        0 finished and unjoined
        0 running and detached
SIGTERM received
SIGTERM received
SIGTERM received
Thanks for any advice,

Matt



Matthew MacManes, Ph.D.
University of New Hampshire? I? Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH? 03824
Phone: 603-862-4052? | Twitter:?@macmanes?| Web:?genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
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From carsonhh at gmail.com  Wed Jun 22 08:52:34 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jun 2016 08:52:34 -0600
Subject: [maker-devel] SegFault with MPI
In-Reply-To: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
References: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
Message-ID: <D75DC8C3-00F8-47B3-AFA8-EB67430EC9AB@gmail.com>

You may have more than one MPI flavor. For example, the mpicc used to compile or the mpi.h referred to during maker setup and compile may be from mpich2 but your running with mpiexec from OpenMPI. Or they may be from a different OpenMPI version than the one you are running with. Also make sure LD_PRELOAD gets exported in your bash_profile or each time before running MAKER (not just during install). Finally if all else fails, you can try installing perl without pthread support, and use that version of Perl to run with instead of /usr/bin/perl. Very very rarely needed, but in cases involving /lib/x86_64-linux-gnu/libpthread.so in a seg fault it can be the source of all grief. Usually indicates that something is broken with your package manager for the MPI install, Perl install, or GNU C library install.

?Carson


> On Jun 20, 2016, at 6:34 AM, Matthew MacManes <macmanes at gmail.com> wrote:
> 
> Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful. 
> 
> I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set 
> 
> export LD_PRELOAD=/openmpi/lib/libmpi.so
> export OMPI_MCA_mpi_warn_on_fork=0
> and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior. 
> 
> /openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> 
> or  
> 
> /openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> lots of output
> ?
> choosing best annotation set
> Choosing best annotations
> deleted:30 hits
> doing blastn of ESTs
> formating database...
> #--------- command -------------#
> Widget::formater:
> /usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
> #-------------------------------#
> processing chunk output
> running  blast search.
> #--------- command -------------#
> Widget::blastn:
> /usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
>  -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
> _46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
> #-------------------------------#
> processing contig output
> examining contents of the fasta file and run log
> [davinci:09219] *** Process received signal ***
> [davinci:09219] Signal: Segmentation fault (11)
> [davinci:09219] Signal code: Address not mapped (1)
> [davinci:09219] Failing at address: 0x50c
> [davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
> [davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 3]
> 
> 
> --Next Contig--
> 
> /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
> [davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
> [davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
> [davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
> [davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
> [davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
> [davinci:09219] *** End of error message ***
> SIGTERM received
> SIGTERM received
> Perl exited with active threads:
>         1 running and unjoined
>         0 finished and unjoined
>         0 running and detached
> SIGTERM received
> SIGTERM received
> SIGTERM received
> Thanks for any advice, 
> 
> Matt
> 
> 
> 
> 
> Matthew MacManes, Ph.D.
> University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
> Department of Molecular, Cellular, & Biomedical Sciences
> Durham, NH  03824
> Phone: 603-862-4052 <tel://Phone:%20603-862-4052>  | Twitter: @macmanes <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_macmanes&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=UqTeeQPXM6sdQU60Nu8UgU2jh30ms8LUeLT76lhbY44&e=> | Web: genomebio.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__genomebio.org_&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=xcTCYRLTnvXh7r_eBb-HmHZgaIA-ba7vE62iQnWHFdk&e=>
> Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
> 
> _______________________________________________
> 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 <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>

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From maker-devel at yandell-lab.org  Wed Jun 22 13:51:20 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 22 Jun 2016 20:51:20 +0100
Subject: [maker-devel] Wanted regional manageres
Message-ID: <001601d1ccc4$02290ba7$3a6d21b2$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Adrian, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

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From maker-devel at yandell-lab.org  Thu Jun 23 17:14:00 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 06:14:00 +0700
Subject: [maker-devel] Wanted regional manageres
Message-ID: <004901d1cda9$04fd272a$3f9f4e93$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Shelia, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Fri Jun 24 02:20:23 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 12:20:23 +0400
Subject: [maker-devel] hi!
Message-ID: <732645530.201606241240@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelsey, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

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From sullis02 at nyu.edu  Fri Jun 24 10:53:25 2016
From: sullis02 at nyu.edu (Steven Sullivan)
Date: Fri, 24 Jun 2016 12:53:25 -0400
Subject: [maker-devel] what is a 'model file' for the web annotation service?
Message-ID: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>

Sorry if this is a dumb question.

Using the MAKER web service I have the option of adding an AUGUSTUS 'model
file' as input

I generated a  training set of genes from my species through use of online
AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
sequences,and a set of protein sequences from those cDNAs, for the species.
I received these files (folders) back from the AUGUSTUS server (in addition
to log and err files):


*Species parameter archive*:  parameters.tar.gz

*Training genes: * training.gb.gz

*Ab initio predictions*:  ab_initio.tar.gz

*predictions with hints:*  hints_pred.tar.gz



The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
train itself. The format is Genbank.

the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
folders), 1 gff and 1 gtf.

Do you know which file would be correct for input to online MAKER as a
'model' file?


(NB there is no UTR predictions file, as my input cDNAs did not have enough
UTR information in them )
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From jason.stajich at gmail.com  Fri Jun 24 19:22:37 2016
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 25 Jun 2016 01:22:37 +0000
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
Message-ID: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>

the parameters.tar.gz should contain this. - untar in the species folder in
you local Augustus install or set the Augustus config env variable to point
to a personal copy of the Augustus config folder and put this there.
Whatever you name this parameters folder is the species name you put in the
maker config.

On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu> wrote:

> Sorry if this is a dumb question.
>
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model
> file' as input
>
> I generated a  training set of genes from my species through use of online
> AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
> input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
> sequences,and a set of protein sequences from those cDNAs, for the species.
> I received these files (folders) back from the AUGUSTUS server (in addition
> to log and err files):
>
>
> *Species parameter archive*:  parameters.tar.gz
>
> *Training genes: * training.gb.gz
>
> *Ab initio predictions*:  ab_initio.tar.gz
>
> *predictions with hints:*  hints_pred.tar.gz
>
>
>
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
> train itself. The format is Genbank.
>
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
> folders), 1 gff and 1 gtf.
>
> Do you know which file would be correct for input to online MAKER as a
> 'model' file?
>
>
> (NB there is no UTR predictions file, as my input cDNAs did not have
> enough UTR information in them )
>
>
>
>
>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Fri Jun 24 17:13:46 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 15:13:46 -0800
Subject: [maker-devel] We offer new vacancy
Message-ID: <576DC40E.8044.C865E3@maker-devel.yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Ericka, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 26 23:12:27 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 26 Jun 2016 23:12:27 -0600
Subject: [maker-devel] The beautiful work in crisis!
Message-ID: <087723970956431164706690@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelvin, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Mon Jun 27 09:32:15 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 27 Jun 2016 09:32:15 -0600
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
	<CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
Message-ID: <4BE66531-1935-4B08-BD84-EB8118EAFBE9@gmail.com>

Also it?s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.

?Carson



> On Jun 24, 2016, at 7:22 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. 
> 
> On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu <mailto:sullis02 at nyu.edu>> wrote:
> Sorry if this is a dumb question.
> 
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input
> 
> I generated a  training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):
> 
> 
> 
> Species parameter archive:  parameters.tar.gz
> 
> Training genes:  training.gb.gz
> 
> Ab initio predictions:  ab_initio.tar.gz
> 
> predictions with hints:  hints_pred.tar.gz
> 
> 
> 
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.
> 
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.
> 
> Do you know which file would be correct for input to online MAKER as a 'model' file?
> 
> 
> (NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )
> 
> 
> 
> 
> 
> _______________________________________________
> 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 <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 maker-devel at yandell-lab.org  Mon Jun 27 05:17:39 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 05:17:39 -0600
Subject: [maker-devel] Cooperation with the great company
Message-ID: <3C4249810B378AC3BDB67EF4C8753C42@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Leigh, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Tue Jun 28 01:35:52 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Tue, 28 Jun 2016 14:35:52 +0700
Subject: [maker-devel] DOC9732563123
Message-ID: <4C1EEB87-FE30-392B-9BC3-8BE15A78C15B@yandell-lab.org>

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From maker-devel at yandell-lab.org  Tue Jun 28 03:40:25 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 28 Jun 2016 09:40:25 +0000
Subject: [maker-devel] The crisis has finished! Work with us!
Message-ID: <98168ECD71005532BC2467DBAAFF9816@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Louisa, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 27 21:03:30 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 19:03:30 -0800
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <134877952880848613282257@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Jerrod, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From mmacd at udel.edu  Tue Jun 28 19:24:12 2016
From: mmacd at udel.edu (Madolyn Macdonald)
Date: Tue, 28 Jun 2016 21:24:12 -0400
Subject: [maker-devel] Segmentation Fault
Message-ID: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>

Hi Maker,
I am trying to run Maker and got the following in my stderr.log file for
one of my scaffolds.

sh: line 1: 34865 Segmentation fault      (core dumped)
/usr/local/exonerate-2.2.0/bin/exonerate -q
/tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m
protein2genome --softmasktarget --percent 20 --showcigar >
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
ERROR: Exonerate failed
--> rank=1, hostname=biomix2.dbi.local
ERROR: Failed while polishing proteins
ERROR: Chunk failed at level:10, tier_type:3
FAILED CONTIG:picr50

I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help
with this issue?
Any other thoughts?
Thanks

-- 
Madolyn Stinner (formerly Madolyn MacDonald)
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'
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From maker-devel at yandell-lab.org  Thu Jun 30 14:16:53 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 1 Jul 2016 03:16:53 +0700
Subject: [maker-devel] hi!
Message-ID: <219003668054710392676282@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Gale, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Thu Jun 30 12:11:31 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 30 Jun 2016 12:11:31 -0600
Subject: [maker-devel] Segmentation Fault
In-Reply-To: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
References: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
Message-ID: <659615D9-BDD3-4BE4-8832-C3129D3E4A37@gmail.com>

Seg faults will be the result of one of the programs used by MAKER or MPI itself.

If using OpenMPI, add '-mca btl ^openib? to your command line.
Example: mpiexec -mca btl ^openib -n 20 maker

Also you nY need to do this before running MAKER ?> export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so

Both steps are explained in the ../maker/INSTALL file.

MAKER is not compatible with MVAPICH2 or Intel MPI.


For external programs that segfault. Just reinstall them or pick different versions.


Finally the error from the forks module. See the following from the devel list ?> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA
It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)

?Carson



> On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd at udel.edu> wrote:
> 
> Hi Maker,
> I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.
> 
> sh: line 1: 34865 Segmentation fault      (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> ERROR: Exonerate failed
> --> rank=1, hostname=biomix2.dbi.local
> ERROR: Failed while polishing proteins
> ERROR: Chunk failed at level:10, tier_type:3
> FAILED CONTIG:picr50
> 
> I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help with this issue?
> Any other thoughts?
> Thanks
> 
> -- 
> Madolyn Stinner (formerly Madolyn MacDonald)
> UDel Bioinformatics and Systems Biology, PhD student
> RIT Alumnus 13'
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 30 15:19:02 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 30 Jun 2016 23:19:02 +0200
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <676D6E4F64644C454F4C6D46466E676D@DL0YF88>

Hello!

We are looking for employees working remotely.

My name is Nelson, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From courtney.stairs at icm.uu.se  Wed Jun 29 03:29:48 2016
From: courtney.stairs at icm.uu.se (Courtney Stairs)
Date: Wed, 29 Jun 2016 11:29:48 +0200
Subject: [maker-devel] Alternative genetic code
Message-ID: <5773950C.8030102@icm.uu.se>

Hello there,

I noticed on the google group that someone has asked about using an 
alternative genetic code with Maker.  Has such a function been 
implemented on the newer versions of Maker?  I understand that this is 
not a straight-forward task. I am interested in using Maker on a genome 
that using code 6.

Thank you very much for your time,

Courtney

-- 
------------------------------------
Courtney Stairs, PhD
Post-doctoral fellow
Laboratory of Dr. Thijs Ettema
Institute for Cell and Molecular Biology
Uppsala University
Sweden




From qlian003 at ucr.edu  Wed Jun  1 13:22:29 2016
From: qlian003 at ucr.edu (Qihua Liang)
Date: Wed, 1 Jun 2016 12:22:29 -0700
Subject: [maker-devel] fasta/gff3_merge problem
Message-ID: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>

Hi Maker developers,

I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
Synopsis:

fasta_merge -d maker_datastore_index.log
fasta_merge -o genome.all -i <fasta1> <fasta2> ...
Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 

Is it any explicit reason for this error?

Thanks
Qihua
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From carsonhh at gmail.com  Fri Jun  3 12:01:26 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 3 Jun 2016 12:01:26 -0600
Subject: [maker-devel] fasta/gff3_merge problem
In-Reply-To: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
References: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
Message-ID: <43A96AEB-DC28-4BBC-BDC2-BAEE35CFAAC9@gmail.com>

If it is just printing out the usage statement, then you have something wrong with your command line.

If you are getting no results back, then you have no gene models (you may have failed to provide an HMM for the gene predictors.).

Thanks,
Carson


> On Jun 1, 2016, at 1:22 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi Maker developers,
> 
> I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
> Synopsis:
> 
> fasta_merge -d maker_datastore_index.log
> fasta_merge -o genome.all -i <fasta1> <fasta2> ...
> Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 
> 
> Is it any explicit reason for this error?
> 
> Thanks
> Qihua
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Mon Jun  6 13:51:45 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Mon, 06 Jun 2016 15:51:45 -0400
Subject: [maker-devel] grab your part right now
Message-ID: <5755D451.1000506@yandell-lab.org>

Hello, 
 
Just wanted to know where I should send you the profits you'll be making?
 
My team is all setup and ready to welcome you on board,
so that we can start you on one of the most amazing pesos making journeys you'll ever take.
 
>>
CLICK HERE TO START YOUR JOURNEY 
Let's not waste another minute, click the link below and your first commissions will be coming in as early as in the next 30 minutes.
 
>>
CLICK HERE TO START EXPEDITION 
To your success, Charley Berger
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From maker-devel at yandell-lab.org  Wed Jun  8 02:11:50 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 8 Jun 2016 15:11:50 +0700
Subject: [maker-devel] look for a companion
Message-ID: <393096489.201606081534@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Darlene Carson, I am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun  9 12:23:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 9 Jun 2016 22:23:15 +0400
Subject: [maker-devel] partial occupation
Message-ID: <001c01d1c280$021aeb65$6c7a7bbe$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Alma, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 12 10:57:19 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 12 Jun 2016 20:57:19 +0400
Subject: [maker-devel] partial occupation
Message-ID: <349471532331748141280616@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Dudley, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From willett4 at email.unc.edu  Mon Jun 13 07:01:09 2016
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 13 Jun 2016 13:01:09 +0000
Subject: [maker-devel] integrating results from Augustus
Message-ID: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>

Hi All-

I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs.

The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:

"ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:Contig149

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:Contig149?


Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?

Thanks for any help you can give me,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: Genome Sciences Building 2252
phone: 919-843-8663
fax: 919-962-1625

http://labs.bio.unc.edu/Willett/

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From carsonhh at gmail.com  Mon Jun 13 12:28:33 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 13 Jun 2016 12:28:33 -0600
Subject: [maker-devel] integrating results from Augustus
In-Reply-To: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
References: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
Message-ID: <BAC5552D-4D70-4E0D-9B8D-10593E19F782@gmail.com>

You need to install augustus and place the species parameter files into the ?/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.

?Carson



> On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi All-
> 
> I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs. 
> 
> The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:
> 
> "ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:Contig149
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:Contig149?
> 
>   
> Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?
> 
> Thanks for any help you can give me,
> 
> Best,
> 
> Chris Willett
> 
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: Genome Sciences Building 2252
> phone: 919-843-8663
> fax: 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> 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 bmoore at genetics.utah.edu  Mon Jun 13 23:36:27 2016
From: bmoore at genetics.utah.edu (Barry Moore)
Date: Tue, 14 Jun 2016 05:36:27 +0000
Subject: [maker-devel] Fwd: possible problems in maker
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
Message-ID: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>

Hi Alexander,

I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.

It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:

sudo cpan forks
sudo cpan Time::HiRes

Regards,

Barry

Begin forwarded message:

From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>
Subject: possible problems in maker
Date: June 13, 2016 at 10:33:25 PM MDT
To: "barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>>
Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>>

Dear All

Please excuse me if you are not the right people to address, but there is no clear support stated in your page.

I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel).
My perl is 5.10 and my set up libraries are:

Here is my dialog:

./Build distclean
Cleaning up build files
Cleaning up configuration files
Not in MANIFEST: bin/AED_cdf_generator.pl
Not in MANIFEST: bin/quality_filter.pl
MANIFEST appears to be out of sync with the distribution

?

Next:

The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 3
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK


Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu

Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)

My PERL libraries are:

?.
Characteristics of this binary (from libperl):
  Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
  Built under linux
  Compiled at Nov 22 2013 18:29:21
  %ENV:
    PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
  @INC:
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /usr/local/lib64/perl5
    /usr/local/share/perl5
    /usr/lib64/perl5/vendor_perl
    /usr/share/perl5/vendor_perl
    /usr/lib64/perl5
    /usr/share/perl5


 The  ./Build install pass without errors.

However when I try to start the maker exacutable I got the following error:

./maker
Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
Compilation failed in require at ./maker line 42.
BEGIN failed--compilation aborted at ./maker line 42.
Undefined subroutine &threads::_END called at (eval 6) line 1.
END failed--call queue aborted at ./maker line 42.

Is there any other mising module which I have to install in order to make this software work. Thank you in advance

Alexander Tzanov



________________________________
Take a picture. Write a caption. Win a prize. Where?s Danny the Dolphin today?<http://www.csi.cuny.edu/wheresdanny/>

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From carsonhh at gmail.com  Wed Jun 15 08:50:54 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 15 Jun 2016 08:50:54 -0600
Subject: [maker-devel] possible problems in maker
In-Reply-To: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
	<A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
Message-ID: <7B96A90D-D5E7-4933-A005-334BFA50AC36@gmail.com>

Yes. I agree. The issue is your copy of some perl modules. You will need to install those via CPAN. Perhaps using the force option.

?Carson



> On Jun 13, 2016, at 11:36 PM, Barry Moore <bmoore at genetics.utah.edu> wrote:
> 
> Hi Alexander,
> 
> I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.
> 
> It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:
> 
> sudo cpan forks
> sudo cpan Time::HiRes
> 
> Regards,
> 
> Barry
> 
>> Begin forwarded message:
>> 
>> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>
>> Subject: possible problems in maker
>> Date: June 13, 2016 at 10:33:25 PM MDT
>> To: "barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>>
>> Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>>
>> 
>> Dear All
>> 
>> Please excuse me if you are not the right people to address, but there is no clear support stated in your page. 
>> 
>> I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel). 
>> My perl is 5.10 and my set up libraries are:
>> 
>> Here is my dialog:
>> 
>> ./Build distclean
>> Cleaning up build files
>> Cleaning up configuration files
>> Not in MANIFEST: bin/AED_cdf_generator.pl
>> Not in MANIFEST: bin/quality_filter.pl
>> MANIFEST appears to be out of sync with the distribution
>> 
>> ? 
>> 
>> Next:
>> 
>> The file 'Build' has been created for you to finish installing MAKER.
>> 
>> 
>> ==============================================================================
>> STATUS MAKER 3
>> ==============================================================================
>> PERL Dependencies:
>> VERIFIED
>> External Programs:
>> VERIFIED
>> External C Libraries:
>> VERIFIED
>> MPI SUPPORT:
>> ENABLED
>> MWAS Web Interface:
>> DISABLED
>> MAKER PACKAGE:
>> CONFIGURATION OK
>> 
>> 
>> Important Commands:
>> ./Build installdeps
>> #installs missing PERL dependencies
>> ./Build installexes
>> #installs all missing external programs
>> ./Build install
>> #installs MAKER
>> ./Build status
>> #Shows this status menu
>> 
>> Other Commands:
>> ./Build repeatmasker
>> #installs RepeatMasker (asks for RepBase)
>> ./Build blast
>> #installs BLAST (NCBI BLAST+)
>> ./Build exonerate
>> #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
>> ./Build snap
>> #installs SNAP
>> ./Build augustus
>> #installs Augustus
>> ./Build apollo
>> #installs Apollo
>> ./Build gbrowse
>> #installs GBrowse (must be root)
>> ./Build jbrowse
>> #installs JBrowse (MAKER copy, not web accecible)
>> ./Build webapollo
>> #installs WebApollo (use maker2wap to create DBs)
>> ./Build mpich2
>> #installs MPICH2 (but manual install recommended)
>> 
>> My PERL libraries are: 
>> 
>> ?.
>> Characteristics of this binary (from libperl): 
>>   Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>>                         PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>>                         USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>>                         USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>>   Built under linux
>>   Compiled at Nov 22 2013 18:29:21
>>   %ENV:
>>     PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
>> ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
>>   @INC:
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /usr/local/lib64/perl5
>>     /usr/local/share/perl5
>>     /usr/lib64/perl5/vendor_perl
>>     /usr/share/perl5/vendor_perl
>>     /usr/lib64/perl5
>>     /usr/share/perl5
>> 
>> 
>>  The  ./Build install pass without errors. 
>> 
>> However when I try to start the maker exacutable I got the following error:
>> 
>> ./maker
>> Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
>> Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
>> BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
>> Compilation failed in require at ./maker line 42.
>> BEGIN failed--compilation aborted at ./maker line 42.
>> Undefined subroutine &threads::_END called at (eval 6) line 1.
>> END failed--call queue aborted at ./maker line 42.
>> 
>> Is there any other mising module which I have to install in order to make this software work. Thank you in advance
>> 
>> Alexander Tzanov
>> 
>> 
>> 
>> Take a picture. Write a caption. Win a prize.  <>Where?s Danny the Dolphin today? <http://www.csi.cuny.edu/wheresdanny/>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 16 06:28:59 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 16 Jun 2016 16:28:59 +0400
Subject: [maker-devel] Healthy Lifestyle Plan Will Help Your Get Back In
	Shape
Message-ID: <004001d1c7cd$06e48b02$22298c96@jjjwfs>

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From maker-devel at yandell-lab.org  Sun Jun 19 04:49:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 19 Jun 2016 16:49:15 +0600
Subject: [maker-devel] Flexible schedule
Message-ID: <003801d1ca1b$07a06da6$05acaba6$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Wendi, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 20 09:41:04 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 20 Jun 2016 18:41:04 +0300
Subject: [maker-devel] Career growth
Message-ID: <D76325B51291F3823670E047C4A6D763@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Elliott, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From macmanes at gmail.com  Mon Jun 20 06:34:49 2016
From: macmanes at gmail.com (Matthew MacManes)
Date: Mon, 20 Jun 2016 07:34:49 -0500
Subject: [maker-devel] SegFault with MPI
Message-ID: <etPan.5767e2ee.49e7393e.19ff@gmail.com>

Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful.

I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set

export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior.

/openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer

or  

/openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
lots of output
?
choosing best annotation set
Choosing best annotations
deleted:30 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
_46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
#-------------------------------#
processing contig output
examining contents of the fasta file and run log
[davinci:09219] *** Process received signal ***
[davinci:09219] Signal: Segmentation fault (11)
[davinci:09219] Signal code: Address not mapped (1)
[davinci:09219] Failing at address: 0x50c
[davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
[davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 3]


--Next Contig--

/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
[davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
[davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
[davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
[davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
[davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
[davinci:09219] *** End of error message ***
SIGTERM received
SIGTERM received
Perl exited with active threads:
        1 running and unjoined
        0 finished and unjoined
        0 running and detached
SIGTERM received
SIGTERM received
SIGTERM received
Thanks for any advice,

Matt



Matthew MacManes, Ph.D.
University of New Hampshire? I? Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH? 03824
Phone: 603-862-4052? | Twitter:?@macmanes?| Web:?genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
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From carsonhh at gmail.com  Wed Jun 22 08:52:34 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jun 2016 08:52:34 -0600
Subject: [maker-devel] SegFault with MPI
In-Reply-To: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
References: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
Message-ID: <D75DC8C3-00F8-47B3-AFA8-EB67430EC9AB@gmail.com>

You may have more than one MPI flavor. For example, the mpicc used to compile or the mpi.h referred to during maker setup and compile may be from mpich2 but your running with mpiexec from OpenMPI. Or they may be from a different OpenMPI version than the one you are running with. Also make sure LD_PRELOAD gets exported in your bash_profile or each time before running MAKER (not just during install). Finally if all else fails, you can try installing perl without pthread support, and use that version of Perl to run with instead of /usr/bin/perl. Very very rarely needed, but in cases involving /lib/x86_64-linux-gnu/libpthread.so in a seg fault it can be the source of all grief. Usually indicates that something is broken with your package manager for the MPI install, Perl install, or GNU C library install.

?Carson


> On Jun 20, 2016, at 6:34 AM, Matthew MacManes <macmanes at gmail.com> wrote:
> 
> Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful. 
> 
> I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set 
> 
> export LD_PRELOAD=/openmpi/lib/libmpi.so
> export OMPI_MCA_mpi_warn_on_fork=0
> and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior. 
> 
> /openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> 
> or  
> 
> /openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> lots of output
> ?
> choosing best annotation set
> Choosing best annotations
> deleted:30 hits
> doing blastn of ESTs
> formating database...
> #--------- command -------------#
> Widget::formater:
> /usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
> #-------------------------------#
> processing chunk output
> running  blast search.
> #--------- command -------------#
> Widget::blastn:
> /usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
>  -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
> _46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
> #-------------------------------#
> processing contig output
> examining contents of the fasta file and run log
> [davinci:09219] *** Process received signal ***
> [davinci:09219] Signal: Segmentation fault (11)
> [davinci:09219] Signal code: Address not mapped (1)
> [davinci:09219] Failing at address: 0x50c
> [davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
> [davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 3]
> 
> 
> --Next Contig--
> 
> /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
> [davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
> [davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
> [davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
> [davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
> [davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
> [davinci:09219] *** End of error message ***
> SIGTERM received
> SIGTERM received
> Perl exited with active threads:
>         1 running and unjoined
>         0 finished and unjoined
>         0 running and detached
> SIGTERM received
> SIGTERM received
> SIGTERM received
> Thanks for any advice, 
> 
> Matt
> 
> 
> 
> 
> Matthew MacManes, Ph.D.
> University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
> Department of Molecular, Cellular, & Biomedical Sciences
> Durham, NH  03824
> Phone: 603-862-4052 <tel://Phone:%20603-862-4052>  | Twitter: @macmanes <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_macmanes&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=UqTeeQPXM6sdQU60Nu8UgU2jh30ms8LUeLT76lhbY44&e=> | Web: genomebio.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__genomebio.org_&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=xcTCYRLTnvXh7r_eBb-HmHZgaIA-ba7vE62iQnWHFdk&e=>
> Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
> 
> _______________________________________________
> 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 <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>

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From maker-devel at yandell-lab.org  Wed Jun 22 13:51:20 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 22 Jun 2016 20:51:20 +0100
Subject: [maker-devel] Wanted regional manageres
Message-ID: <001601d1ccc4$02290ba7$3a6d21b2$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Adrian, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun 23 17:14:00 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 06:14:00 +0700
Subject: [maker-devel] Wanted regional manageres
Message-ID: <004901d1cda9$04fd272a$3f9f4e93$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Shelia, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Fri Jun 24 02:20:23 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 12:20:23 +0400
Subject: [maker-devel] hi!
Message-ID: <732645530.201606241240@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelsey, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From sullis02 at nyu.edu  Fri Jun 24 10:53:25 2016
From: sullis02 at nyu.edu (Steven Sullivan)
Date: Fri, 24 Jun 2016 12:53:25 -0400
Subject: [maker-devel] what is a 'model file' for the web annotation service?
Message-ID: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>

Sorry if this is a dumb question.

Using the MAKER web service I have the option of adding an AUGUSTUS 'model
file' as input

I generated a  training set of genes from my species through use of online
AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
sequences,and a set of protein sequences from those cDNAs, for the species.
I received these files (folders) back from the AUGUSTUS server (in addition
to log and err files):


*Species parameter archive*:  parameters.tar.gz

*Training genes: * training.gb.gz

*Ab initio predictions*:  ab_initio.tar.gz

*predictions with hints:*  hints_pred.tar.gz



The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
train itself. The format is Genbank.

the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
folders), 1 gff and 1 gtf.

Do you know which file would be correct for input to online MAKER as a
'model' file?


(NB there is no UTR predictions file, as my input cDNAs did not have enough
UTR information in them )
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From jason.stajich at gmail.com  Fri Jun 24 19:22:37 2016
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 25 Jun 2016 01:22:37 +0000
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
Message-ID: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>

the parameters.tar.gz should contain this. - untar in the species folder in
you local Augustus install or set the Augustus config env variable to point
to a personal copy of the Augustus config folder and put this there.
Whatever you name this parameters folder is the species name you put in the
maker config.

On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu> wrote:

> Sorry if this is a dumb question.
>
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model
> file' as input
>
> I generated a  training set of genes from my species through use of online
> AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
> input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
> sequences,and a set of protein sequences from those cDNAs, for the species.
> I received these files (folders) back from the AUGUSTUS server (in addition
> to log and err files):
>
>
> *Species parameter archive*:  parameters.tar.gz
>
> *Training genes: * training.gb.gz
>
> *Ab initio predictions*:  ab_initio.tar.gz
>
> *predictions with hints:*  hints_pred.tar.gz
>
>
>
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
> train itself. The format is Genbank.
>
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
> folders), 1 gff and 1 gtf.
>
> Do you know which file would be correct for input to online MAKER as a
> 'model' file?
>
>
> (NB there is no UTR predictions file, as my input cDNAs did not have
> enough UTR information in them )
>
>
>
>
>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Fri Jun 24 17:13:46 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 15:13:46 -0800
Subject: [maker-devel] We offer new vacancy
Message-ID: <576DC40E.8044.C865E3@maker-devel.yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Ericka, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 26 23:12:27 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 26 Jun 2016 23:12:27 -0600
Subject: [maker-devel] The beautiful work in crisis!
Message-ID: <087723970956431164706690@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelvin, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Mon Jun 27 09:32:15 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 27 Jun 2016 09:32:15 -0600
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
	<CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
Message-ID: <4BE66531-1935-4B08-BD84-EB8118EAFBE9@gmail.com>

Also it?s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.

?Carson



> On Jun 24, 2016, at 7:22 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. 
> 
> On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu <mailto:sullis02 at nyu.edu>> wrote:
> Sorry if this is a dumb question.
> 
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input
> 
> I generated a  training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):
> 
> 
> 
> Species parameter archive:  parameters.tar.gz
> 
> Training genes:  training.gb.gz
> 
> Ab initio predictions:  ab_initio.tar.gz
> 
> predictions with hints:  hints_pred.tar.gz
> 
> 
> 
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.
> 
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.
> 
> Do you know which file would be correct for input to online MAKER as a 'model' file?
> 
> 
> (NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )
> 
> 
> 
> 
> 
> _______________________________________________
> 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 <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 maker-devel at yandell-lab.org  Mon Jun 27 05:17:39 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 05:17:39 -0600
Subject: [maker-devel] Cooperation with the great company
Message-ID: <3C4249810B378AC3BDB67EF4C8753C42@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Leigh, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Tue Jun 28 01:35:52 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Tue, 28 Jun 2016 14:35:52 +0700
Subject: [maker-devel] DOC9732563123
Message-ID: <4C1EEB87-FE30-392B-9BC3-8BE15A78C15B@yandell-lab.org>

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From maker-devel at yandell-lab.org  Tue Jun 28 03:40:25 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 28 Jun 2016 09:40:25 +0000
Subject: [maker-devel] The crisis has finished! Work with us!
Message-ID: <98168ECD71005532BC2467DBAAFF9816@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Louisa, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 27 21:03:30 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 19:03:30 -0800
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <134877952880848613282257@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Jerrod, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From mmacd at udel.edu  Tue Jun 28 19:24:12 2016
From: mmacd at udel.edu (Madolyn Macdonald)
Date: Tue, 28 Jun 2016 21:24:12 -0400
Subject: [maker-devel] Segmentation Fault
Message-ID: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>

Hi Maker,
I am trying to run Maker and got the following in my stderr.log file for
one of my scaffolds.

sh: line 1: 34865 Segmentation fault      (core dumped)
/usr/local/exonerate-2.2.0/bin/exonerate -q
/tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m
protein2genome --softmasktarget --percent 20 --showcigar >
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
ERROR: Exonerate failed
--> rank=1, hostname=biomix2.dbi.local
ERROR: Failed while polishing proteins
ERROR: Chunk failed at level:10, tier_type:3
FAILED CONTIG:picr50

I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help
with this issue?
Any other thoughts?
Thanks

-- 
Madolyn Stinner (formerly Madolyn MacDonald)
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'
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From maker-devel at yandell-lab.org  Thu Jun 30 14:16:53 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 1 Jul 2016 03:16:53 +0700
Subject: [maker-devel] hi!
Message-ID: <219003668054710392676282@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Gale, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Thu Jun 30 12:11:31 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 30 Jun 2016 12:11:31 -0600
Subject: [maker-devel] Segmentation Fault
In-Reply-To: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
References: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
Message-ID: <659615D9-BDD3-4BE4-8832-C3129D3E4A37@gmail.com>

Seg faults will be the result of one of the programs used by MAKER or MPI itself.

If using OpenMPI, add '-mca btl ^openib? to your command line.
Example: mpiexec -mca btl ^openib -n 20 maker

Also you nY need to do this before running MAKER ?> export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so

Both steps are explained in the ../maker/INSTALL file.

MAKER is not compatible with MVAPICH2 or Intel MPI.


For external programs that segfault. Just reinstall them or pick different versions.


Finally the error from the forks module. See the following from the devel list ?> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA
It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)

?Carson



> On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd at udel.edu> wrote:
> 
> Hi Maker,
> I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.
> 
> sh: line 1: 34865 Segmentation fault      (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> ERROR: Exonerate failed
> --> rank=1, hostname=biomix2.dbi.local
> ERROR: Failed while polishing proteins
> ERROR: Chunk failed at level:10, tier_type:3
> FAILED CONTIG:picr50
> 
> I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help with this issue?
> Any other thoughts?
> Thanks
> 
> -- 
> Madolyn Stinner (formerly Madolyn MacDonald)
> UDel Bioinformatics and Systems Biology, PhD student
> RIT Alumnus 13'
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 30 15:19:02 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 30 Jun 2016 23:19:02 +0200
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <676D6E4F64644C454F4C6D46466E676D@DL0YF88>

Hello!

We are looking for employees working remotely.

My name is Nelson, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From courtney.stairs at icm.uu.se  Wed Jun 29 03:29:48 2016
From: courtney.stairs at icm.uu.se (Courtney Stairs)
Date: Wed, 29 Jun 2016 11:29:48 +0200
Subject: [maker-devel] Alternative genetic code
Message-ID: <5773950C.8030102@icm.uu.se>

Hello there,

I noticed on the google group that someone has asked about using an 
alternative genetic code with Maker.  Has such a function been 
implemented on the newer versions of Maker?  I understand that this is 
not a straight-forward task. I am interested in using Maker on a genome 
that using code 6.

Thank you very much for your time,

Courtney

-- 
------------------------------------
Courtney Stairs, PhD
Post-doctoral fellow
Laboratory of Dr. Thijs Ettema
Institute for Cell and Molecular Biology
Uppsala University
Sweden




From qlian003 at ucr.edu  Wed Jun  1 13:22:29 2016
From: qlian003 at ucr.edu (Qihua Liang)
Date: Wed, 1 Jun 2016 12:22:29 -0700
Subject: [maker-devel] fasta/gff3_merge problem
Message-ID: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>

Hi Maker developers,

I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
Synopsis:

fasta_merge -d maker_datastore_index.log
fasta_merge -o genome.all -i <fasta1> <fasta2> ...
Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 

Is it any explicit reason for this error?

Thanks
Qihua
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From carsonhh at gmail.com  Fri Jun  3 12:01:26 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 3 Jun 2016 12:01:26 -0600
Subject: [maker-devel] fasta/gff3_merge problem
In-Reply-To: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
References: <C3621DE9-2D0A-4C5C-8881-34DA69458217@icloud.com>
Message-ID: <43A96AEB-DC28-4BBC-BDC2-BAEE35CFAAC9@gmail.com>

If it is just printing out the usage statement, then you have something wrong with your command line.

If you are getting no results back, then you have no gene models (you may have failed to provide an HMM for the gene predictors.).

Thanks,
Carson


> On Jun 1, 2016, at 1:22 PM, Qihua Liang <qlian003 at ucr.edu> wrote:
> 
> Hi Maker developers,
> 
> I am trying to get merged fasta/gff3 results. gff3_merge works perfect, but for the same datastore_index.log file, fast_merge doesn?t work as expect. There is no explicit error messages, but printing out 
> Synopsis:
> 
> fasta_merge -d maker_datastore_index.log
> fasta_merge -o genome.all -i <fasta1> <fasta2> ...
> Actually, I do run as the synopsis indicates, and similar steps work for gff3_merge and I could get the gff3 file. 
> 
> Is it any explicit reason for this error?
> 
> Thanks
> Qihua
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Mon Jun  6 13:51:45 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Mon, 06 Jun 2016 15:51:45 -0400
Subject: [maker-devel] grab your part right now
Message-ID: <5755D451.1000506@yandell-lab.org>

Hello, 
 
Just wanted to know where I should send you the profits you'll be making?
 
My team is all setup and ready to welcome you on board,
so that we can start you on one of the most amazing pesos making journeys you'll ever take.
 
>>
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Let's not waste another minute, click the link below and your first commissions will be coming in as early as in the next 30 minutes.
 
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To your success, Charley Berger
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From maker-devel at yandell-lab.org  Wed Jun  8 02:11:50 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 8 Jun 2016 15:11:50 +0700
Subject: [maker-devel] look for a companion
Message-ID: <393096489.201606081534@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Darlene Carson, I am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Thu Jun  9 12:23:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 9 Jun 2016 22:23:15 +0400
Subject: [maker-devel] partial occupation
Message-ID: <001c01d1c280$021aeb65$6c7a7bbe$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Alma, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 12 10:57:19 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 12 Jun 2016 20:57:19 +0400
Subject: [maker-devel] partial occupation
Message-ID: <349471532331748141280616@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Dudley, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From willett4 at email.unc.edu  Mon Jun 13 07:01:09 2016
From: willett4 at email.unc.edu (Willett, Christopher S)
Date: Mon, 13 Jun 2016 13:01:09 +0000
Subject: [maker-devel] integrating results from Augustus
Message-ID: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>

Hi All-

I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs.

The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:

"ERROR: Failed while prepare section files
ERROR: Chunk failed at level:12, tier_type:3
FAILED CONTIG:Contig149

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:Contig149?


Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?

Thanks for any help you can give me,

Best,

Chris Willett




~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Research Associate Professor
Department of Biology
CB#3280 Coker Hall
University of North Carolina, Chapel Hill
Chapel Hill, NC, 27599-3280

Office: Genome Sciences Building 2252
phone: 919-843-8663
fax: 919-962-1625

http://labs.bio.unc.edu/Willett/

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From carsonhh at gmail.com  Mon Jun 13 12:28:33 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 13 Jun 2016 12:28:33 -0600
Subject: [maker-devel] integrating results from Augustus
In-Reply-To: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
References: <8FD57CB5-C4A4-4A27-8EC7-E398F2198825@email.unc.edu>
Message-ID: <BAC5552D-4D70-4E0D-9B8D-10593E19F782@gmail.com>

You need to install augustus and place the species parameter files into the ?/augustus/config/species directory. They should be downloadable from the augustus online training tool. If you try and use GFF3 from augustus as input instead, you will lose the ability to use evidence alignments to inform the annotations.

?Carson



> On Jun 13, 2016, at 7:01 AM, Willett, Christopher S <willett4 at email.unc.edu> wrote:
> 
> Hi All-
> 
> I was trying to figure out if it is possible to integrate predictions from the web version of Augustus into a Maker run. I am working on a species of copepod and have a decent set of gene models that I used to train Augustus on its website. That seemed to work okay but I was having trouble figuring out how use these predictions in Maker. I tried generating predictions on the web service and then using the gff file generated from this with the pred_gff option but that doesn?t seem to be working. Is this the best way to do this? It looks like we don?t currently have Augustus installed on our server where I am running these programs. 
> 
> The problem that I am having with this approach is that each contig is failing and it looks like there are several errors. Including "ERROR: Non-unique top level ID?, "BLAST engine error: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence?, and this chunk:
> 
> "ERROR: Failed while prepare section files
> ERROR: Chunk failed at level:12, tier_type:3
> FAILED CONTIG:Contig149
> 
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:Contig149?
> 
>   
> Is there a better way of doing this, perhaps using a different file from the Augustus prediction output?
> 
> Thanks for any help you can give me,
> 
> Best,
> 
> Chris Willett
> 
> 
> 
> 
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Research Associate Professor
> Department of Biology
> CB#3280 Coker Hall
> University of North Carolina, Chapel Hill
> Chapel Hill, NC, 27599-3280 
> 
> Office: Genome Sciences Building 2252
> phone: 919-843-8663
> fax: 919-962-1625
> 
> http://labs.bio.unc.edu/Willett/ <http://labs.bio.unc.edu/Willett/>
> _______________________________________________
> 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 bmoore at genetics.utah.edu  Mon Jun 13 23:36:27 2016
From: bmoore at genetics.utah.edu (Barry Moore)
Date: Tue, 14 Jun 2016 05:36:27 +0000
Subject: [maker-devel] Fwd: possible problems in maker
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
Message-ID: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>

Hi Alexander,

I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.

It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:

sudo cpan forks
sudo cpan Time::HiRes

Regards,

Barry

Begin forwarded message:

From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>
Subject: possible problems in maker
Date: June 13, 2016 at 10:33:25 PM MDT
To: "barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu<mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu<mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com<mailto:shawn.rynearson at gmail.com>>
Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu<mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu<mailto:Zaid.MK at brooklyn.cuny.edu>>

Dear All

Please excuse me if you are not the right people to address, but there is no clear support stated in your page.

I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel).
My perl is 5.10 and my set up libraries are:

Here is my dialog:

./Build distclean
Cleaning up build files
Cleaning up configuration files
Not in MANIFEST: bin/AED_cdf_generator.pl
Not in MANIFEST: bin/quality_filter.pl
MANIFEST appears to be out of sync with the distribution

?

Next:

The file 'Build' has been created for you to finish installing MAKER.


==============================================================================
STATUS MAKER 3
==============================================================================
PERL Dependencies: VERIFIED
External Programs: VERIFIED
External C Libraries: VERIFIED
MPI SUPPORT: ENABLED
MWAS Web Interface: DISABLED
MAKER PACKAGE: CONFIGURATION OK


Important Commands:
./Build installdeps #installs missing PERL dependencies
./Build installexes #installs all missing external programs
./Build install #installs MAKER
./Build status #Shows this status menu

Other Commands:
./Build repeatmasker #installs RepeatMasker (asks for RepBase)
./Build blast #installs BLAST (NCBI BLAST+)
./Build exonerate #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
./Build snap #installs SNAP
./Build augustus #installs Augustus
./Build apollo #installs Apollo
./Build gbrowse #installs GBrowse (must be root)
./Build jbrowse #installs JBrowse (MAKER copy, not web accecible)
./Build webapollo #installs WebApollo (use maker2wap to create DBs)
./Build mpich2 #installs MPICH2 (but manual install recommended)

My PERL libraries are:

?.
Characteristics of this binary (from libperl):
  Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
                        PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
                        USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
                        USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
  Built under linux
  Compiled at Nov 22 2013 18:29:21
  %ENV:
    PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
  @INC:
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /share/apps/syssigaction/0.21/blib/lib
    /share/apps/listmoreutils/0.415/blib/lib
    /share/apps/exportertiny/0.042/blib/lib
    /share/apps/bioperl/1.6.923
    /usr/local/lib64/perl5
    /usr/local/share/perl5
    /usr/lib64/perl5/vendor_perl
    /usr/share/perl5/vendor_perl
    /usr/lib64/perl5
    /usr/share/perl5


 The  ./Build install pass without errors.

However when I try to start the maker exacutable I got the following error:

./maker
Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
Compilation failed in require at ./maker line 42.
BEGIN failed--compilation aborted at ./maker line 42.
Undefined subroutine &threads::_END called at (eval 6) line 1.
END failed--call queue aborted at ./maker line 42.

Is there any other mising module which I have to install in order to make this software work. Thank you in advance

Alexander Tzanov



________________________________
Take a picture. Write a caption. Win a prize. Where?s Danny the Dolphin today?<http://www.csi.cuny.edu/wheresdanny/>

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From carsonhh at gmail.com  Wed Jun 15 08:50:54 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 15 Jun 2016 08:50:54 -0600
Subject: [maker-devel] possible problems in maker
In-Reply-To: <A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
References: <F7C48569-0CED-4A19-B27D-5D6CDF08FCA7@csi.cuny.edu>
	<A4A359F1-4903-4477-A9A6-03ED37CA967B@genetics.utah.edu>
Message-ID: <7B96A90D-D5E7-4933-A005-334BFA50AC36@gmail.com>

Yes. I agree. The issue is your copy of some perl modules. You will need to install those via CPAN. Perhaps using the force option.

?Carson



> On Jun 13, 2016, at 11:36 PM, Barry Moore <bmoore at genetics.utah.edu> wrote:
> 
> Hi Alexander,
> 
> I?ve forwarded your e-mail to the maker-devel mailing list where it will reach a broad community of maker users.
> 
> It looks like your build is complete, but the error message suggest problems with the forks module calling Time::HiRes.  A manual install of the forks and Time::HiRes module would be where I would start.  If you have root access, try this:
> 
> sudo cpan forks
> sudo cpan Time::HiRes
> 
> Regards,
> 
> Barry
> 
>> Begin forwarded message:
>> 
>> From: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>
>> Subject: possible problems in maker
>> Date: June 13, 2016 at 10:33:25 PM MDT
>> To: "barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>" <barry.moore at genetics.utah.edu <mailto:barry.moore at genetics.utah.edu>>, "myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>" <myandell at genetics.utah.edu <mailto:myandell at genetics.utah.edu>>, "shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>" <shawn.rynearson at gmail.com <mailto:shawn.rynearson at gmail.com>>
>> Cc: Alexander Tzanov <Alexander.Tzanov at csi.cuny.edu <mailto:Alexander.Tzanov at csi.cuny.edu>>, "Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>" <Zaid.MK at brooklyn.cuny.edu <mailto:Zaid.MK at brooklyn.cuny.edu>>
>> 
>> Dear All
>> 
>> Please excuse me if you are not the right people to address, but there is no clear support stated in your page. 
>> 
>> I am trying to install MAKER (both versions give me the same error, ACADEMIC) on our HPC cluster  (OpenMpi 1.8.4_intel). 
>> My perl is 5.10 and my set up libraries are:
>> 
>> Here is my dialog:
>> 
>> ./Build distclean
>> Cleaning up build files
>> Cleaning up configuration files
>> Not in MANIFEST: bin/AED_cdf_generator.pl
>> Not in MANIFEST: bin/quality_filter.pl
>> MANIFEST appears to be out of sync with the distribution
>> 
>> ? 
>> 
>> Next:
>> 
>> The file 'Build' has been created for you to finish installing MAKER.
>> 
>> 
>> ==============================================================================
>> STATUS MAKER 3
>> ==============================================================================
>> PERL Dependencies:
>> VERIFIED
>> External Programs:
>> VERIFIED
>> External C Libraries:
>> VERIFIED
>> MPI SUPPORT:
>> ENABLED
>> MWAS Web Interface:
>> DISABLED
>> MAKER PACKAGE:
>> CONFIGURATION OK
>> 
>> 
>> Important Commands:
>> ./Build installdeps
>> #installs missing PERL dependencies
>> ./Build installexes
>> #installs all missing external programs
>> ./Build install
>> #installs MAKER
>> ./Build status
>> #Shows this status menu
>> 
>> Other Commands:
>> ./Build repeatmasker
>> #installs RepeatMasker (asks for RepBase)
>> ./Build blast
>> #installs BLAST (NCBI BLAST+)
>> ./Build exonerate
>> #installs Exonerate (v2 on UNIX / v1 on Mac OSX)
>> ./Build snap
>> #installs SNAP
>> ./Build augustus
>> #installs Augustus
>> ./Build apollo
>> #installs Apollo
>> ./Build gbrowse
>> #installs GBrowse (must be root)
>> ./Build jbrowse
>> #installs JBrowse (MAKER copy, not web accecible)
>> ./Build webapollo
>> #installs WebApollo (use maker2wap to create DBs)
>> ./Build mpich2
>> #installs MPICH2 (but manual install recommended)
>> 
>> My PERL libraries are: 
>> 
>> ?.
>> Characteristics of this binary (from libperl): 
>>   Compile-time options: MULTIPLICITY PERL_DONT_CREATE_GVSV
>>                         PERL_IMPLICIT_CONTEXT PERL_MALLOC_WRAP USE_64_BIT_ALL
>>                         USE_64_BIT_INT USE_ITHREADS USE_LARGE_FILES
>>                         USE_PERLIO USE_REENTRANT_API USE_SITECUSTOMIZE
>>   Built under linux
>>   Compiled at Nov 22 2013 18:29:21
>>   %ENV:
>>     PERL5LIB="/share/apps/syssigaction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:/share/apps/syssiga
>> ction/0.21/blib/lib:/share/apps/listmoreutils/0.415/blib/lib:/share/apps/exportertiny/0.042/blib/lib:/share/apps/bioperl/1.6.923:"
>>   @INC:
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /share/apps/syssigaction/0.21/blib/lib
>>     /share/apps/listmoreutils/0.415/blib/lib
>>     /share/apps/exportertiny/0.042/blib/lib
>>     /share/apps/bioperl/1.6.923
>>     /usr/local/lib64/perl5
>>     /usr/local/share/perl5
>>     /usr/lib64/perl5/vendor_perl
>>     /usr/share/perl5/vendor_perl
>>     /usr/lib64/perl5
>>     /usr/share/perl5
>> 
>> 
>>  The  ./Build install pass without errors. 
>> 
>> However when I try to start the maker exacutable I got the following error:
>> 
>> ./maker
>> Use of inherited AUTOLOAD for non-method Time::HiRes::d_usleep() is deprecated at /usr/local/lib64/perl5/forks.pm line 638.
>> Can't locate auto/Time/HiRes/d_usleep.al in @INC (@INC contains: /share/apps/maker/3.0.B/build/maker/bin/../perl/lib /share/apps/maker/3.0.B/build/maker/bin/../lib /share/apps/maker/3.0.B/build/maker/bin/../src/inc/perl/lib /share/apps/syssigaction/0.21/blib/lib /share/apps/listmoreutils/0.415/blib/lib /share/apps/exportertiny/0.042/blib/lib /share/apps/bioperl/1.6.923 /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /usr/local/lib64/perl5/forks.pm line 638.
>> BEGIN failed--compilation aborted at /usr/local/lib64/perl5/forks.pm line 681.
>> Compilation failed in require at ./maker line 42.
>> BEGIN failed--compilation aborted at ./maker line 42.
>> Undefined subroutine &threads::_END called at (eval 6) line 1.
>> END failed--call queue aborted at ./maker line 42.
>> 
>> Is there any other mising module which I have to install in order to make this software work. Thank you in advance
>> 
>> Alexander Tzanov
>> 
>> 
>> 
>> Take a picture. Write a caption. Win a prize.  <>Where?s Danny the Dolphin today? <http://www.csi.cuny.edu/wheresdanny/>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Thu Jun 16 06:28:59 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 16 Jun 2016 16:28:59 +0400
Subject: [maker-devel] Healthy Lifestyle Plan Will Help Your Get Back In
	Shape
Message-ID: <004001d1c7cd$06e48b02$22298c96@jjjwfs>

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From maker-devel at yandell-lab.org  Sun Jun 19 04:49:15 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 19 Jun 2016 16:49:15 +0600
Subject: [maker-devel] Flexible schedule
Message-ID: <003801d1ca1b$07a06da6$05acaba6$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Wendi, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

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Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 20 09:41:04 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 20 Jun 2016 18:41:04 +0300
Subject: [maker-devel] Career growth
Message-ID: <D76325B51291F3823670E047C4A6D763@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Elliott, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From macmanes at gmail.com  Mon Jun 20 06:34:49 2016
From: macmanes at gmail.com (Matthew MacManes)
Date: Mon, 20 Jun 2016 07:34:49 -0500
Subject: [maker-devel] SegFault with MPI
Message-ID: <etPan.5767e2ee.49e7393e.19ff@gmail.com>

Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful.

I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set

export LD_PRELOAD=/openmpi/lib/libmpi.so
export OMPI_MCA_mpi_warn_on_fork=0
and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior.

/openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer

or  

/openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
lots of output
?
choosing best annotation set
Choosing best annotations
deleted:30 hits
doing blastn of ESTs
formating database...
#--------- command -------------#
Widget::formater:
/usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
#-------------------------------#
processing chunk output
running  blast search.
#--------- command -------------#
Widget::blastn:
/usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
 -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
_46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
#-------------------------------#
processing contig output
examining contents of the fasta file and run log
[davinci:09219] *** Process received signal ***
[davinci:09219] Signal: Segmentation fault (11)
[davinci:09219] Signal code: Address not mapped (1)
[davinci:09219] Failing at address: 0x50c
[davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
[davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
[davinci:09219] [ 3]


--Next Contig--

/lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
[davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
[davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
[davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
[davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
[davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
[davinci:09219] *** End of error message ***
SIGTERM received
SIGTERM received
Perl exited with active threads:
        1 running and unjoined
        0 finished and unjoined
        0 running and detached
SIGTERM received
SIGTERM received
SIGTERM received
Thanks for any advice,

Matt



Matthew MacManes, Ph.D.
University of New Hampshire? I? Assistant Professor of Genome Enabled Biology
Department of Molecular, Cellular, & Biomedical Sciences
Durham, NH? 03824
Phone: 603-862-4052? | Twitter:?@macmanes?| Web:?genomebio.org
Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
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From carsonhh at gmail.com  Wed Jun 22 08:52:34 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 22 Jun 2016 08:52:34 -0600
Subject: [maker-devel] SegFault with MPI
In-Reply-To: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
References: <etPan.5767e2ee.49e7393e.19ff@gmail.com>
Message-ID: <D75DC8C3-00F8-47B3-AFA8-EB67430EC9AB@gmail.com>

You may have more than one MPI flavor. For example, the mpicc used to compile or the mpi.h referred to during maker setup and compile may be from mpich2 but your running with mpiexec from OpenMPI. Or they may be from a different OpenMPI version than the one you are running with. Also make sure LD_PRELOAD gets exported in your bash_profile or each time before running MAKER (not just during install). Finally if all else fails, you can try installing perl without pthread support, and use that version of Perl to run with instead of /usr/bin/perl. Very very rarely needed, but in cases involving /lib/x86_64-linux-gnu/libpthread.so in a seg fault it can be the source of all grief. Usually indicates that something is broken with your package manager for the MPI install, Perl install, or GNU C library install.

?Carson


> On Jun 20, 2016, at 6:34 AM, Matthew MacManes <macmanes at gmail.com> wrote:
> 
> Hello, I am having a strange SegFault that is related to MPI use - invoking maker without MPI seems to be fine, tho obviously slow. The issue is that the segfault occurs seemingly non-deterministically after 5?10 contigs are processed. If I restart after a fail, another 5?10 contigs are processed, then another.. It does not seem to be a specific contig that is causing failure. I?m pretty confident that I?ve followed the directions, and not quite sure how to troubleshoot from here, so any advice would be helpful. 
> 
> I?m using Ubuntu 14.04, Maker 3 (similar behavior with Maker 2.31.8), OpenMPI 1.10.3 (I?ve tried a few different versions), augustus?3.2, EVM 1.1.1 on a large system with lots of RAM. I set 
> 
> export LD_PRELOAD=/openmpi/lib/libmpi.so
> export OMPI_MCA_mpi_warn_on_fork=0
> and did this before installing Maker. I attempt to run maker like this, with both showing the same behavior. 
> 
> /openmpi/bin/mpirun -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> 
> or  
> 
> /openmpi/bin/mpirun -mca btl ^openib -np 30 /share/maker3/maker/bin/maker -fix_nucleotides -base peer
> lots of output
> ?
> choosing best annotation set
> Choosing best annotations
> deleted:30 hits
> doing blastn of ESTs
> formating database...
> #--------- command -------------#
> Widget::formater:
> /usr/bin/makeblastdb -dbtype nucl -in /tmp/maker_dFW8I4/28/blastprep/Pero%2EBLTK%2Efasta.mpi.10.2
> #-------------------------------#
> processing chunk output
> running  blast search.
> #--------- command -------------#
> Widget::blastn:
> /usr/bin/blastn -db /tmp/maker_dFW8I4/Pero%2EBLTK%2Efasta.mpi.10.2 -query /tmp/maker_dFW8I4/28/scaffold_46.0 -num_alignments 10000 -num_descriptions 10000 -evalue 1e-10 -word_size 28 -reward 1 -penalty -5
>  -gapopen 5 -gapextend 5 -dbsize 1000 -searchsp 500000000 -num_threads 1 -lcase_masking -dust yes -soft_masking true -show_gis -out /mouse/pero_genome/maker/peer.maker.output/peer_datastore/B4/81/scaffold
> _46//theVoid.scaffold_46/0/scaffold_46.0.Pero%2EBLTK%2Efasta.blastn.temp_dir/Pero%2EBLTK%2Efasta.mpi.10.2.blastn
> #-------------------------------#
> processing contig output
> examining contents of the fasta file and run log
> [davinci:09219] *** Process received signal ***
> [davinci:09219] Signal: Segmentation fault (11)
> [davinci:09219] Signal code: Address not mapped (1)
> [davinci:09219] Failing at address: 0x50c
> [davinci:09219] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 1] /usr/lib/libperl.so.5.18(Perl_csighandler+0x22)[0x7f3ba9d5d982]
> [davinci:09219] [ 2] /lib/x86_64-linux-gnu/libc.so.6(+0x36d40)[0x7f3ba992ed40]
> [davinci:09219] [ 3]
> 
> 
> --Next Contig--
> 
> /lib/x86_64-linux-gnu/libc.so.6(__poll+0x2d)[0x7f3ba99e512d]
> [davinci:09219] [ 4] /openmpi/lib/libopen-pal.so.13(+0x6b738)[0x7f3ba9403738]
> [davinci:09219] [ 5] /openmpi/lib/libopen-pal.so.13(opal_libevent2021_event_base_loop+0x1b2)[0x7f3ba93fa862]
> [davinci:09219] [ 6] /openmpi/lib/libopen-rte.so.12(+0x381fe)[0x7f3ba96b01fe]
> [davinci:09219] [ 7] /lib/x86_64-linux-gnu/libpthread.so.0(+0x8182)[0x7f3ba9180182]
> [davinci:09219] [ 8] /lib/x86_64-linux-gnu/libc.so.6(clone+0x6d)[0x7f3ba99f247d]
> [davinci:09219] *** End of error message ***
> SIGTERM received
> SIGTERM received
> Perl exited with active threads:
>         1 running and unjoined
>         0 finished and unjoined
>         0 running and detached
> SIGTERM received
> SIGTERM received
> SIGTERM received
> Thanks for any advice, 
> 
> Matt
> 
> 
> 
> 
> Matthew MacManes, Ph.D.
> University of New Hampshire  I  Assistant Professor of Genome Enabled Biology
> Department of Molecular, Cellular, & Biomedical Sciences
> Durham, NH  03824
> Phone: 603-862-4052 <tel://Phone:%20603-862-4052>  | Twitter: @macmanes <https://urldefense.proofpoint.com/v2/url?u=http-3A__twitter.com_macmanes&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=UqTeeQPXM6sdQU60Nu8UgU2jh30ms8LUeLT76lhbY44&e=> | Web: genomebio.org <https://urldefense.proofpoint.com/v2/url?u=http-3A__genomebio.org_&d=CwMFAg&c=c6MrceVCY5m5A_KAUkrdoA&r=FM3LJfYXZ1h-_Ot21HFFtqNXBqfGYyBrUQLf9mLeTOQ&m=RETSVWfQxdoWK0IcpUZloxNf7eGuKdm90EFhZQi67PY&s=xcTCYRLTnvXh7r_eBb-HmHZgaIA-ba7vE62iQnWHFdk&e=>
> Office: 189 Rudman Hall | Laboratory: 145 Rudman Hall
> 
> _______________________________________________
> 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 <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>

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From maker-devel at yandell-lab.org  Wed Jun 22 13:51:20 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 22 Jun 2016 20:51:20 +0100
Subject: [maker-devel] Wanted regional manageres
Message-ID: <001601d1ccc4$02290ba7$3a6d21b2$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Adrian, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

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From maker-devel at yandell-lab.org  Thu Jun 23 17:14:00 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 06:14:00 +0700
Subject: [maker-devel] Wanted regional manageres
Message-ID: <004901d1cda9$04fd272a$3f9f4e93$@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Shelia, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Fri Jun 24 02:20:23 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 12:20:23 +0400
Subject: [maker-devel] hi!
Message-ID: <732645530.201606241240@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelsey, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From sullis02 at nyu.edu  Fri Jun 24 10:53:25 2016
From: sullis02 at nyu.edu (Steven Sullivan)
Date: Fri, 24 Jun 2016 12:53:25 -0400
Subject: [maker-devel] what is a 'model file' for the web annotation service?
Message-ID: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>

Sorry if this is a dumb question.

Using the MAKER web service I have the option of adding an AUGUSTUS 'model
file' as input

I generated a  training set of genes from my species through use of online
AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
sequences,and a set of protein sequences from those cDNAs, for the species.
I received these files (folders) back from the AUGUSTUS server (in addition
to log and err files):


*Species parameter archive*:  parameters.tar.gz

*Training genes: * training.gb.gz

*Ab initio predictions*:  ab_initio.tar.gz

*predictions with hints:*  hints_pred.tar.gz



The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
train itself. The format is Genbank.

the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
folders), 1 gff and 1 gtf.

Do you know which file would be correct for input to online MAKER as a
'model' file?


(NB there is no UTR predictions file, as my input cDNAs did not have enough
UTR information in them )
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From jason.stajich at gmail.com  Fri Jun 24 19:22:37 2016
From: jason.stajich at gmail.com (Jason Stajich)
Date: Sat, 25 Jun 2016 01:22:37 +0000
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
Message-ID: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>

the parameters.tar.gz should contain this. - untar in the species folder in
you local Augustus install or set the Augustus config env variable to point
to a personal copy of the Augustus config folder and put this there.
Whatever you name this parameters folder is the species name you put in the
maker config.

On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu> wrote:

> Sorry if this is a dumb question.
>
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model
> file' as input
>
> I generated a  training set of genes from my species through use of online
> AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I
> input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA
> sequences,and a set of protein sequences from those cDNAs, for the species.
> I received these files (folders) back from the AUGUSTUS server (in addition
> to log and err files):
>
>
> *Species parameter archive*:  parameters.tar.gz
>
> *Training genes: * training.gb.gz
>
> *Ab initio predictions*:  ab_initio.tar.gz
>
> *predictions with hints:*  hints_pred.tar.gz
>
>
>
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to
> train itself. The format is Genbank.
>
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both
> folders), 1 gff and 1 gtf.
>
> Do you know which file would be correct for input to online MAKER as a
> 'model' file?
>
>
> (NB there is no UTR predictions file, as my input cDNAs did not have
> enough UTR information in them )
>
>
>
>
>
> _______________________________________________
> 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 maker-devel at yandell-lab.org  Fri Jun 24 17:13:46 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 24 Jun 2016 15:13:46 -0800
Subject: [maker-devel] We offer new vacancy
Message-ID: <576DC40E.8044.C865E3@maker-devel.yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Ericka, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Sun Jun 26 23:12:27 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 26 Jun 2016 23:12:27 -0600
Subject: [maker-devel] The beautiful work in crisis!
Message-ID: <087723970956431164706690@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Kelvin, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Mon Jun 27 09:32:15 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 27 Jun 2016 09:32:15 -0600
Subject: [maker-devel] what is a 'model file' for the web annotation
	service?
In-Reply-To: <CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
References: <CAF=9aSKUwph1400vd=4Bc6H87L8=Y79H8GTSEdACPSELWLb6nw@mail.gmail.com>
	<CALf8LpzD1wjSr7e+qaiEef411rCr-MbS_axqWFWKRbZCanuLvQ@mail.gmail.com>
Message-ID: <4BE66531-1935-4B08-BD84-EB8118EAFBE9@gmail.com>

Also it?s worth mentioning, that you will need to use the command line version of MAKER. The web version has limited capability, and does not support uploading new Augustus training files.

?Carson



> On Jun 24, 2016, at 7:22 PM, Jason Stajich <jason.stajich at gmail.com> wrote:
> 
> the parameters.tar.gz should contain this. - untar in the species folder in you local Augustus install or set the Augustus config env variable to point to a personal copy of the Augustus config folder and put this there. Whatever you name this parameters folder is the species name you put in the maker config. 
> 
> On Fri, Jun 24, 2016 at 11:53 AM Steven Sullivan <sullis02 at nyu.edu <mailto:sullis02 at nyu.edu>> wrote:
> Sorry if this is a dumb question.
> 
> Using the MAKER web service I have the option of adding an AUGUSTUS 'model file' as input
> 
> I generated a  training set of genes from my species through use of online AUGUSTUS in 'training' mode, because I am dealing with a 'new' species.  I input a set of scaffolds, a set of ESTs, a set of 'high confidence' cDNA sequences,and a set of protein sequences from those cDNAs, for the species. I received these files (folders) back from the AUGUSTUS server (in addition to log and err files):
> 
> 
> 
> Species parameter archive:  parameters.tar.gz
> 
> Training genes:  training.gb.gz
> 
> Ab initio predictions:  ab_initio.tar.gz
> 
> predictions with hints:  hints_pred.tar.gz
> 
> 
> 
> The 'training genes'  (n=178) are the gene models AUGUSTUS generated to train itself. The format is Genbank.
> 
> the two 'predictions' folders contain 1 amino acid fasta (n=15,939 in both folders), 1 gff and 1 gtf.
> 
> Do you know which file would be correct for input to online MAKER as a 'model' file?
> 
> 
> (NB there is no UTR predictions file, as my input cDNAs did not have enough UTR information in them )
> 
> 
> 
> 
> 
> _______________________________________________
> 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 <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 maker-devel at yandell-lab.org  Mon Jun 27 05:17:39 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 05:17:39 -0600
Subject: [maker-devel] Cooperation with the great company
Message-ID: <3C4249810B378AC3BDB67EF4C8753C42@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Leigh, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Tue Jun 28 01:35:52 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: Tue, 28 Jun 2016 14:35:52 +0700
Subject: [maker-devel] DOC9732563123
Message-ID: <4C1EEB87-FE30-392B-9BC3-8BE15A78C15B@yandell-lab.org>

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From maker-devel at yandell-lab.org  Tue Jun 28 03:40:25 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 28 Jun 2016 09:40:25 +0000
Subject: [maker-devel] The crisis has finished! Work with us!
Message-ID: <98168ECD71005532BC2467DBAAFF9816@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Louisa, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From maker-devel at yandell-lab.org  Mon Jun 27 21:03:30 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 27 Jun 2016 19:03:30 -0800
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <134877952880848613282257@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Jerrod, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From mmacd at udel.edu  Tue Jun 28 19:24:12 2016
From: mmacd at udel.edu (Madolyn Macdonald)
Date: Tue, 28 Jun 2016 21:24:12 -0400
Subject: [maker-devel] Segmentation Fault
Message-ID: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>

Hi Maker,
I am trying to run Maker and got the following in my stderr.log file for
one of my scaffolds.

sh: line 1: 34865 Segmentation fault      (core dumped)
/usr/local/exonerate-2.2.0/bin/exonerate -q
/tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m
protein2genome --softmasktarget --percent 20 --showcigar >
/tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
Use of each() on hash after insertion without resetting hash iterator
results in undefined behavior, Perl interpreter: 0x1846010 at
/usr/lib64/perl5/vendor_perl/forks.pm line 1736.
ERROR: Exonerate failed
--> rank=1, hostname=biomix2.dbi.local
ERROR: Failed while polishing proteins
ERROR: Chunk failed at level:10, tier_type:3
FAILED CONTIG:picr50

I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help
with this issue?
Any other thoughts?
Thanks

-- 
Madolyn Stinner (formerly Madolyn MacDonald)
UDel Bioinformatics and Systems Biology, PhD student
RIT Alumnus 13'
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From maker-devel at yandell-lab.org  Thu Jun 30 14:16:53 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 1 Jul 2016 03:16:53 +0700
Subject: [maker-devel] hi!
Message-ID: <219003668054710392676282@yandell-lab.org>

Hello!

We are looking for employees working remotely.

My name is Gale, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From carsonhh at gmail.com  Thu Jun 30 12:11:31 2016
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 30 Jun 2016 12:11:31 -0600
Subject: [maker-devel] Segmentation Fault
In-Reply-To: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
References: <CALTaXCX-wtZ7iDz71wA2uV7ManROf8SRPa4GwiLEjqp7GjrQVw@mail.gmail.com>
Message-ID: <659615D9-BDD3-4BE4-8832-C3129D3E4A37@gmail.com>

Seg faults will be the result of one of the programs used by MAKER or MPI itself.

If using OpenMPI, add '-mca btl ^openib? to your command line.
Example: mpiexec -mca btl ^openib -n 20 maker

Also you nY need to do this before running MAKER ?> export LD_PRELOAD=/location/of/openmpi/lib/libmpi.so

Both steps are explained in the ../maker/INSTALL file.

MAKER is not compatible with MVAPICH2 or Intel MPI.


For external programs that segfault. Just reinstall them or pick different versions.


Finally the error from the forks module. See the following from the devel list ?> https://groups.google.com/forum/#!topic/maker-devel/2kYQ90TCuXA
It can be fixed with a small edit to the forks.pm file from CPAN (or a change in perl version)

?Carson



> On Jun 28, 2016, at 7:24 PM, Madolyn Macdonald <mmacd at udel.edu> wrote:
> 
> Hi Maker,
> I am trying to run Maker and got the following in my stderr.log file for one of my scaffolds.
> 
> sh: line 1: 34865 Segmentation fault      (core dumped) /usr/local/exonerate-2.2.0/bin/exonerate -q /tmp/maker_kqNxYt/1/NP_001233663%2E1.for.11692140-11693047.1.fasta -t /tmp/maker_kqNxYt/1/picr50.11692140-11693047.1.fasta -Q protein -T dna -m protein2genome --softmasktarget --percent 20 --showcigar > /tmp/maker_kqNxYt/1/picr50.11692140-11693047.NP_001233663%2E1.p.exonerate
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> Use of each() on hash after insertion without resetting hash iterator results in undefined behavior, Perl interpreter: 0x1846010 at /usr/lib64/perl5/vendor_perl/forks.pm <http://forks.pm/> line 1736.
> ERROR: Exonerate failed
> --> rank=1, hostname=biomix2.dbi.local
> ERROR: Failed while polishing proteins
> ERROR: Chunk failed at level:10, tier_type:3
> FAILED CONTIG:picr50
> 
> I am running exonerate-2.2.0, anyone know if updating to 2.4.0 would help with this issue?
> Any other thoughts?
> Thanks
> 
> -- 
> Madolyn Stinner (formerly Madolyn MacDonald)
> UDel Bioinformatics and Systems Biology, PhD student
> RIT Alumnus 13'
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
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From maker-devel at yandell-lab.org  Thu Jun 30 15:19:02 2016
From: maker-devel at yandell-lab.org (maker-devel at yandell-lab.org)
Date: 30 Jun 2016 23:19:02 +0200
Subject: [maker-devel] Cooperarion with a large firm
Message-ID: <676D6E4F64644C454F4C6D46466E676D@DL0YF88>

Hello!

We are looking for employees working remotely.

My name is Nelson, am the personnel manager of a large International company.
Most of the work you can do from home, that is, at a distance.

Salary is $2500-$5000.

If you are interested in this offer, please visit 
Our Site

Best regards!
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From courtney.stairs at icm.uu.se  Wed Jun 29 03:29:48 2016
From: courtney.stairs at icm.uu.se (Courtney Stairs)
Date: Wed, 29 Jun 2016 11:29:48 +0200
Subject: [maker-devel] Alternative genetic code
Message-ID: <5773950C.8030102@icm.uu.se>

Hello there,

I noticed on the google group that someone has asked about using an 
alternative genetic code with Maker.  Has such a function been 
implemented on the newer versions of Maker?  I understand that this is 
not a straight-forward task. I am interested in using Maker on a genome 
that using code 6.

Thank you very much for your time,

Courtney

-- 
------------------------------------
Courtney Stairs, PhD
Post-doctoral fellow
Laboratory of Dr. Thijs Ettema
Institute for Cell and Molecular Biology
Uppsala University
Sweden