From weckalba at asu.edu  Tue Apr  3 18:28:28 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 3 Apr 2012 16:28:28 -0700
Subject: [maker-devel] gff3_preds2models usage question
Message-ID: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a
few issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
 I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
chado yet, and it does not appear trivial.

Thanks for the help,

Walter
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From ranjani at uga.edu  Tue Apr  3 21:24:49 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Wed, 4 Apr 2012 02:24:49 +0000
Subject: [maker-devel] mRNA-seq data
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>

Hi,



I am using to MAKER to annotate a genome and I would like a couple of clarifications.



In the previous version of MAKER, under EST_evidence in maker_opts. ctl the user could input est and est_reads- the mRNAseq reads (although this was not fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation quality.

I have assembled transcriptome data from Sanger,454 and Illumina



Do I just provide all this data in a fasta file format to the 'est' option? Is this is the best way to provide the mRNA-seq evidence?Will this assure the mRNA-seq data is used to improve the annotations?



Thanks!



Ranjani
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From carsonhh at gmail.com  Tue Apr  3 21:39:02 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 03 Apr 2012 22:39:02 -0400
Subject: [maker-devel] mRNA-seq data
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>
Message-ID: <CBA12B6C.AA4A%carsonhh@gmail.com>

Yes.  If you have them in fasta format, just provide them to the est= option
and let MAEKR align them with exonerate.  If you used something like
cufflinks or trinity, to process them you can provide them to the est_gff
option (MAKER comes with a cufflinks2gff3 converter to make that easy).

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Wed, 4 Apr 2012 02:24:49 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mRNA-seq data

Hi,

 

I am using to MAKER to annotate a genome and I would like a couple of
clarifications.

 

In the previous version of MAKER, under EST_evidence in maker_opts. ctl the
user could input est and est_reads- the mRNAseq reads (although this was not
fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation
quality.

I have assembled transcriptome data from Sanger,454 and Illumina

 

Do I just provide all this data in a fasta file format to the 'est' option?
Is this is the best way to provide the mRNA-seq evidence?Will this assure
the mRNA-seq data is used to improve the annotations?

 

Thanks!

 

Ranjani
_______________________________________________ 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 pingouinandsheep at gmail.com  Thu Apr  5 09:14:39 2012
From: pingouinandsheep at gmail.com (pingouinandsheep at gmail.com)
Date: Thu, 5 Apr 2012 07:14:39 -0700 (PDT)
Subject: [maker-devel] Huge memory usage
Message-ID: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>

Hello,

When I try to run the test provided with maker2, maker start to use a
huge amount of memory. I stoped it after it reach ~100go of memory
used. I believe the test should not use that amount of memory.

In an other message someone suggest that the bioperl version installed
could be the cause of the problem, but the bioperl installed on my
cluster is already at version 1.6.

perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006901

Unfortunately I don't have an error message to provide, that could
clarify my problem.

But maybe it is a recurrent problem and you know a few things I should
check.

Thanks,

Ismael



From carsonhh at gmail.com  Thu Apr  5 09:26:17 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 05 Apr 2012 10:26:17 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>
Message-ID: <CBA321AA.AB7A%carsonhh@gmail.com>

The test should not use up more then a few megabytes of RAM.  Even on very
large datasets you should never really use more that 1 or 2 gig of RAM
perl MAKER instance

It's possible that their may be other perl modules that are broken need to
be reinstalled on your system.  This can happen when perl gets updated,
but you are pointing to modules built for a different perl version with
the PERL5LIB environmental variable.  Make sure you you have the latest
version of MAKER and run with --debug set.  Collect that output and send
it to me (the --debug option does some dependancy checking).

I know there is an issue on Macs with updating perl's DB_File module that
causes it to gobble up big sections of the hard drive (it will eventually
fill the drive if you let it).  It's not a memory issue but just one
example of how broken modules can cause weird behavior.

Thanks,
Carson




On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
<pingouinandsheep at gmail.com> wrote:

>Hello,
>
>When I try to run the test provided with maker2, maker start to use a
>huge amount of memory. I stoped it after it reach ~100go of memory
>used. I believe the test should not use that amount of memory.
>
>In an other message someone suggest that the bioperl version installed
>could be the cause of the problem, but the bioperl installed on my
>cluster is already at version 1.6.
>
>perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>1.006901
>
>Unfortunately I don't have an error message to provide, that could
>clarify my problem.
>
>But maybe it is a recurrent problem and you know a few things I should
>check.
>
>Thanks,
>
>Ismael
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From eernst at cshl.edu  Sun Apr  8 17:09:22 2012
From: eernst at cshl.edu (Evan Ernst)
Date: Sun, 8 Apr 2012 18:09:22 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log under
	openMPI
Message-ID: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker
instances, each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no
actual processing is required apart from marking the scaffolds FINISHED.
Comparing the result to a single, non-MPI maker instance running on the
same completed hierarchy reveals that many entries aren't being written to
the log at all when running under MPI. The single process instance runs
just fine, generating a complete log that can be used for the downstream
scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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From carsonhh at gmail.com  Tue Apr 10 09:26:40 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 10 Apr 2012 10:26:40 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log
 under openMPI
In-Reply-To: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>
Message-ID: <CBA9B62E.AE4E%carsonhh@gmail.com>

Depending on if your using NFS and other architecture design you can get
race conditions with the datastore log file.  This primarily happens when
you have multiple instances of MAKER running at the same time or thousands
of short contigs running in parallel so many finish at the same time.  In a
future release, I plan on having the last MAKER job to exit just rebuild the
log at the end of a run to ensure it is complete. For now though, just run
'maker -dsindex' at the end of a run when it happens.  It will rebbuild the
log and only takes a few seconds.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Sun, 8 Apr 2012 18:09:22 -0400
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Incomplete/Missing lines in datastore index log
under openMPI

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker instances,
each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no actual
processing is required apart from marking the scaffolds FINISHED. Comparing
the result to a single, non-MPI maker instance running on the same completed
hierarchy reveals that many entries aren't being written to the log at all
when running under MPI. The single process instance runs just fine,
generating a complete log that can be used for the downstream scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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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 smg283 at gmail.com  Fri Apr 13 14:00:29 2012
From: smg283 at gmail.com (Scott Geib)
Date: Fri, 13 Apr 2012 09:00:29 -1000
Subject: [maker-devel] mpi issue on computing cluster
Message-ID: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>

Hi,
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first,

Thanks
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From sbrubaker at solazyme.com  Fri Apr 13 15:12:24 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 20:12:24 +0000
Subject: [maker-devel] Functional annotation pipeline
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>

Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane



From joseph.fass at gmail.com  Fri Apr 13 15:42:51 2012
From: joseph.fass at gmail.com (Joseph Fass)
Date: Fri, 13 Apr 2012 13:42:51 -0700
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
References: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
Message-ID: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:

> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
>
> Thanks,
> Shane
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)
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From carsonhh at gmail.com  Fri Apr 13 14:51:38 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 15:51:38 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <CADNSSgBwH1-wbqpC3_EC+92yzLoi-f5CVwMVaewV=xCK3qkPaA@mail.gmail.com>
Message-ID: <CBADFB12.B16B%carsonhh@gmail.com>

You can pre-mask the genome, convert the RepaetMasker results to GFF3 and
pass them in, or just run the ./configure script in the RepeatMasker
directory to configure wublast to be the default.

You can also let MAKER install it's own separate installation of
RepeatMasker using rmblast.  Just go to the maker/src/ directory and run
this command --> ./Build repeatmasker

MAKER will use that installation preferentially if you let it install that.

Thanks,
Carson

From:  padioleau isma?l <ismpadioleau at gmail.com>
Date:  Fri, 13 Apr 2012 17:42:20 +0200
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Huge memory usage

Dear Carson,

I have a problem with RepeatMasker on my cluster. It work with wublast but
not with Crossmatch. As maker try to run RepeatMasker with default I can not
successfully run maker.

I wanted to know if I can provide to maker the genome already masked (if I
run with wublast externally), I though it was possible but I can't found in
the configuration files where I should provide it i.e : In maker_opts.ctl,
should I provide the result from RepeatMasker to 'genome_gff:' and set
'rm_pass' to 1, or set rm_gff in the 'Repeat Masking' part of the file?
Or maybe I should provide directly the masked fasta as genome reference.

An other solution could be to ask maker to run RepeatMasker with the option
'-e wublast'.

Is it possible to use one of these solutions?

Thanks,

Ismael

2012/4/5 padioleau isma?l <ismpadioleau at gmail.com>
> Dear Carson,
> 
> Thank you for your very quick answering.
> 
> I realised that I missed some error messages and the problem seems to be
> linked to the DB_file package as you suggested. The person in charge of
> installation told me that he will recover the configuration.
> 
> I will test it after the Easter weekend and come back to you if we have other
> issues.
> 
> Have a nice Easter weekend,
> 
> Ismael
> 
> Here Is the error message:
> Use of uninitialized value $DB_File::db_version in numeric ge (>=) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 276.
> Use of uninitialized value $DB_File::db_version in numeric gt (>) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 280.
> Deep recursion on subroutine "DB_File::AUTOLOAD" at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 235.
> 
> 
> 
> 2012/4/5 Carson Holt <carsonhh at gmail.com>
>> The test should not use up more then a few megabytes of RAM.  Even on very
>> large datasets you should never really use more that 1 or 2 gig of RAM
>> perl MAKER instance
>> 
>> It's possible that their may be other perl modules that are broken need to
>> be reinstalled on your system.  This can happen when perl gets updated,
>> but you are pointing to modules built for a different perl version with
>> the PERL5LIB environmental variable.  Make sure you you have the latest
>> version of MAKER and run with --debug set.  Collect that output and send
>> it to me (the --debug option does some dependancy checking).
>> 
>> I know there is an issue on Macs with updating perl's DB_File module that
>> causes it to gobble up big sections of the hard drive (it will eventually
>> fill the drive if you let it).  It's not a memory issue but just one
>> example of how broken modules can cause weird behavior.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> 
>> On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
>> <pingouinandsheep at gmail.com> wrote:
>> 
>>> >Hello,
>>> >
>>> >When I try to run the test provided with maker2, maker start to use a
>>> >huge amount of memory. I stoped it after it reach ~100go of memory
>>> >used. I believe the test should not use that amount of memory.
>>> >
>>> >In an other message someone suggest that the bioperl version installed
>>> >could be the cause of the problem, but the bioperl installed on my
>>> >cluster is already at version 1.6.
>>> >
>>> >perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>>> >1.006901
>>> >
>>> >Unfortunately I don't have an error message to provide, that could
>>> >clarify my problem.
>>> >
>>> >But maybe it is a recurrent problem and you know a few things I should
>>> >check.
>>> >
>>> >Thanks,
>>> >
>>> >Ismael
>>> >
>>> >_______________________________________________
>>> >maker-devel mailing list
>>> >maker-devel at box290.bluehost.com
>>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> 
> -- 
> Isma?l Padioleau
> Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
> Emmanouil Dermitzakis Group
> Dpt de M?decine G?n?tique et D?veloppement
> Universit? de Gen?ve - Facult? de M?decine
> CMU -  Rue Michel-Servet 1
> CH 1211 Gen?ve 4
> Tel: 0041 22 379 59 74
> ismael.padioleau at unige.ch
> 
> --
> Tel. 0041 78 77 69 561
> ismpadioleau at gmail.com



-- 
Isma?l Padioleau
Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
Emmanouil Dermitzakis Group
Dpt de M?decine G?n?tique et D?veloppement
Universit? de Gen?ve - Facult? de M?decine
CMU -  Rue Michel-Servet 1
CH 1211 Gen?ve 4
Tel: 0041 22 379 59 74
ismael.padioleau at unige.ch

--
Tel. 0041 78 77 69 561
ismpadioleau at gmail.com


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From carsonhh at gmail.com  Fri Apr 13 16:02:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 17:02:51 -0400
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
Message-ID: <CBAE0B9F.B1D2%carsonhh@gmail.com>

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
integrate interproscan results in the GFF3 files.  There are also a couple
of scripts maker_functional_gff and maker_functional_fasta that can do
putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From:  Joseph Fass <joseph.fass at gmail.com>
Date:  Fri, 13 Apr 2012 13:42:51 -0700
To:  Shane Brubaker <sbrubaker at solazyme.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>
wrote:
> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
> 
> Thanks,
> Shane
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com <http://gmail.com>  (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ 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 sbrubaker at solazyme.com  Fri Apr 13 16:18:10 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 21:18:10 +0000
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065BBA@EXCHANGE-05.internal.solazyme.com>

Great thank you ... I will take a look at those.

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Friday, April 13, 2012 2:03 PM
To: Joseph Fass; Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Functional annotation pipeline

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files.  There are also a couple of scripts maker_functional_gff and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From: Joseph Fass <joseph.fass at gmail.com<mailto:joseph.fass at gmail.com>>
Date: Fri, 13 Apr 2012 13:42:51 -0700
To: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>> wrote:
Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane

_______________________________________________
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



--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com<http://gmail.com> (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From dsth at ebi.ac.uk  Fri Apr 13 16:22:37 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:22:37 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>

Careful of interproscan atm.. I believe the executable is still in beta and
they definitely aren't recommending it for production use yet. If you do
use it be sure to check output file if using the lookup service as when i
used it recently it would sometimes exit normally despite lookup failures
(the lookup problems may have had something to do with running ~800 in
parallel - they're looking into the issue atm.).

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Carson Holt <carsonhh at gmail.com>

> I would agree blast2go.
>
> You can also try interproscan fro the EBI
>
> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
> integrate interproscan results in the GFF3 files.  There are also a couple
> of scripts maker_functional_gff and maker_functional_fasta that can do
> putative functional annotation using uniprot/swiss-prot.
>
> Thanks,
> Carson
>
>
>
> From: Joseph Fass <joseph.fass at gmail.com>
> Date: Fri, 13 Apr 2012 13:42:51 -0700
> To: Shane Brubaker <sbrubaker at solazyme.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Functional annotation pipeline
>
> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
> HTH,
> ~Joe
>
> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>
>> Hi, can you recommend any open source functional annotation pipelines -
>> to assign function, GO terms, pathways, etc. to gene models?
>>
>> Thanks,
>> Shane
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
> --
> Joseph Fass
> Lead Data Analyst
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From dsth at ebi.ac.uk  Fri Apr 13 16:37:06 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:37:06 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
	<CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
Message-ID: <CAP8X9uKOcovWFAetQTaGgQ6Mpb-rg_8PB5RCkfrhsev6Mx03bQ@mail.gmail.com>

sorry, that's the new version of course.

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Daniel Hughes <dsth at ebi.ac.uk>

> Careful of interproscan atm.. I believe the executable is still in beta
> and they definitely aren't recommending it for production use yet. If you
> do use it be sure to check output file if using the lookup service as when
> i used it recently it would sometimes exit normally despite lookup failures
> (the lookup problems may have had something to do with running ~800 in
> parallel - they're looking into the issue atm.).
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
>
> 2012/4/13 Carson Holt <carsonhh at gmail.com>
>
>> I would agree blast2go.
>>
>> You can also try interproscan fro the EBI
>>
>> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
>> integrate interproscan results in the GFF3 files.  There are also a couple
>> of scripts maker_functional_gff and maker_functional_fasta that can do
>> putative functional annotation using uniprot/swiss-prot.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: Joseph Fass <joseph.fass at gmail.com>
>> Date: Fri, 13 Apr 2012 13:42:51 -0700
>> To: Shane Brubaker <sbrubaker at solazyme.com>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] Functional annotation pipeline
>>
>> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
>> HTH,
>> ~Joe
>>
>> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>>
>>> Hi, can you recommend any open source functional annotation pipelines -
>>> to assign function, GO terms, pathways, etc. to gene models?
>>>
>>> Thanks,
>>> Shane
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>>
>>
>> --
>> Joseph Fass
>> Lead Data Analyst
>> UC Davis Bioinformatics Core
>> joseph.fass -at- gmail.com (professional)
>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
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From kd7gwt at exchange.usfood.com  Sat Apr 14 01:50:28 2012
From: kd7gwt at exchange.usfood.com (Liz Douglas)
Date: Sat, 14 Apr 2012 14:50:28 +0800
Subject: [maker-devel] Incredible effect on your possibilities in bed
Message-ID: <002801cd1a0b$727fe840$5047c36a@SAMrc6umq>

http://sten-stil.dk/require.html Do you wish to satisfy your babe tonight?




From ranjani at uga.edu  Tue Apr 17 11:46:40 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Tue, 17 Apr 2012 16:46:40 +0000
Subject: [maker-devel] MAKER2.23 output
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>

Hi,

I tried running the latest version of Maker 2.23 with my dataset but with out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2 /usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further details

I was able run the previous version of Maker 2.10 successfully with my dataset.

Thanks,
Ranjani


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From carsonhh at gmail.com  Tue Apr 17 11:56:11 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 12:56:11 -0400
Subject: [maker-devel] MAKER2.23 output
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>
Message-ID: <CBB31716.B317%carsonhh@gmail.com>

Segmentation fault means there was a failure with C code.  It was likely in
one of the modules being used.

These are all potential culprits

Inline::C
Proc::ProcessTable
DB_file
forks

Based on when the error occurred.  I would lean more toward DB_File.  Is it
possible that BerkleyDB has been updated on your system, perhaps as part of
another installation or a system update?  That sometimes breaks this module
(which is part of the perl core).

You can try reinstalling that module from CPAN.  Also if you run MAKER
version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug')
to get more information just before the error occurs.  You can then capture
the error log send that to me.

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tue, 17 Apr 2012 16:46:40 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER2.23 output

Hi, 

I tried running the latest version of Maker 2.23 with my dataset but with
out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output
files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2
/usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further
details

I was able run the previous version of Maker 2.10 successfully with my
dataset.

Thanks,
Ranjani


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

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From carsonhh at gmail.com  Tue Apr 17 12:09:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 13:09:32 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>
Message-ID: <CBB31953.B329%carsonhh@gmail.com>

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    }

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

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

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From carsonhh at gmail.com  Tue Apr 17 15:25:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 16:25:51 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CBB31953.B329%carsonhh@gmail.com>
Message-ID: <CBB349BE.B364%carsonhh@gmail.com>

Sorry missed the ';' at the end of the eval block.

Should be this -->

    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


--Carson

From:  Carson Holt <carsonhh at gmail.com>
Date:  Tue, 17 Apr 2012 13:09:32 -0400
To:  Scott Geib <smg283 at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] mpi issue on computing cluster

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

Thanks
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From elzedliu at gmail.com  Tue Apr 17 18:22:53 2012
From: elzedliu at gmail.com (Huanle)
Date: Tue, 17 Apr 2012 16:22:53 -0700 (PDT)
Subject: [maker-devel] gene predictors in MARKER
Message-ID: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>

I am using MAKER to annotate a recently assembled plant genome.
Hi There,

I am using MAKER to annotate a recently assembled plant genome.

I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial

The denovo gene predictors i included in the maker_exe.ctl file are
#-----Ab-initio Gene Prediction Algorithms
snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
augustus executable

However, I am not sure whether they were really used.

During the running, i could see repeatmasker, exonerate and wublast
were called. But i did see any information popped up for those gene
predictors.

So i am wondering if they were actually used.

Could you please let me know how to know if all or one of those gene
predictors were called by marker?

Kind Regards,
Huanle



From carsonhh at gmail.com  Mon Apr 23 16:04:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 23 Apr 2012 17:04:16 -0400
Subject: [maker-devel] gene predictors in MARKER
In-Reply-To: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>
Message-ID: <CBBB3AB1.BC17%carsonhh@gmail.com>

The gene predictors have to be trained first, and when they are trained
they produce an HMM file that can be supplied to MAKER.  You can either
use MAKER's protein2genome option or est2genome option to produce rough
models to train with, or you can try one of the models that come
prepackaged with those algorithms.

SNAP models will be in --> /sw/maker/2.10/bin/../exe/snap/HMM
Augustus --> run this to see species in augustus -->
/sw/maker/2.10/bin/../exe/augustus/bin/augustus --species=help
GeneMark is self training.  Run it one directly on your genome fasta or
for speed just a chromosome or two of the assembly and it will produce a
file called es.mod as part of it's results.  That is the file you need.

If you have any questions or issues with training just let us know.

Thanks,
Carson



On 12-04-17 7:22 PM, "Huanle" <elzedliu at gmail.com> wrote:

>I am using MAKER to annotate a recently assembled plant genome.
>Hi There,
>
>I am using MAKER to annotate a recently assembled plant genome.
>
>I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial
>
>The denovo gene predictors i included in the maker_exe.ctl file are
>#-----Ab-initio Gene Prediction Algorithms
>snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
>gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
>genemark executable
>gmhmmp= #location of prokaryotic genemark executable
>augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
>augustus executable
>
>However, I am not sure whether they were really used.
>
>During the running, i could see repeatmasker, exonerate and wublast
>were called. But i did see any information popped up for those gene
>predictors.
>
>So i am wondering if they were actually used.
>
>Could you please let me know how to know if all or one of those gene
>predictors were called by marker?
>
>Kind Regards,
>Huanle
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From anastasia.gioti at scilifelab.se  Wed Apr 25 04:09:36 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:09:36 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
Message-ID: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 04:22:03 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:22:03 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>

For cross-species comparisons you might have be better off including the
actual peptide sequences of the other fungi too in the annotation run - I'd
be very surprised if you really did get the same result.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> I  have a set of predicted proteins from the genome of a fungus annotated
> by MAKER  using EST data from a closely related species and 3 ab initio
> predictors  (snap iterativelly trained 3 times, genemark trained directly
> on the assembly and augustus with a model from a less closely related
> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
> when I compare to the species i used EST data from, and there is good
> evidence from alignments that these genes exist. The question is how to
> proceed from Blast hits to actual gene models here. The idea would be to
> add these genes to the existing dataset, rather than reannotate the genome.
> I believe that reannotating it without any further evidence such as RNA-seq
> from the species itself would not change much,and i d rather stick with
> actual predictions that i trust and have used in subsequent analyses. The
> 1000 genes I can accept to annotate with a less stringent and reliable way
> than MAKER, I just want to add them so that the difference in gene count
> gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the
> legacy annotations scheme to do it, by providing GFF3 of the alignments
> between the two species in the regions where genes were missed, but as i
> said, I would not like to reannotate the whole genome, and running MAKER2
> might cause slight changes that i d like to avoid. Is this possible? First,
> is it possible to provide a Gff3 file of specific locations and not the
> entire genome alignment? (I guess so..) Second, how can I tag the existing
> annotations as 'not to be changed' or alternatively, tag the new models
> only? How should I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
> _______________________________________________
> 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 anastasia.gioti at scilifelab.se  Wed Apr 25 04:29:30 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:29:30 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
Message-ID: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>

Hi, 
Do you mean that I should have not include the proteins of the closely related species in my fungal protein fasta file that I used as evidence in MAKER? i do not see why... What I have been trying to do now is further 'bias' the annotations in favor of this species, so as to get the missing genes. Can you explain a bit more whta you mean?
Thanks, 
Anastasia
On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:

> For cross-species comparisons you might have be better off including the actual peptide sequences of the other fungi too in the annotation run - I'd be very surprised if you really did get the same result.
> 
> dan.
> 
> 
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
> 
> 
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Hi, 
> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
> Thanks, 
> Anastasia
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 04:39:49 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:39:49 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
	<A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
Message-ID: <CAP8X9u+BvAG8xRqd_DHwdoiFAbWu0nZ0Get-UNkbGrU_qOEHXA@mail.gmail.com>

sorry my bad, i missed the part about you having already included the
fungal proteins as fasta ;/ - too early for me.

in that case have you viewed the full gff output for specific instances of
such missing proteins in something like apollo to try and work out why
maker hasn't made a call at those loci (aed score...)?

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> Do you mean that I should have not include the proteins of the closely
> related species in my fungal protein fasta file that I used as evidence in
> MAKER? i do not see why... What I have been trying to do now is further
> 'bias' the annotations in favor of this species, so as to get the missing
> genes. Can you explain a bit more whta you mean?
> Thanks,
> Anastasia
>
> On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:
>
> For cross-species comparisons you might have be better off including the
> actual peptide sequences of the other fungi too in the annotation run - I'd
> be very surprised if you really did get the same result.
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
>
>> Hi,
>> I  have a set of predicted proteins from the genome of a fungus annotated
>> by MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly
>> on the assembly and augustus with a model from a less closely related
>> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
>> when I compare to the species i used EST data from, and there is good
>> evidence from alignments that these genes exist. The question is how to
>> proceed from Blast hits to actual gene models here. The idea would be to
>> add these genes to the existing dataset, rather than reannotate the genome.
>> I believe that reannotating it without any further evidence such as RNA-seq
>> from the species itself would not change much,and i d rather stick with
>> actual predictions that i trust and have used in subsequent analyses. The
>> 1000 genes I can accept to annotate with a less stringent and reliable way
>> than MAKER, I just want to add them so that the difference in gene count
>> gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the
>> legacy annotations scheme to do it, by providing GFF3 of the alignments
>> between the two species in the regions where genes were missed, but as i
>> said, I would not like to reannotate the whole genome, and running MAKER2
>> might cause slight changes that i d like to avoid. Is this possible? First,
>> is it possible to provide a Gff3 file of specific locations and not the
>> entire genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models
>> only? How should I run maker2, with which predictors on and which off?
>> Thanks,
>> Anastasia
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
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From carsonhh at gmail.com  Wed Apr 25 09:29:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Apr 2012 10:29:01 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CBBD7372.BD57%carsonhh@gmail.com>

The way you proceed depends on why the genes are not there to begin with.
Are they not there because of a lack of evidence?  If that's the case just
adding the new fasta file should do the trick.  Or are they not there
because an assembly error makes it impossible to get a logical model for the
region (I.e reading frame breaks).  Are there ab initio models already
called in those regions that could just be promoted to the annotation tier?
You can test that one by blasting against the nonoverlaping_abinits.fasta
files.

For any of the cases described, you can provide the existing annotation set
as the input in GFF3 format, and previous models will be maintained
preferentially.  If you know which ab initio predictions you want to add
(I.e. the ab initio promoting scenario I descibed), you can provide those
predictions to the use the pred_gff option and then set keep_preds=1 and
they will be maintained even without evidence.  Attached is a script that
would make selecting those easier.  It take the MAKER generated GFF3 and a
list of predictions to keep (one name per line).  These might be the results
of a BLAST analysis for example.  It will then return the GFF3 entries for
just those models selected.

If the situation is more complex, just provide more detail, and I am sure we
can help you come up with a plan.

Thanks,
Carson

From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Date:  Wed, 25 Apr 2012 11:09:36 +0200
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Use pass-through system to add missing genes

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by
MAKER  using EST data from a closely related species and 3 ab initio
predictors  (snap iterativelly trained 3 times, genemark trained directly on
the assembly and augustus with a model from a less closely related species),
along with a set of fungal proteins. I am missing ~ 1000 proteins when I
compare to the species i used EST data from, and there is good evidence from
alignments that these genes exist. The question is how to proceed from Blast
hits to actual gene models here. The idea would be to add these genes to the
existing dataset, rather than reannotate the genome. I believe that
reannotating it without any further evidence such as RNA-seq from the
species itself would not change much,and i d rather stick with actual
predictions that i trust and have used in subsequent analyses. The 1000
genes I can accept to annotate with a less stringent and reliable way than
MAKER, I just want to add them so that the difference in gene count gets
corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy
annotations scheme to do it, by providing GFF3 of the alignments between the
two species in the regions where genes were missed, but as i said, I would
not like to reannotate the whole genome, and running MAKER2 might cause
slight changes that i d like to avoid. Is this possible? First, is it
possible to provide a Gff3 file of specific locations and not the entire
genome alignment? (I guess so..) Second, how can I tag the existing
annotations as 'not to be changed' or alternatively, tag the new models
only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



_______________________________________________ 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 anastasia.gioti at scilifelab.se  Fri Apr 27 03:43:14 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Fri, 27 Apr 2012 10:43:14 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CBBD7372.BD57%carsonhh@gmail.com>
References: <CBBD7372.BD57%carsonhh@gmail.com>
Message-ID: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>

Hi Carlson,
Thanks for your help!

> The way you proceed depends on why the genes are not there to begin  
> with.  Are they not there because of a lack of evidence?

It is a mixture of cases, and I can only look at some examples to say  
that. There are cases where all 3 used ab initio predictors provide  
models, there are blastx hits, or both blastx and protein2 genome, but  
no EST evidence, thus  no model is retained. i guess my default  
parameters could be responsible for these cases at least.

> If that's the case just adding the new fasta file should do the trick.

which fasta do you refer to? The proteins file I use as evidence  
contains all proteins i can actually use.

> Or are they not there because an assembly error makes it impossible  
> to get a logical model for the region (I.e reading frame breaks).

This is not the case in general.

> Are there ab initio models already called in those regions that  
> could just be promoted to the annotation tier?  You can test that  
> one by blasting against the nonoverlaping_abinits.fasta files.

I have not done this, will do!

>
> For any of the cases described, you can provide the existing  
> annotation set as the input in GFF3 format, and previous models will  
> be maintained preferentially.

You mean in a new maker run? is this possible with the old maker as  
well, not maker2, right?

> If you know which ab initio predictions you want to add (I.e. the ab  
> initio promoting scenario I descibed), you can provide those  
> predictions to the use the pred_gff option and then set keep_preds=1  
> and they will be maintained even without evidence.  Attached is a  
> script that would make selecting those easier.  It take the MAKER  
> generated GFF3 and a list of predictions to keep (one name per  
> line).  These might be the results of a BLAST analysis for example.   
> It will then return the GFF3 entries for just those models selected.

The thing is, for the few cases I have looked at, I cannot really  
decide which model is the best, and the 3 models from the ab initio  
predictors do not agree on the exact intron-exon junctions or the  
start and stop codons.
>
> If the situation is more complex, just provide more detail, and I am  
> sure we can help you come up with a plan.
>
What i was thinking to do was to provide a gff file of alignments (eg  
by exonerate) to the proteins of the closely related species that i  
am  missing, and somehow keep the previous annotations and get the  
extra ones by this gff file. But how exactly maker should be run to do  
this I am not sure. if I want to keep the previous annotations I  need  
the gff file of the last maker run as input, but then how do I  
discriminate with the exonerate gff file? And which mode of rediction  
should be on, and with which parameters? You mention keep_preds=1  for  
the existing annotations, but how do i also promote evidence from  
alignments on the same way in the same run?
Looks feasible though. Thanks again,
Anastasia

> Thanks,
> Carson
>
> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Date: Wed, 25 Apr 2012 11:09:36 +0200
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Use pass-through system to add missing genes
>
> Hi,
> I  have a set of predicted proteins from the genome of a fungus  
> annotated by MAKER  using EST data from a closely related species  
> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
> genemark trained directly on the assembly and augustus with a model  
> from a less closely related species), along with a set of fungal  
> proteins. I am missing ~ 1000 proteins when I compare to the species  
> i used EST data from, and there is good evidence from alignments  
> that these genes exist. The question is how to proceed from Blast  
> hits to actual gene models here. The idea would be to add these  
> genes to the existing dataset, rather than reannotate the genome. I  
> believe that reannotating it without any further evidence such as  
> RNA-seq from the species itself would not change much,and i d rather  
> stick with actual predictions that i trust and have used in  
> subsequent analyses. The 1000 genes I can accept to annotate with a  
> less stringent and reliable way than MAKER, I just want to add them  
> so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the  
> legacy annotations scheme to do it, by providing GFF3 of the  
> alignments between the two species in the regions where genes were  
> missed, but as i said, I would not like to reannotate the whole  
> genome, and running MAKER2 might cause slight changes that i d like  
> to avoid. Is this possible? First, is it possible to provide a Gff3  
> file of specific locations and not the entire genome alignment? (I  
> guess so..) Second, how can I tag the existing annotations as 'not  
> to be changed' or alternatively, tag the new models only? How should  
> I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
> _______________________________________________ maker-devel mailing  
> list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> <gff3_select>

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From barry.moore at genetics.utah.edu  Fri Apr 27 06:57:01 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 27 Apr 2012 05:57:01 -0600
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
Message-ID: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.  Are they not there because of a lack of evidence?  
> 
> It is a mixture of cases, and I can only look at some examples to say that. There are cases where all 3 used ab initio predictors provide models, there are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus  no model is retained. i guess my default parameters could be responsible for these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein evidence overlapping them you should get a model retained.  I know for the EST evidence that it has to support a splice site before it will be promoted and I can't remember if protein evidence is the same but certainly if you pass back those protein2genome predictions and the original proteins as evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.  
> 
> which fasta do you refer to? The proteins file I use as evidence contains all proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a logical model for the region (I.e reading frame breaks).  
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be promoted to the annotation tier?  You can test that one by blasting against the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set as the input in GFF3 format, and previous models will be maintained preferentially.  
> 
> You mean in a new maker run? is this possible with the old maker as well, not maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which model is the best, and the 3 models from the ab initio predictors do not agree on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by exonerate) to the proteins of the closely related species that i am  missing, and somehow keep the previous annotations and get the extra ones by this gff file. But how exactly maker should be run to do this I am not sure. if I want to keep the previous annotations I  need the gff file of the last maker run as input, but then how do I discriminate with the exonerate gff file? And which mode of rediction should be on, and with which parameters? You mention keep_preds=1  for the existing annotations, but how do i also promote evidence from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct about what you've already done.  You have run Maker with SNAP, Genemark and Augustus using EST from a closely related species (passed to altest) and protein evidence from other fungi.  You are missing about 1,000 genes compared to the species that provided the EST alignments.  You say their is good evidence that these genes exist from the alignments and I assume by this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's proteins in the evidence set that you provided to Maker.  If you haven't provided these proteins as evidence to maker then you should do this.  You can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta and blast them directly against your closely related proteins.  Presumably they don't hit too well because if they did they should have been promoted to predictions by Maker the first time, but here you can decide yourself what thresholds to allow to keep the abinit predictions that hit the closely related species proteins.  If you filter you blast hits the way you want and keep the names of the abinit predictions that pass your filter, then use the script Carson attached it it will generate a abinit precidtion GFF file with only the predictions you selected.  You can then pass those predictions back to Maker and force it to keep them and Maker will turn them from predictions (match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Fri Apr 27 08:27:24 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 09:27:24 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <CBC01559.BF45%carsonhh@gmail.com>

> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.

The only way you should be able to get BLASTX overlap and still not get a
model for the region is if 1.  The protein alignment in in a different
reading frame then your models for every single base pair of the alignment
(in which case it's not true overlap).  2. The BLASTX HSPs are stacked on
each other again and again in weird rearranged overlaps to produce a very
deep alignment which would mean this is a repetitive region and is not
really a significant alignment.  Otherwise this should not happen unless you
have the AED_threshold set to some value where MAKER will ignore genes
unless they have a minimum amount of support (by default this option is
always off).  The other two possibilities can be tested by just looking at
the alignments manually in Apollo.  Also take a look at the AED and eAED
values for your missing genes.  Anything below 1 should always be kept by
MAKER by default because it has at least some evidence supported.

> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.

If they are already in your current run ignore this.

Barry provided detailed instructions on how to configure MAKER, for your
particular case.  So just follow his excellent instructions.

Thanks,
Carson



From:  Barry Moore <barry.moore at genetics.utah.edu>
Date:  Friday, 27 April, 2012 7:57 AM
To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Use pass-through system to add missing genes

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.
>> Are they not there because of a lack of evidence?
> 
> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein
evidence overlapping them you should get a model retained.  I know for the
EST evidence that it has to support a splice site before it will be promoted
and I can't remember if protein evidence is the same but certainly if you
pass back those protein2genome predictions and the original proteins as
evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.
> 
> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I
think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a
>> logical model for the region (I.e reading frame breaks).
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be
>> promoted to the annotation tier?  You can test that one by blasting against
>> the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set
>> as the input in GFF3 format, and previous models will be maintained
>> preferentially. 
> 
> You mean in a new maker run? is this possible with the old maker as well, not
> maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio
>> promoting scenario I descibed), you can provide those predictions to the use
>> the pred_gff option and then set keep_preds=1 and they will be maintained
>> even without evidence.  Attached is a script that would make selecting those
>> easier.  It take the MAKER generated GFF3 and a list of predictions to keep
>> (one name per line).  These might be the results of a BLAST analysis for
>> example.  It will then return the GFF3 entries for just those models
>> selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which
> model is the best, and the 3 models from the ab initio predictors do not agree
> on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we
>> can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by
> exonerate) to the proteins of the closely related species that i am  missing,
> and somehow keep the previous annotations and get the extra ones by this gff
> file. But how exactly maker should be run to do this I am not sure. if I want
> to keep the previous annotations I  need the gff file of the last maker run as
> input, but then how do I discriminate with the exonerate gff file? And which
> mode of rediction should be on, and with which parameters? You mention
> keep_preds=1  for the existing annotations, but how do i also promote evidence
> from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct
about what you've already done.  You have run Maker with SNAP, Genemark and
Augustus using EST from a closely related species (passed to altest) and
protein evidence from other fungi.  You are missing about 1,000 genes
compared to the species that provided the EST alignments.  You say their is
good evidence that these genes exist from the alignments and I assume by
this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's
proteins in the evidence set that you provided to Maker.  If you haven't
provided these proteins as evidence to maker then you should do this.  You
can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but
still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta
and blast them directly against your closely related proteins.  Presumably
they don't hit too well because if they did they should have been promoted
to predictions by Maker the first time, but here you can decide yourself
what thresholds to allow to keep the abinit predictions that hit the closely
related species proteins.  If you filter you blast hits the way you want and
keep the names of the abinit predictions that pass your filter, then use the
script Carson attached it it will generate a abinit precidtion GFF file with
only the predictions you selected.  You can then pass those predictions back
to Maker and force it to keep them and Maker will turn them from predictions
(match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> To:  <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by
>> MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly on
>> the assembly and augustus with a model from a less closely related species),
>> along with a set of fungal proteins. I am missing ~ 1000 proteins when I
>> compare to the species i used EST data from, and there is good evidence from
>> alignments that these genes exist. The question is how to proceed from Blast
>> hits to actual gene models here. The idea would be to add these genes to the
>> existing dataset, rather than reannotate the genome. I believe that
>> reannotating it without any further evidence such as RNA-seq from the species
>> itself would not change much,and i d rather stick with actual predictions
>> that i trust and have used in subsequent analyses. The 1000 genes I can
>> accept to annotate with a less stringent and reliable way than MAKER, I just
>> want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy
>> annotations scheme to do it, by providing GFF3 of the alignments between the
>> two species in the regions where genes were missed, but as i said, I would
>> not like to reannotate the whole genome, and running MAKER2 might cause
>> slight changes that i d like to avoid. Is this possible? First, is it
>> possible to provide a Gff3 file of specific locations and not the entire
>> genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models only?
>> How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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






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From james.collett at pnnl.gov  Fri Apr 27 11:51:05 2012
From: james.collett at pnnl.gov (Collett, James R)
Date: Fri, 27 Apr 2012 09:51:05 -0700
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
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Hi Carson,

Could you please send me (or make available for download) the perl script that you mentioned in this previous post in this thread?

>> Attached is a 
>> script that would make selecting those easier.  It take the MAKER 
>> generated GFF3 and a list of predictions to keep (one name per line).  
>> These might be the results of a BLAST analysis for example.  It will 
>> then return the GFF3 entries for just those models selected.

Thanks,

Jim
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory

> -----Original Message-----
> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
> lab.org
> Sent: Friday, April 27, 2012 6:48 AM
> To: maker-devel at yandell-lab.org
> Subject: maker-devel Digest, Vol 47, Issue 14
> 
> Send maker-devel mailing list submissions to
> 	maker-devel at yandell-lab.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.org
> 
> or, via email, send a message with subject or body 'help' to
> 	maker-devel-request at yandell-lab.org
> 
> You can reach the person managing the list at
> 	maker-devel-owner at yandell-lab.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of maker-devel digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Use pass-through system to add missing genes (Carson Holt)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 27 Apr 2012 09:27:24 -0400
> From: Carson Holt <carsonhh at gmail.com>
> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
> 	<anastasia.gioti at scilifelab.se>
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] Use pass-through system to add missing
> 	genes
> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> 
> The only way you should be able to get BLASTX overlap and still not get
> a model for the region is if 1.  The protein alignment in in a
> different reading frame then your models for every single base pair of
> the alignment (in which case it's not true overlap).  2. The BLASTX
> HSPs are stacked on each other again and again in weird rearranged
> overlaps to produce a very deep alignment which would mean this is a
> repetitive region and is not really a significant alignment.  Otherwise
> this should not happen unless you have the AED_threshold set to some
> value where MAKER will ignore genes unless they have a minimum amount
> of support (by default this option is always off).  The other two
> possibilities can be tested by just looking at the alignments manually
> in Apollo.  Also take a look at the AED and eAED values for your
> missing genes.  Anything below 1 should always be kept by MAKER by
> default because it has at least some evidence supported.
> 
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> 
> If they are already in your current run ignore this.
> 
> Barry provided detailed instructions on how to configure MAKER, for
> your particular case.  So just follow his excellent instructions.
> 
> Thanks,
> Carson
> 
> 
> 
> From:  Barry Moore <barry.moore at genetics.utah.edu>
> Date:  Friday, 27 April, 2012 7:57 AM
> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Use pass-through system to add missing
> genes
> 
> Hi Anastasia,
> 
> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
> 
> > Hi Carlson,
> > Thanks for your help!
> >
> >> The way you proceed depends on why the genes are not there to begin
> with.
> >> Are they not there because of a lack of evidence?
> >
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> >
> 
> This doesn't sound right.  If there are predicted models and blastx
> protein evidence overlapping them you should get a model retained.  I
> know for the EST evidence that it has to support a splice site before
> it will be promoted and I can't remember if protein evidence is the
> same but certainly if you pass back those protein2genome predictions
> and the original proteins as evidence then they will be retained as
> models.
> 
> >> If that's the case just adding the new fasta file should do the
> trick.
> >
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> >
> 
> Yes using the protein fasta from the closely related species as
> evidence.  I think you said you've already done that right?
> 
> 
> >> Or are they not there because an assembly error makes it impossible
> >> to get a logical model for the region (I.e reading frame breaks).
> >
> > This is not the case in general.
> >
> >> Are there ab initio models already called in those regions that
> could
> >> just be promoted to the annotation tier?  You can test that one by
> >> blasting against the nonoverlaping_abinits.fasta files.
> >
> > I have not done this, will do!
> >
> >>
> >> For any of the cases described, you can provide the existing
> >> annotation set as the input in GFF3 format, and previous models will
> >> be maintained preferentially.
> >
> > You mean in a new maker run? is this possible with the old maker as
> > well, not maker2, right?
> >
> 
> Yes, the original MAKER will do this.
> 
> 
> >> If you know which ab initio predictions you want to add (I.e. the ab
> >> initio promoting scenario I descibed), you can provide those
> >> predictions to the use the pred_gff option and then set keep_preds=1
> >> and they will be maintained even without evidence.  Attached is a
> >> script that would make selecting those easier.  It take the MAKER
> >> generated GFF3 and a list of predictions to keep (one name per
> line).
> >> These might be the results of a BLAST analysis for example.  It will
> >> then return the GFF3 entries for just those models selected.
> >
> > The thing is, for the few cases I have looked at, I cannot really
> > decide which model is the best, and the 3 models from the ab initio
> > predictors do not agree on the exact intron-exon junctions or the
> start and stop codons.
> >>
> >> If the situation is more complex, just provide more detail, and I am
> >> sure we can help you come up with a plan.
> >>
> > What i was thinking to do was to provide a gff file of alignments (eg
> > by
> > exonerate) to the proteins of the closely related species that i am
> > missing, and somehow keep the previous annotations and get the extra
> > ones by this gff file. But how exactly maker should be run to do this
> > I am not sure. if I want to keep the previous annotations I  need the
> > gff file of the last maker run as input, but then how do I
> > discriminate with the exonerate gff file? And which mode of rediction
> > should be on, and with which parameters? You mention
> > keep_preds=1  for the existing annotations, but how do i also promote
> > evidence from alignments on the same way in the same run?
> > Looks feasible though. Thanks again,
> > Anastasia
> >
> 
> Let me just restate what you've said so that I can be sure that I am
> correct about what you've already done.  You have run Maker with SNAP,
> Genemark and Augustus using EST from a closely related species (passed
> to altest) and protein evidence from other fungi.  You are missing
> about 1,000 genes compared to the species that provided the EST
> alignments.  You say their is good evidence that these genes exist from
> the alignments and I assume by this that you mean the EST/protein
> alignments that Maker produced.
> 
> 1) Is the closely related fungus annotated and if so have you included
> it's proteins in the evidence set that you provided to Maker.  If you
> haven't provided these proteins as evidence to maker then you should do
> this.  You can re-run maker passing your original models back through
> like this:
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
> 
> #-----Protein Homology Evidence (for best results provide a file for at
> least one) protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
> 
> 2) If you've already included those closely related species proteins
> but still didn't get the 1,000 genes, then take your
> nonoverlaping_abinits.fasta and blast them directly against your
> closely related proteins.  Presumably they don't hit too well because
> if they did they should have been promoted to predictions by Maker the
> first time, but here you can decide yourself what thresholds to allow
> to keep the abinit predictions that hit the closely related species
> proteins.  If you filter you blast hits the way you want and keep the
> names of the abinit predictions that pass your filter, then use the
> script Carson attached it it will generate a abinit precidtion GFF file
> with only the predictions you selected.  You can then pass those
> predictions back to Maker and force it to keep them and Maker will turn
> them from predictions
> (match/match_part) into gene models.
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
> 
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
> 
> keep_preds=1
> 
> Barry
> 
> >> Thanks,
> >> Carson
> >>
> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
> >> To:  <maker-devel at yandell-lab.org>
> >> Subject:  [maker-devel] Use pass-through system to add missing genes
> >>
> >> Hi,
> >> I  have a set of predicted proteins from the genome of a fungus
> >> annotated by MAKER  using EST data from a closely related species
> and
> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
> >> trained directly on the assembly and augustus with a model from a
> >> less closely related species), along with a set of fungal proteins.
> I
> >> am missing ~ 1000 proteins when I compare to the species i used EST
> >> data from, and there is good evidence from alignments that these
> >> genes exist. The question is how to proceed from Blast hits to
> actual
> >> gene models here. The idea would be to add these genes to the
> >> existing dataset, rather than reannotate the genome. I believe that
> >> reannotating it without any further evidence such as RNA-seq from
> the
> >> species itself would not change much,and i d rather stick with
> actual
> >> predictions that i trust and have used in subsequent analyses. The
> >> 1000 genes I can accept to annotate with a less stringent and
> reliable way than MAKER, I just want to add them so that the difference
> in gene count gets corrected.
> >> I was reading the MAKER 2 paper and i was wondering if I can use the
> >> legacy annotations scheme to do it, by providing GFF3 of the
> >> alignments between the two species in the regions where genes were
> >> missed, but as i said, I would not like to reannotate the whole
> >> genome, and running MAKER2 might cause slight changes that i d like
> >> to avoid. Is this possible? First, is it possible to provide a Gff3
> >> file of specific locations and not the entire genome alignment? (I
> >> guess so..) Second, how can I tag the existing annotations as 'not
> to be changed' or alternatively, tag the new models only?
> >> How should I run maker2, with which predictors on and which off?
> >> Thanks,
> >> Anastasia
> >>
> >> Anastasia Gioti
> >> Post-doctoral Researcher
> >>
> >> anastasia.gioti at scilifelab.se
> >> anastasia.gioti at ebc.uu.se
> >>
> >>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
> >> /
> >>
> >>
> >>
> >> _______________________________________________ maker-devel mailing
> >> list
> >> maker-
> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
> >> tinfo/ma
> >> ker-devel_yandell-lab.org
> >> <gff3_select>
> >
> > Anastasia Gioti
> > Post-doctoral Researcher
> >
> > anastasia.gioti at scilifelab.se
> > anastasia.gioti at ebc.uu.se
> >
> >
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> >
> >
> >
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.or
> > g
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
> 
> 
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> End of maker-devel Digest, Vol 47, Issue 14
> *******************************************



From carsonhh at gmail.com  Fri Apr 27 12:18:23 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 13:18:23 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>
Message-ID: <CBC04C5D.BF73%carsonhh@gmail.com>

Here you go.  This will also be part of the next MAKER release in some
form.

Thanks,
Carson



On 12-04-27 12:51 PM, "Collett, James R" <james.collett at pnnl.gov> wrote:

>Hi Carson,
>
>Could you please send me (or make available for download) the perl script
>that you mentioned in this previous post in this thread?
>
>>> Attached is a 
>>> script that would make selecting those easier.  It take the MAKER
>>> generated GFF3 and a list of predictions to keep (one name per line).
>>> These might be the results of a BLAST analysis for example.  It will
>>> then return the GFF3 entries for just those models selected.
>
>Thanks,
>
>Jim
>__________________________________________________
>James R. Collett, Ph.D.
>Senior Scientist
>Chemical and Biological Process Development Group
>Energy and Environment Directorate
>Pacific Northwest National Laboratory
>
>> -----Original Message-----
>> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
>> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
>> lab.org
>> Sent: Friday, April 27, 2012 6:48 AM
>> To: maker-devel at yandell-lab.org
>> Subject: maker-devel Digest, Vol 47, Issue 14
>> 
>> Send maker-devel mailing list submissions to
>> 	maker-devel at yandell-lab.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.org
>> 
>> or, via email, send a message with subject or body 'help' to
>> 	maker-devel-request at yandell-lab.org
>> 
>> You can reach the person managing the list at
>> 	maker-devel-owner at yandell-lab.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of maker-devel digest..."
>> 
>> 
>> Today's Topics:
>> 
>>    1. Re: Use pass-through system to add missing genes (Carson Holt)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Fri, 27 Apr 2012 09:27:24 -0400
>> From: Carson Holt <carsonhh at gmail.com>
>> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
>> 	<anastasia.gioti at scilifelab.se>
>> Cc: maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] Use pass-through system to add missing
>> 	genes
>> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> 
>> The only way you should be able to get BLASTX overlap and still not get
>> a model for the region is if 1.  The protein alignment in in a
>> different reading frame then your models for every single base pair of
>> the alignment (in which case it's not true overlap).  2. The BLASTX
>> HSPs are stacked on each other again and again in weird rearranged
>> overlaps to produce a very deep alignment which would mean this is a
>> repetitive region and is not really a significant alignment.  Otherwise
>> this should not happen unless you have the AED_threshold set to some
>> value where MAKER will ignore genes unless they have a minimum amount
>> of support (by default this option is always off).  The other two
>> possibilities can be tested by just looking at the alignments manually
>> in Apollo.  Also take a look at the AED and eAED values for your
>> missing genes.  Anything below 1 should always be kept by MAKER by
>> default because it has at least some evidence supported.
>> 
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> 
>> If they are already in your current run ignore this.
>> 
>> Barry provided detailed instructions on how to configure MAKER, for
>> your particular case.  So just follow his excellent instructions.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Barry Moore <barry.moore at genetics.utah.edu>
>> Date:  Friday, 27 April, 2012 7:57 AM
>> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
>> Subject:  Re: [maker-devel] Use pass-through system to add missing
>> genes
>> 
>> Hi Anastasia,
>> 
>> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
>> 
>> > Hi Carlson,
>> > Thanks for your help!
>> >
>> >> The way you proceed depends on why the genes are not there to begin
>> with.
>> >> Are they not there because of a lack of evidence?
>> >
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> >
>> 
>> This doesn't sound right.  If there are predicted models and blastx
>> protein evidence overlapping them you should get a model retained.  I
>> know for the EST evidence that it has to support a splice site before
>> it will be promoted and I can't remember if protein evidence is the
>> same but certainly if you pass back those protein2genome predictions
>> and the original proteins as evidence then they will be retained as
>> models.
>> 
>> >> If that's the case just adding the new fasta file should do the
>> trick.
>> >
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> >
>> 
>> Yes using the protein fasta from the closely related species as
>> evidence.  I think you said you've already done that right?
>> 
>> 
>> >> Or are they not there because an assembly error makes it impossible
>> >> to get a logical model for the region (I.e reading frame breaks).
>> >
>> > This is not the case in general.
>> >
>> >> Are there ab initio models already called in those regions that
>> could
>> >> just be promoted to the annotation tier?  You can test that one by
>> >> blasting against the nonoverlaping_abinits.fasta files.
>> >
>> > I have not done this, will do!
>> >
>> >>
>> >> For any of the cases described, you can provide the existing
>> >> annotation set as the input in GFF3 format, and previous models will
>> >> be maintained preferentially.
>> >
>> > You mean in a new maker run? is this possible with the old maker as
>> > well, not maker2, right?
>> >
>> 
>> Yes, the original MAKER will do this.
>> 
>> 
>> >> If you know which ab initio predictions you want to add (I.e. the ab
>> >> initio promoting scenario I descibed), you can provide those
>> >> predictions to the use the pred_gff option and then set keep_preds=1
>> >> and they will be maintained even without evidence.  Attached is a
>> >> script that would make selecting those easier.  It take the MAKER
>> >> generated GFF3 and a list of predictions to keep (one name per
>> line).
>> >> These might be the results of a BLAST analysis for example.  It will
>> >> then return the GFF3 entries for just those models selected.
>> >
>> > The thing is, for the few cases I have looked at, I cannot really
>> > decide which model is the best, and the 3 models from the ab initio
>> > predictors do not agree on the exact intron-exon junctions or the
>> start and stop codons.
>> >>
>> >> If the situation is more complex, just provide more detail, and I am
>> >> sure we can help you come up with a plan.
>> >>
>> > What i was thinking to do was to provide a gff file of alignments (eg
>> > by
>> > exonerate) to the proteins of the closely related species that i am
>> > missing, and somehow keep the previous annotations and get the extra
>> > ones by this gff file. But how exactly maker should be run to do this
>> > I am not sure. if I want to keep the previous annotations I  need the
>> > gff file of the last maker run as input, but then how do I
>> > discriminate with the exonerate gff file? And which mode of rediction
>> > should be on, and with which parameters? You mention
>> > keep_preds=1  for the existing annotations, but how do i also promote
>> > evidence from alignments on the same way in the same run?
>> > Looks feasible though. Thanks again,
>> > Anastasia
>> >
>> 
>> Let me just restate what you've said so that I can be sure that I am
>> correct about what you've already done.  You have run Maker with SNAP,
>> Genemark and Augustus using EST from a closely related species (passed
>> to altest) and protein evidence from other fungi.  You are missing
>> about 1,000 genes compared to the species that provided the EST
>> alignments.  You say their is good evidence that these genes exist from
>> the alignments and I assume by this that you mean the EST/protein
>> alignments that Maker produced.
>> 
>> 1) Is the closely related fungus annotated and if so have you included
>> it's proteins in the evidence set that you provided to Maker.  If you
>> haven't provided these proteins as evidence to maker then you should do
>> this.  You can re-run maker passing your original models back through
>> like this:
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=1
>> other_pass=1
>> 
>> #-----Protein Homology Evidence (for best results provide a file for at
>> least one) protein=proteins_from_closely_related.fasta
>> ## OR it sounds like you've already aligned these with exonerate?
>> protein_gff=proteins_from_closely_related_already_aligned.gff
>> 
>> 2) If you've already included those closely related species proteins
>> but still didn't get the 1,000 genes, then take your
>> nonoverlaping_abinits.fasta and blast them directly against your
>> closely related proteins.  Presumably they don't hit too well because
>> if they did they should have been promoted to predictions by Maker the
>> first time, but here you can decide yourself what thresholds to allow
>> to keep the abinit predictions that hit the closely related species
>> proteins.  If you filter you blast hits the way you want and keep the
>> names of the abinit predictions that pass your filter, then use the
>> script Carson attached it it will generate a abinit precidtion GFF file
>> with only the predictions you selected.  You can then pass those
>> predictions back to Maker and force it to keep them and Maker will turn
>> them from predictions
>> (match/match_part) into gene models.
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=0
>> other_pass=1
>> 
>> #-----Gene Prediction
>> snaphmm=
>> gmhmm=
>> augustus_species=
>> fgenesh_par_file=
>> pred_gff=ab_init_predictions_rescued_by_blast.gff
>> 
>> keep_preds=1
>> 
>> Barry
>> 
>> >> Thanks,
>> >> Carson
>> >>
>> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> >> To:  <maker-devel at yandell-lab.org>
>> >> Subject:  [maker-devel] Use pass-through system to add missing genes
>> >>
>> >> Hi,
>> >> I  have a set of predicted proteins from the genome of a fungus
>> >> annotated by MAKER  using EST data from a closely related species
>> and
>> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
>> >> trained directly on the assembly and augustus with a model from a
>> >> less closely related species), along with a set of fungal proteins.
>> I
>> >> am missing ~ 1000 proteins when I compare to the species i used EST
>> >> data from, and there is good evidence from alignments that these
>> >> genes exist. The question is how to proceed from Blast hits to
>> actual
>> >> gene models here. The idea would be to add these genes to the
>> >> existing dataset, rather than reannotate the genome. I believe that
>> >> reannotating it without any further evidence such as RNA-seq from
>> the
>> >> species itself would not change much,and i d rather stick with
>> actual
>> >> predictions that i trust and have used in subsequent analyses. The
>> >> 1000 genes I can accept to annotate with a less stringent and
>> reliable way than MAKER, I just want to add them so that the difference
>> in gene count gets corrected.
>> >> I was reading the MAKER 2 paper and i was wondering if I can use the
>> >> legacy annotations scheme to do it, by providing GFF3 of the
>> >> alignments between the two species in the regions where genes were
>> >> missed, but as i said, I would not like to reannotate the whole
>> >> genome, and running MAKER2 might cause slight changes that i d like
>> >> to avoid. Is this possible? First, is it possible to provide a Gff3
>> >> file of specific locations and not the entire genome alignment? (I
>> >> guess so..) Second, how can I tag the existing annotations as 'not
>> to be changed' or alternatively, tag the new models only?
>> >> How should I run maker2, with which predictors on and which off?
>> >> Thanks,
>> >> Anastasia
>> >>
>> >> Anastasia Gioti
>> >> Post-doctoral Researcher
>> >>
>> >> anastasia.gioti at scilifelab.se
>> >> anastasia.gioti at ebc.uu.se
>> >>
>> >>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
>> >> /
>> >>
>> >>
>> >>
>> >> _______________________________________________ maker-devel mailing
>> >> list
>> >> maker-
>> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
>> >> tinfo/ma
>> >> ker-devel_yandell-lab.org
>> >> <gff3_select>
>> >
>> > Anastasia Gioti
>> > Post-doctoral Researcher
>> >
>> > anastasia.gioti at scilifelab.se
>> > anastasia.gioti at ebc.uu.se
>> >
>> >
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> >
>> >
>> >
>> > _______________________________________________
>> > maker-devel mailing list
>> > maker-devel at box290.bluehost.com
>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.or
>> > g
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> End of maker-devel Digest, Vol 47, Issue 14
>> *******************************************
>
>_______________________________________________
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>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From weckalba at asu.edu  Tue Apr  3 17:28:28 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 3 Apr 2012 16:28:28 -0700
Subject: [maker-devel] gff3_preds2models usage question
Message-ID: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a
few issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
 I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
chado yet, and it does not appear trivial.

Thanks for the help,

Walter
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From ranjani at uga.edu  Tue Apr  3 20:24:49 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Wed, 4 Apr 2012 02:24:49 +0000
Subject: [maker-devel] mRNA-seq data
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>

Hi,



I am using to MAKER to annotate a genome and I would like a couple of clarifications.



In the previous version of MAKER, under EST_evidence in maker_opts. ctl the user could input est and est_reads- the mRNAseq reads (although this was not fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation quality.

I have assembled transcriptome data from Sanger,454 and Illumina



Do I just provide all this data in a fasta file format to the 'est' option? Is this is the best way to provide the mRNA-seq evidence?Will this assure the mRNA-seq data is used to improve the annotations?



Thanks!



Ranjani
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From carsonhh at gmail.com  Tue Apr  3 20:39:02 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 03 Apr 2012 22:39:02 -0400
Subject: [maker-devel] mRNA-seq data
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>
Message-ID: <CBA12B6C.AA4A%carsonhh@gmail.com>

Yes.  If you have them in fasta format, just provide them to the est= option
and let MAEKR align them with exonerate.  If you used something like
cufflinks or trinity, to process them you can provide them to the est_gff
option (MAKER comes with a cufflinks2gff3 converter to make that easy).

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Wed, 4 Apr 2012 02:24:49 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mRNA-seq data

Hi,

 

I am using to MAKER to annotate a genome and I would like a couple of
clarifications.

 

In the previous version of MAKER, under EST_evidence in maker_opts. ctl the
user could input est and est_reads- the mRNAseq reads (although this was not
fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation
quality.

I have assembled transcriptome data from Sanger,454 and Illumina

 

Do I just provide all this data in a fasta file format to the 'est' option?
Is this is the best way to provide the mRNA-seq evidence?Will this assure
the mRNA-seq data is used to improve the annotations?

 

Thanks!

 

Ranjani
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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 pingouinandsheep at gmail.com  Thu Apr  5 08:14:39 2012
From: pingouinandsheep at gmail.com (pingouinandsheep at gmail.com)
Date: Thu, 5 Apr 2012 07:14:39 -0700 (PDT)
Subject: [maker-devel] Huge memory usage
Message-ID: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>

Hello,

When I try to run the test provided with maker2, maker start to use a
huge amount of memory. I stoped it after it reach ~100go of memory
used. I believe the test should not use that amount of memory.

In an other message someone suggest that the bioperl version installed
could be the cause of the problem, but the bioperl installed on my
cluster is already at version 1.6.

perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006901

Unfortunately I don't have an error message to provide, that could
clarify my problem.

But maybe it is a recurrent problem and you know a few things I should
check.

Thanks,

Ismael



From carsonhh at gmail.com  Thu Apr  5 08:26:17 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 05 Apr 2012 10:26:17 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>
Message-ID: <CBA321AA.AB7A%carsonhh@gmail.com>

The test should not use up more then a few megabytes of RAM.  Even on very
large datasets you should never really use more that 1 or 2 gig of RAM
perl MAKER instance

It's possible that their may be other perl modules that are broken need to
be reinstalled on your system.  This can happen when perl gets updated,
but you are pointing to modules built for a different perl version with
the PERL5LIB environmental variable.  Make sure you you have the latest
version of MAKER and run with --debug set.  Collect that output and send
it to me (the --debug option does some dependancy checking).

I know there is an issue on Macs with updating perl's DB_File module that
causes it to gobble up big sections of the hard drive (it will eventually
fill the drive if you let it).  It's not a memory issue but just one
example of how broken modules can cause weird behavior.

Thanks,
Carson




On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
<pingouinandsheep at gmail.com> wrote:

>Hello,
>
>When I try to run the test provided with maker2, maker start to use a
>huge amount of memory. I stoped it after it reach ~100go of memory
>used. I believe the test should not use that amount of memory.
>
>In an other message someone suggest that the bioperl version installed
>could be the cause of the problem, but the bioperl installed on my
>cluster is already at version 1.6.
>
>perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>1.006901
>
>Unfortunately I don't have an error message to provide, that could
>clarify my problem.
>
>But maybe it is a recurrent problem and you know a few things I should
>check.
>
>Thanks,
>
>Ismael
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From eernst at cshl.edu  Sun Apr  8 16:09:22 2012
From: eernst at cshl.edu (Evan Ernst)
Date: Sun, 8 Apr 2012 18:09:22 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log under
	openMPI
Message-ID: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker
instances, each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no
actual processing is required apart from marking the scaffolds FINISHED.
Comparing the result to a single, non-MPI maker instance running on the
same completed hierarchy reveals that many entries aren't being written to
the log at all when running under MPI. The single process instance runs
just fine, generating a complete log that can be used for the downstream
scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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From carsonhh at gmail.com  Tue Apr 10 08:26:40 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 10 Apr 2012 10:26:40 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log
 under openMPI
In-Reply-To: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>
Message-ID: <CBA9B62E.AE4E%carsonhh@gmail.com>

Depending on if your using NFS and other architecture design you can get
race conditions with the datastore log file.  This primarily happens when
you have multiple instances of MAKER running at the same time or thousands
of short contigs running in parallel so many finish at the same time.  In a
future release, I plan on having the last MAKER job to exit just rebuild the
log at the end of a run to ensure it is complete. For now though, just run
'maker -dsindex' at the end of a run when it happens.  It will rebbuild the
log and only takes a few seconds.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Sun, 8 Apr 2012 18:09:22 -0400
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Incomplete/Missing lines in datastore index log
under openMPI

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker instances,
each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no actual
processing is required apart from marking the scaffolds FINISHED. Comparing
the result to a single, non-MPI maker instance running on the same completed
hierarchy reveals that many entries aren't being written to the log at all
when running under MPI. The single process instance runs just fine,
generating a complete log that can be used for the downstream scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
_______________________________________________ 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 smg283 at gmail.com  Fri Apr 13 13:00:29 2012
From: smg283 at gmail.com (Scott Geib)
Date: Fri, 13 Apr 2012 09:00:29 -1000
Subject: [maker-devel] mpi issue on computing cluster
Message-ID: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>

Hi,
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first,

Thanks
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From sbrubaker at solazyme.com  Fri Apr 13 14:12:24 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 20:12:24 +0000
Subject: [maker-devel] Functional annotation pipeline
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>

Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane



From joseph.fass at gmail.com  Fri Apr 13 14:42:51 2012
From: joseph.fass at gmail.com (Joseph Fass)
Date: Fri, 13 Apr 2012 13:42:51 -0700
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
References: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
Message-ID: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:

> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
>
> Thanks,
> Shane
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)
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From carsonhh at gmail.com  Fri Apr 13 13:51:38 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 15:51:38 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <CADNSSgBwH1-wbqpC3_EC+92yzLoi-f5CVwMVaewV=xCK3qkPaA@mail.gmail.com>
Message-ID: <CBADFB12.B16B%carsonhh@gmail.com>

You can pre-mask the genome, convert the RepaetMasker results to GFF3 and
pass them in, or just run the ./configure script in the RepeatMasker
directory to configure wublast to be the default.

You can also let MAKER install it's own separate installation of
RepeatMasker using rmblast.  Just go to the maker/src/ directory and run
this command --> ./Build repeatmasker

MAKER will use that installation preferentially if you let it install that.

Thanks,
Carson

From:  padioleau isma?l <ismpadioleau at gmail.com>
Date:  Fri, 13 Apr 2012 17:42:20 +0200
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Huge memory usage

Dear Carson,

I have a problem with RepeatMasker on my cluster. It work with wublast but
not with Crossmatch. As maker try to run RepeatMasker with default I can not
successfully run maker.

I wanted to know if I can provide to maker the genome already masked (if I
run with wublast externally), I though it was possible but I can't found in
the configuration files where I should provide it i.e : In maker_opts.ctl,
should I provide the result from RepeatMasker to 'genome_gff:' and set
'rm_pass' to 1, or set rm_gff in the 'Repeat Masking' part of the file?
Or maybe I should provide directly the masked fasta as genome reference.

An other solution could be to ask maker to run RepeatMasker with the option
'-e wublast'.

Is it possible to use one of these solutions?

Thanks,

Ismael

2012/4/5 padioleau isma?l <ismpadioleau at gmail.com>
> Dear Carson,
> 
> Thank you for your very quick answering.
> 
> I realised that I missed some error messages and the problem seems to be
> linked to the DB_file package as you suggested. The person in charge of
> installation told me that he will recover the configuration.
> 
> I will test it after the Easter weekend and come back to you if we have other
> issues.
> 
> Have a nice Easter weekend,
> 
> Ismael
> 
> Here Is the error message:
> Use of uninitialized value $DB_File::db_version in numeric ge (>=) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 276.
> Use of uninitialized value $DB_File::db_version in numeric gt (>) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 280.
> Deep recursion on subroutine "DB_File::AUTOLOAD" at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 235.
> 
> 
> 
> 2012/4/5 Carson Holt <carsonhh at gmail.com>
>> The test should not use up more then a few megabytes of RAM.  Even on very
>> large datasets you should never really use more that 1 or 2 gig of RAM
>> perl MAKER instance
>> 
>> It's possible that their may be other perl modules that are broken need to
>> be reinstalled on your system.  This can happen when perl gets updated,
>> but you are pointing to modules built for a different perl version with
>> the PERL5LIB environmental variable.  Make sure you you have the latest
>> version of MAKER and run with --debug set.  Collect that output and send
>> it to me (the --debug option does some dependancy checking).
>> 
>> I know there is an issue on Macs with updating perl's DB_File module that
>> causes it to gobble up big sections of the hard drive (it will eventually
>> fill the drive if you let it).  It's not a memory issue but just one
>> example of how broken modules can cause weird behavior.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> 
>> On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
>> <pingouinandsheep at gmail.com> wrote:
>> 
>>> >Hello,
>>> >
>>> >When I try to run the test provided with maker2, maker start to use a
>>> >huge amount of memory. I stoped it after it reach ~100go of memory
>>> >used. I believe the test should not use that amount of memory.
>>> >
>>> >In an other message someone suggest that the bioperl version installed
>>> >could be the cause of the problem, but the bioperl installed on my
>>> >cluster is already at version 1.6.
>>> >
>>> >perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>>> >1.006901
>>> >
>>> >Unfortunately I don't have an error message to provide, that could
>>> >clarify my problem.
>>> >
>>> >But maybe it is a recurrent problem and you know a few things I should
>>> >check.
>>> >
>>> >Thanks,
>>> >
>>> >Ismael
>>> >
>>> >_______________________________________________
>>> >maker-devel mailing list
>>> >maker-devel at box290.bluehost.com
>>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> 
> -- 
> Isma?l Padioleau
> Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
> Emmanouil Dermitzakis Group
> Dpt de M?decine G?n?tique et D?veloppement
> Universit? de Gen?ve - Facult? de M?decine
> CMU -  Rue Michel-Servet 1
> CH 1211 Gen?ve 4
> Tel: 0041 22 379 59 74
> ismael.padioleau at unige.ch
> 
> --
> Tel. 0041 78 77 69 561
> ismpadioleau at gmail.com



-- 
Isma?l Padioleau
Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
Emmanouil Dermitzakis Group
Dpt de M?decine G?n?tique et D?veloppement
Universit? de Gen?ve - Facult? de M?decine
CMU -  Rue Michel-Servet 1
CH 1211 Gen?ve 4
Tel: 0041 22 379 59 74
ismael.padioleau at unige.ch

--
Tel. 0041 78 77 69 561
ismpadioleau at gmail.com


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From carsonhh at gmail.com  Fri Apr 13 15:02:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 17:02:51 -0400
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
Message-ID: <CBAE0B9F.B1D2%carsonhh@gmail.com>

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
integrate interproscan results in the GFF3 files.  There are also a couple
of scripts maker_functional_gff and maker_functional_fasta that can do
putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From:  Joseph Fass <joseph.fass at gmail.com>
Date:  Fri, 13 Apr 2012 13:42:51 -0700
To:  Shane Brubaker <sbrubaker at solazyme.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>
wrote:
> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
> 
> Thanks,
> Shane
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com <http://gmail.com>  (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ 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 sbrubaker at solazyme.com  Fri Apr 13 15:18:10 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 21:18:10 +0000
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065BBA@EXCHANGE-05.internal.solazyme.com>

Great thank you ... I will take a look at those.

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Friday, April 13, 2012 2:03 PM
To: Joseph Fass; Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Functional annotation pipeline

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files.  There are also a couple of scripts maker_functional_gff and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From: Joseph Fass <joseph.fass at gmail.com<mailto:joseph.fass at gmail.com>>
Date: Fri, 13 Apr 2012 13:42:51 -0700
To: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>> wrote:
Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane

_______________________________________________
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



--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com<http://gmail.com> (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From dsth at ebi.ac.uk  Fri Apr 13 15:22:37 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:22:37 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>

Careful of interproscan atm.. I believe the executable is still in beta and
they definitely aren't recommending it for production use yet. If you do
use it be sure to check output file if using the lookup service as when i
used it recently it would sometimes exit normally despite lookup failures
(the lookup problems may have had something to do with running ~800 in
parallel - they're looking into the issue atm.).

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Carson Holt <carsonhh at gmail.com>

> I would agree blast2go.
>
> You can also try interproscan fro the EBI
>
> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
> integrate interproscan results in the GFF3 files.  There are also a couple
> of scripts maker_functional_gff and maker_functional_fasta that can do
> putative functional annotation using uniprot/swiss-prot.
>
> Thanks,
> Carson
>
>
>
> From: Joseph Fass <joseph.fass at gmail.com>
> Date: Fri, 13 Apr 2012 13:42:51 -0700
> To: Shane Brubaker <sbrubaker at solazyme.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Functional annotation pipeline
>
> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
> HTH,
> ~Joe
>
> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>
>> Hi, can you recommend any open source functional annotation pipelines -
>> to assign function, GO terms, pathways, etc. to gene models?
>>
>> Thanks,
>> Shane
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
> --
> Joseph Fass
> Lead Data Analyst
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From dsth at ebi.ac.uk  Fri Apr 13 15:37:06 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:37:06 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
	<CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
Message-ID: <CAP8X9uKOcovWFAetQTaGgQ6Mpb-rg_8PB5RCkfrhsev6Mx03bQ@mail.gmail.com>

sorry, that's the new version of course.

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Daniel Hughes <dsth at ebi.ac.uk>

> Careful of interproscan atm.. I believe the executable is still in beta
> and they definitely aren't recommending it for production use yet. If you
> do use it be sure to check output file if using the lookup service as when
> i used it recently it would sometimes exit normally despite lookup failures
> (the lookup problems may have had something to do with running ~800 in
> parallel - they're looking into the issue atm.).
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
>
> 2012/4/13 Carson Holt <carsonhh at gmail.com>
>
>> I would agree blast2go.
>>
>> You can also try interproscan fro the EBI
>>
>> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
>> integrate interproscan results in the GFF3 files.  There are also a couple
>> of scripts maker_functional_gff and maker_functional_fasta that can do
>> putative functional annotation using uniprot/swiss-prot.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: Joseph Fass <joseph.fass at gmail.com>
>> Date: Fri, 13 Apr 2012 13:42:51 -0700
>> To: Shane Brubaker <sbrubaker at solazyme.com>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] Functional annotation pipeline
>>
>> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
>> HTH,
>> ~Joe
>>
>> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>>
>>> Hi, can you recommend any open source functional annotation pipelines -
>>> to assign function, GO terms, pathways, etc. to gene models?
>>>
>>> Thanks,
>>> Shane
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>>
>>
>> --
>> Joseph Fass
>> Lead Data Analyst
>> UC Davis Bioinformatics Core
>> joseph.fass -at- gmail.com (professional)
>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
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From kd7gwt at exchange.usfood.com  Sat Apr 14 00:50:28 2012
From: kd7gwt at exchange.usfood.com (Liz Douglas)
Date: Sat, 14 Apr 2012 14:50:28 +0800
Subject: [maker-devel] Incredible effect on your possibilities in bed
Message-ID: <002801cd1a0b$727fe840$5047c36a@SAMrc6umq>

http://sten-stil.dk/require.html Do you wish to satisfy your babe tonight?




From ranjani at uga.edu  Tue Apr 17 10:46:40 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Tue, 17 Apr 2012 16:46:40 +0000
Subject: [maker-devel] MAKER2.23 output
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>

Hi,

I tried running the latest version of Maker 2.23 with my dataset but with out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2 /usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further details

I was able run the previous version of Maker 2.10 successfully with my dataset.

Thanks,
Ranjani


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From carsonhh at gmail.com  Tue Apr 17 10:56:11 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 12:56:11 -0400
Subject: [maker-devel] MAKER2.23 output
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>
Message-ID: <CBB31716.B317%carsonhh@gmail.com>

Segmentation fault means there was a failure with C code.  It was likely in
one of the modules being used.

These are all potential culprits

Inline::C
Proc::ProcessTable
DB_file
forks

Based on when the error occurred.  I would lean more toward DB_File.  Is it
possible that BerkleyDB has been updated on your system, perhaps as part of
another installation or a system update?  That sometimes breaks this module
(which is part of the perl core).

You can try reinstalling that module from CPAN.  Also if you run MAKER
version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug')
to get more information just before the error occurs.  You can then capture
the error log send that to me.

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tue, 17 Apr 2012 16:46:40 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER2.23 output

Hi, 

I tried running the latest version of Maker 2.23 with my dataset but with
out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output
files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2
/usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further
details

I was able run the previous version of Maker 2.10 successfully with my
dataset.

Thanks,
Ranjani


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

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From carsonhh at gmail.com  Tue Apr 17 11:09:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 13:09:32 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>
Message-ID: <CBB31953.B329%carsonhh@gmail.com>

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    }

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

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

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From carsonhh at gmail.com  Tue Apr 17 14:25:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 16:25:51 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CBB31953.B329%carsonhh@gmail.com>
Message-ID: <CBB349BE.B364%carsonhh@gmail.com>

Sorry missed the ';' at the end of the eval block.

Should be this -->

    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


--Carson

From:  Carson Holt <carsonhh at gmail.com>
Date:  Tue, 17 Apr 2012 13:09:32 -0400
To:  Scott Geib <smg283 at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] mpi issue on computing cluster

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

Thanks
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From elzedliu at gmail.com  Tue Apr 17 17:22:53 2012
From: elzedliu at gmail.com (Huanle)
Date: Tue, 17 Apr 2012 16:22:53 -0700 (PDT)
Subject: [maker-devel] gene predictors in MARKER
Message-ID: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>

I am using MAKER to annotate a recently assembled plant genome.
Hi There,

I am using MAKER to annotate a recently assembled plant genome.

I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial

The denovo gene predictors i included in the maker_exe.ctl file are
#-----Ab-initio Gene Prediction Algorithms
snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
augustus executable

However, I am not sure whether they were really used.

During the running, i could see repeatmasker, exonerate and wublast
were called. But i did see any information popped up for those gene
predictors.

So i am wondering if they were actually used.

Could you please let me know how to know if all or one of those gene
predictors were called by marker?

Kind Regards,
Huanle



From carsonhh at gmail.com  Mon Apr 23 15:04:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 23 Apr 2012 17:04:16 -0400
Subject: [maker-devel] gene predictors in MARKER
In-Reply-To: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>
Message-ID: <CBBB3AB1.BC17%carsonhh@gmail.com>

The gene predictors have to be trained first, and when they are trained
they produce an HMM file that can be supplied to MAKER.  You can either
use MAKER's protein2genome option or est2genome option to produce rough
models to train with, or you can try one of the models that come
prepackaged with those algorithms.

SNAP models will be in --> /sw/maker/2.10/bin/../exe/snap/HMM
Augustus --> run this to see species in augustus -->
/sw/maker/2.10/bin/../exe/augustus/bin/augustus --species=help
GeneMark is self training.  Run it one directly on your genome fasta or
for speed just a chromosome or two of the assembly and it will produce a
file called es.mod as part of it's results.  That is the file you need.

If you have any questions or issues with training just let us know.

Thanks,
Carson



On 12-04-17 7:22 PM, "Huanle" <elzedliu at gmail.com> wrote:

>I am using MAKER to annotate a recently assembled plant genome.
>Hi There,
>
>I am using MAKER to annotate a recently assembled plant genome.
>
>I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial
>
>The denovo gene predictors i included in the maker_exe.ctl file are
>#-----Ab-initio Gene Prediction Algorithms
>snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
>gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
>genemark executable
>gmhmmp= #location of prokaryotic genemark executable
>augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
>augustus executable
>
>However, I am not sure whether they were really used.
>
>During the running, i could see repeatmasker, exonerate and wublast
>were called. But i did see any information popped up for those gene
>predictors.
>
>So i am wondering if they were actually used.
>
>Could you please let me know how to know if all or one of those gene
>predictors were called by marker?
>
>Kind Regards,
>Huanle
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From anastasia.gioti at scilifelab.se  Wed Apr 25 03:09:36 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:09:36 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
Message-ID: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:22:03 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:22:03 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>

For cross-species comparisons you might have be better off including the
actual peptide sequences of the other fungi too in the annotation run - I'd
be very surprised if you really did get the same result.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> I  have a set of predicted proteins from the genome of a fungus annotated
> by MAKER  using EST data from a closely related species and 3 ab initio
> predictors  (snap iterativelly trained 3 times, genemark trained directly
> on the assembly and augustus with a model from a less closely related
> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
> when I compare to the species i used EST data from, and there is good
> evidence from alignments that these genes exist. The question is how to
> proceed from Blast hits to actual gene models here. The idea would be to
> add these genes to the existing dataset, rather than reannotate the genome.
> I believe that reannotating it without any further evidence such as RNA-seq
> from the species itself would not change much,and i d rather stick with
> actual predictions that i trust and have used in subsequent analyses. The
> 1000 genes I can accept to annotate with a less stringent and reliable way
> than MAKER, I just want to add them so that the difference in gene count
> gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the
> legacy annotations scheme to do it, by providing GFF3 of the alignments
> between the two species in the regions where genes were missed, but as i
> said, I would not like to reannotate the whole genome, and running MAKER2
> might cause slight changes that i d like to avoid. Is this possible? First,
> is it possible to provide a Gff3 file of specific locations and not the
> entire genome alignment? (I guess so..) Second, how can I tag the existing
> annotations as 'not to be changed' or alternatively, tag the new models
> only? How should I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
> _______________________________________________
> 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 anastasia.gioti at scilifelab.se  Wed Apr 25 03:29:30 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:29:30 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
Message-ID: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>

Hi, 
Do you mean that I should have not include the proteins of the closely related species in my fungal protein fasta file that I used as evidence in MAKER? i do not see why... What I have been trying to do now is further 'bias' the annotations in favor of this species, so as to get the missing genes. Can you explain a bit more whta you mean?
Thanks, 
Anastasia
On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:

> For cross-species comparisons you might have be better off including the actual peptide sequences of the other fungi too in the annotation run - I'd be very surprised if you really did get the same result.
> 
> dan.
> 
> 
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
> 
> 
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Hi, 
> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
> Thanks, 
> Anastasia
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:39:49 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:39:49 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
	<A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
Message-ID: <CAP8X9u+BvAG8xRqd_DHwdoiFAbWu0nZ0Get-UNkbGrU_qOEHXA@mail.gmail.com>

sorry my bad, i missed the part about you having already included the
fungal proteins as fasta ;/ - too early for me.

in that case have you viewed the full gff output for specific instances of
such missing proteins in something like apollo to try and work out why
maker hasn't made a call at those loci (aed score...)?

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> Do you mean that I should have not include the proteins of the closely
> related species in my fungal protein fasta file that I used as evidence in
> MAKER? i do not see why... What I have been trying to do now is further
> 'bias' the annotations in favor of this species, so as to get the missing
> genes. Can you explain a bit more whta you mean?
> Thanks,
> Anastasia
>
> On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:
>
> For cross-species comparisons you might have be better off including the
> actual peptide sequences of the other fungi too in the annotation run - I'd
> be very surprised if you really did get the same result.
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
>
>> Hi,
>> I  have a set of predicted proteins from the genome of a fungus annotated
>> by MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly
>> on the assembly and augustus with a model from a less closely related
>> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
>> when I compare to the species i used EST data from, and there is good
>> evidence from alignments that these genes exist. The question is how to
>> proceed from Blast hits to actual gene models here. The idea would be to
>> add these genes to the existing dataset, rather than reannotate the genome.
>> I believe that reannotating it without any further evidence such as RNA-seq
>> from the species itself would not change much,and i d rather stick with
>> actual predictions that i trust and have used in subsequent analyses. The
>> 1000 genes I can accept to annotate with a less stringent and reliable way
>> than MAKER, I just want to add them so that the difference in gene count
>> gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the
>> legacy annotations scheme to do it, by providing GFF3 of the alignments
>> between the two species in the regions where genes were missed, but as i
>> said, I would not like to reannotate the whole genome, and running MAKER2
>> might cause slight changes that i d like to avoid. Is this possible? First,
>> is it possible to provide a Gff3 file of specific locations and not the
>> entire genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models
>> only? How should I run maker2, with which predictors on and which off?
>> Thanks,
>> Anastasia
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
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From carsonhh at gmail.com  Wed Apr 25 08:29:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Apr 2012 10:29:01 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CBBD7372.BD57%carsonhh@gmail.com>

The way you proceed depends on why the genes are not there to begin with.
Are they not there because of a lack of evidence?  If that's the case just
adding the new fasta file should do the trick.  Or are they not there
because an assembly error makes it impossible to get a logical model for the
region (I.e reading frame breaks).  Are there ab initio models already
called in those regions that could just be promoted to the annotation tier?
You can test that one by blasting against the nonoverlaping_abinits.fasta
files.

For any of the cases described, you can provide the existing annotation set
as the input in GFF3 format, and previous models will be maintained
preferentially.  If you know which ab initio predictions you want to add
(I.e. the ab initio promoting scenario I descibed), you can provide those
predictions to the use the pred_gff option and then set keep_preds=1 and
they will be maintained even without evidence.  Attached is a script that
would make selecting those easier.  It take the MAKER generated GFF3 and a
list of predictions to keep (one name per line).  These might be the results
of a BLAST analysis for example.  It will then return the GFF3 entries for
just those models selected.

If the situation is more complex, just provide more detail, and I am sure we
can help you come up with a plan.

Thanks,
Carson

From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Date:  Wed, 25 Apr 2012 11:09:36 +0200
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Use pass-through system to add missing genes

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by
MAKER  using EST data from a closely related species and 3 ab initio
predictors  (snap iterativelly trained 3 times, genemark trained directly on
the assembly and augustus with a model from a less closely related species),
along with a set of fungal proteins. I am missing ~ 1000 proteins when I
compare to the species i used EST data from, and there is good evidence from
alignments that these genes exist. The question is how to proceed from Blast
hits to actual gene models here. The idea would be to add these genes to the
existing dataset, rather than reannotate the genome. I believe that
reannotating it without any further evidence such as RNA-seq from the
species itself would not change much,and i d rather stick with actual
predictions that i trust and have used in subsequent analyses. The 1000
genes I can accept to annotate with a less stringent and reliable way than
MAKER, I just want to add them so that the difference in gene count gets
corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy
annotations scheme to do it, by providing GFF3 of the alignments between the
two species in the regions where genes were missed, but as i said, I would
not like to reannotate the whole genome, and running MAKER2 might cause
slight changes that i d like to avoid. Is this possible? First, is it
possible to provide a Gff3 file of specific locations and not the entire
genome alignment? (I guess so..) Second, how can I tag the existing
annotations as 'not to be changed' or alternatively, tag the new models
only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



_______________________________________________ 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 anastasia.gioti at scilifelab.se  Fri Apr 27 02:43:14 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Fri, 27 Apr 2012 10:43:14 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CBBD7372.BD57%carsonhh@gmail.com>
References: <CBBD7372.BD57%carsonhh@gmail.com>
Message-ID: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>

Hi Carlson,
Thanks for your help!

> The way you proceed depends on why the genes are not there to begin  
> with.  Are they not there because of a lack of evidence?

It is a mixture of cases, and I can only look at some examples to say  
that. There are cases where all 3 used ab initio predictors provide  
models, there are blastx hits, or both blastx and protein2 genome, but  
no EST evidence, thus  no model is retained. i guess my default  
parameters could be responsible for these cases at least.

> If that's the case just adding the new fasta file should do the trick.

which fasta do you refer to? The proteins file I use as evidence  
contains all proteins i can actually use.

> Or are they not there because an assembly error makes it impossible  
> to get a logical model for the region (I.e reading frame breaks).

This is not the case in general.

> Are there ab initio models already called in those regions that  
> could just be promoted to the annotation tier?  You can test that  
> one by blasting against the nonoverlaping_abinits.fasta files.

I have not done this, will do!

>
> For any of the cases described, you can provide the existing  
> annotation set as the input in GFF3 format, and previous models will  
> be maintained preferentially.

You mean in a new maker run? is this possible with the old maker as  
well, not maker2, right?

> If you know which ab initio predictions you want to add (I.e. the ab  
> initio promoting scenario I descibed), you can provide those  
> predictions to the use the pred_gff option and then set keep_preds=1  
> and they will be maintained even without evidence.  Attached is a  
> script that would make selecting those easier.  It take the MAKER  
> generated GFF3 and a list of predictions to keep (one name per  
> line).  These might be the results of a BLAST analysis for example.   
> It will then return the GFF3 entries for just those models selected.

The thing is, for the few cases I have looked at, I cannot really  
decide which model is the best, and the 3 models from the ab initio  
predictors do not agree on the exact intron-exon junctions or the  
start and stop codons.
>
> If the situation is more complex, just provide more detail, and I am  
> sure we can help you come up with a plan.
>
What i was thinking to do was to provide a gff file of alignments (eg  
by exonerate) to the proteins of the closely related species that i  
am  missing, and somehow keep the previous annotations and get the  
extra ones by this gff file. But how exactly maker should be run to do  
this I am not sure. if I want to keep the previous annotations I  need  
the gff file of the last maker run as input, but then how do I  
discriminate with the exonerate gff file? And which mode of rediction  
should be on, and with which parameters? You mention keep_preds=1  for  
the existing annotations, but how do i also promote evidence from  
alignments on the same way in the same run?
Looks feasible though. Thanks again,
Anastasia

> Thanks,
> Carson
>
> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Date: Wed, 25 Apr 2012 11:09:36 +0200
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Use pass-through system to add missing genes
>
> Hi,
> I  have a set of predicted proteins from the genome of a fungus  
> annotated by MAKER  using EST data from a closely related species  
> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
> genemark trained directly on the assembly and augustus with a model  
> from a less closely related species), along with a set of fungal  
> proteins. I am missing ~ 1000 proteins when I compare to the species  
> i used EST data from, and there is good evidence from alignments  
> that these genes exist. The question is how to proceed from Blast  
> hits to actual gene models here. The idea would be to add these  
> genes to the existing dataset, rather than reannotate the genome. I  
> believe that reannotating it without any further evidence such as  
> RNA-seq from the species itself would not change much,and i d rather  
> stick with actual predictions that i trust and have used in  
> subsequent analyses. The 1000 genes I can accept to annotate with a  
> less stringent and reliable way than MAKER, I just want to add them  
> so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the  
> legacy annotations scheme to do it, by providing GFF3 of the  
> alignments between the two species in the regions where genes were  
> missed, but as i said, I would not like to reannotate the whole  
> genome, and running MAKER2 might cause slight changes that i d like  
> to avoid. Is this possible? First, is it possible to provide a Gff3  
> file of specific locations and not the entire genome alignment? (I  
> guess so..) Second, how can I tag the existing annotations as 'not  
> to be changed' or alternatively, tag the new models only? How should  
> I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
> _______________________________________________ maker-devel mailing  
> list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> <gff3_select>

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From barry.moore at genetics.utah.edu  Fri Apr 27 05:57:01 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 27 Apr 2012 05:57:01 -0600
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
Message-ID: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.  Are they not there because of a lack of evidence?  
> 
> It is a mixture of cases, and I can only look at some examples to say that. There are cases where all 3 used ab initio predictors provide models, there are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus  no model is retained. i guess my default parameters could be responsible for these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein evidence overlapping them you should get a model retained.  I know for the EST evidence that it has to support a splice site before it will be promoted and I can't remember if protein evidence is the same but certainly if you pass back those protein2genome predictions and the original proteins as evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.  
> 
> which fasta do you refer to? The proteins file I use as evidence contains all proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a logical model for the region (I.e reading frame breaks).  
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be promoted to the annotation tier?  You can test that one by blasting against the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set as the input in GFF3 format, and previous models will be maintained preferentially.  
> 
> You mean in a new maker run? is this possible with the old maker as well, not maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which model is the best, and the 3 models from the ab initio predictors do not agree on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by exonerate) to the proteins of the closely related species that i am  missing, and somehow keep the previous annotations and get the extra ones by this gff file. But how exactly maker should be run to do this I am not sure. if I want to keep the previous annotations I  need the gff file of the last maker run as input, but then how do I discriminate with the exonerate gff file? And which mode of rediction should be on, and with which parameters? You mention keep_preds=1  for the existing annotations, but how do i also promote evidence from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct about what you've already done.  You have run Maker with SNAP, Genemark and Augustus using EST from a closely related species (passed to altest) and protein evidence from other fungi.  You are missing about 1,000 genes compared to the species that provided the EST alignments.  You say their is good evidence that these genes exist from the alignments and I assume by this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's proteins in the evidence set that you provided to Maker.  If you haven't provided these proteins as evidence to maker then you should do this.  You can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta and blast them directly against your closely related proteins.  Presumably they don't hit too well because if they did they should have been promoted to predictions by Maker the first time, but here you can decide yourself what thresholds to allow to keep the abinit predictions that hit the closely related species proteins.  If you filter you blast hits the way you want and keep the names of the abinit predictions that pass your filter, then use the script Carson attached it it will generate a abinit precidtion GFF file with only the predictions you selected.  You can then pass those predictions back to Maker and force it to keep them and Maker will turn them from predictions (match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Fri Apr 27 07:27:24 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 09:27:24 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <CBC01559.BF45%carsonhh@gmail.com>

> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.

The only way you should be able to get BLASTX overlap and still not get a
model for the region is if 1.  The protein alignment in in a different
reading frame then your models for every single base pair of the alignment
(in which case it's not true overlap).  2. The BLASTX HSPs are stacked on
each other again and again in weird rearranged overlaps to produce a very
deep alignment which would mean this is a repetitive region and is not
really a significant alignment.  Otherwise this should not happen unless you
have the AED_threshold set to some value where MAKER will ignore genes
unless they have a minimum amount of support (by default this option is
always off).  The other two possibilities can be tested by just looking at
the alignments manually in Apollo.  Also take a look at the AED and eAED
values for your missing genes.  Anything below 1 should always be kept by
MAKER by default because it has at least some evidence supported.

> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.

If they are already in your current run ignore this.

Barry provided detailed instructions on how to configure MAKER, for your
particular case.  So just follow his excellent instructions.

Thanks,
Carson



From:  Barry Moore <barry.moore at genetics.utah.edu>
Date:  Friday, 27 April, 2012 7:57 AM
To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Use pass-through system to add missing genes

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.
>> Are they not there because of a lack of evidence?
> 
> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein
evidence overlapping them you should get a model retained.  I know for the
EST evidence that it has to support a splice site before it will be promoted
and I can't remember if protein evidence is the same but certainly if you
pass back those protein2genome predictions and the original proteins as
evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.
> 
> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I
think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a
>> logical model for the region (I.e reading frame breaks).
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be
>> promoted to the annotation tier?  You can test that one by blasting against
>> the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set
>> as the input in GFF3 format, and previous models will be maintained
>> preferentially. 
> 
> You mean in a new maker run? is this possible with the old maker as well, not
> maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio
>> promoting scenario I descibed), you can provide those predictions to the use
>> the pred_gff option and then set keep_preds=1 and they will be maintained
>> even without evidence.  Attached is a script that would make selecting those
>> easier.  It take the MAKER generated GFF3 and a list of predictions to keep
>> (one name per line).  These might be the results of a BLAST analysis for
>> example.  It will then return the GFF3 entries for just those models
>> selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which
> model is the best, and the 3 models from the ab initio predictors do not agree
> on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we
>> can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by
> exonerate) to the proteins of the closely related species that i am  missing,
> and somehow keep the previous annotations and get the extra ones by this gff
> file. But how exactly maker should be run to do this I am not sure. if I want
> to keep the previous annotations I  need the gff file of the last maker run as
> input, but then how do I discriminate with the exonerate gff file? And which
> mode of rediction should be on, and with which parameters? You mention
> keep_preds=1  for the existing annotations, but how do i also promote evidence
> from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct
about what you've already done.  You have run Maker with SNAP, Genemark and
Augustus using EST from a closely related species (passed to altest) and
protein evidence from other fungi.  You are missing about 1,000 genes
compared to the species that provided the EST alignments.  You say their is
good evidence that these genes exist from the alignments and I assume by
this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's
proteins in the evidence set that you provided to Maker.  If you haven't
provided these proteins as evidence to maker then you should do this.  You
can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but
still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta
and blast them directly against your closely related proteins.  Presumably
they don't hit too well because if they did they should have been promoted
to predictions by Maker the first time, but here you can decide yourself
what thresholds to allow to keep the abinit predictions that hit the closely
related species proteins.  If you filter you blast hits the way you want and
keep the names of the abinit predictions that pass your filter, then use the
script Carson attached it it will generate a abinit precidtion GFF file with
only the predictions you selected.  You can then pass those predictions back
to Maker and force it to keep them and Maker will turn them from predictions
(match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> To:  <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by
>> MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly on
>> the assembly and augustus with a model from a less closely related species),
>> along with a set of fungal proteins. I am missing ~ 1000 proteins when I
>> compare to the species i used EST data from, and there is good evidence from
>> alignments that these genes exist. The question is how to proceed from Blast
>> hits to actual gene models here. The idea would be to add these genes to the
>> existing dataset, rather than reannotate the genome. I believe that
>> reannotating it without any further evidence such as RNA-seq from the species
>> itself would not change much,and i d rather stick with actual predictions
>> that i trust and have used in subsequent analyses. The 1000 genes I can
>> accept to annotate with a less stringent and reliable way than MAKER, I just
>> want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy
>> annotations scheme to do it, by providing GFF3 of the alignments between the
>> two species in the regions where genes were missed, but as i said, I would
>> not like to reannotate the whole genome, and running MAKER2 might cause
>> slight changes that i d like to avoid. Is this possible? First, is it
>> possible to provide a Gff3 file of specific locations and not the entire
>> genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models only?
>> How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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






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From james.collett at pnnl.gov  Fri Apr 27 10:51:05 2012
From: james.collett at pnnl.gov (Collett, James R)
Date: Fri, 27 Apr 2012 09:51:05 -0700
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>

Hi Carson,

Could you please send me (or make available for download) the perl script that you mentioned in this previous post in this thread?

>> Attached is a 
>> script that would make selecting those easier.  It take the MAKER 
>> generated GFF3 and a list of predictions to keep (one name per line).  
>> These might be the results of a BLAST analysis for example.  It will 
>> then return the GFF3 entries for just those models selected.

Thanks,

Jim
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory

> -----Original Message-----
> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
> lab.org
> Sent: Friday, April 27, 2012 6:48 AM
> To: maker-devel at yandell-lab.org
> Subject: maker-devel Digest, Vol 47, Issue 14
> 
> Send maker-devel mailing list submissions to
> 	maker-devel at yandell-lab.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.org
> 
> or, via email, send a message with subject or body 'help' to
> 	maker-devel-request at yandell-lab.org
> 
> You can reach the person managing the list at
> 	maker-devel-owner at yandell-lab.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of maker-devel digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Use pass-through system to add missing genes (Carson Holt)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 27 Apr 2012 09:27:24 -0400
> From: Carson Holt <carsonhh at gmail.com>
> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
> 	<anastasia.gioti at scilifelab.se>
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] Use pass-through system to add missing
> 	genes
> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> 
> The only way you should be able to get BLASTX overlap and still not get
> a model for the region is if 1.  The protein alignment in in a
> different reading frame then your models for every single base pair of
> the alignment (in which case it's not true overlap).  2. The BLASTX
> HSPs are stacked on each other again and again in weird rearranged
> overlaps to produce a very deep alignment which would mean this is a
> repetitive region and is not really a significant alignment.  Otherwise
> this should not happen unless you have the AED_threshold set to some
> value where MAKER will ignore genes unless they have a minimum amount
> of support (by default this option is always off).  The other two
> possibilities can be tested by just looking at the alignments manually
> in Apollo.  Also take a look at the AED and eAED values for your
> missing genes.  Anything below 1 should always be kept by MAKER by
> default because it has at least some evidence supported.
> 
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> 
> If they are already in your current run ignore this.
> 
> Barry provided detailed instructions on how to configure MAKER, for
> your particular case.  So just follow his excellent instructions.
> 
> Thanks,
> Carson
> 
> 
> 
> From:  Barry Moore <barry.moore at genetics.utah.edu>
> Date:  Friday, 27 April, 2012 7:57 AM
> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Use pass-through system to add missing
> genes
> 
> Hi Anastasia,
> 
> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
> 
> > Hi Carlson,
> > Thanks for your help!
> >
> >> The way you proceed depends on why the genes are not there to begin
> with.
> >> Are they not there because of a lack of evidence?
> >
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> >
> 
> This doesn't sound right.  If there are predicted models and blastx
> protein evidence overlapping them you should get a model retained.  I
> know for the EST evidence that it has to support a splice site before
> it will be promoted and I can't remember if protein evidence is the
> same but certainly if you pass back those protein2genome predictions
> and the original proteins as evidence then they will be retained as
> models.
> 
> >> If that's the case just adding the new fasta file should do the
> trick.
> >
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> >
> 
> Yes using the protein fasta from the closely related species as
> evidence.  I think you said you've already done that right?
> 
> 
> >> Or are they not there because an assembly error makes it impossible
> >> to get a logical model for the region (I.e reading frame breaks).
> >
> > This is not the case in general.
> >
> >> Are there ab initio models already called in those regions that
> could
> >> just be promoted to the annotation tier?  You can test that one by
> >> blasting against the nonoverlaping_abinits.fasta files.
> >
> > I have not done this, will do!
> >
> >>
> >> For any of the cases described, you can provide the existing
> >> annotation set as the input in GFF3 format, and previous models will
> >> be maintained preferentially.
> >
> > You mean in a new maker run? is this possible with the old maker as
> > well, not maker2, right?
> >
> 
> Yes, the original MAKER will do this.
> 
> 
> >> If you know which ab initio predictions you want to add (I.e. the ab
> >> initio promoting scenario I descibed), you can provide those
> >> predictions to the use the pred_gff option and then set keep_preds=1
> >> and they will be maintained even without evidence.  Attached is a
> >> script that would make selecting those easier.  It take the MAKER
> >> generated GFF3 and a list of predictions to keep (one name per
> line).
> >> These might be the results of a BLAST analysis for example.  It will
> >> then return the GFF3 entries for just those models selected.
> >
> > The thing is, for the few cases I have looked at, I cannot really
> > decide which model is the best, and the 3 models from the ab initio
> > predictors do not agree on the exact intron-exon junctions or the
> start and stop codons.
> >>
> >> If the situation is more complex, just provide more detail, and I am
> >> sure we can help you come up with a plan.
> >>
> > What i was thinking to do was to provide a gff file of alignments (eg
> > by
> > exonerate) to the proteins of the closely related species that i am
> > missing, and somehow keep the previous annotations and get the extra
> > ones by this gff file. But how exactly maker should be run to do this
> > I am not sure. if I want to keep the previous annotations I  need the
> > gff file of the last maker run as input, but then how do I
> > discriminate with the exonerate gff file? And which mode of rediction
> > should be on, and with which parameters? You mention
> > keep_preds=1  for the existing annotations, but how do i also promote
> > evidence from alignments on the same way in the same run?
> > Looks feasible though. Thanks again,
> > Anastasia
> >
> 
> Let me just restate what you've said so that I can be sure that I am
> correct about what you've already done.  You have run Maker with SNAP,
> Genemark and Augustus using EST from a closely related species (passed
> to altest) and protein evidence from other fungi.  You are missing
> about 1,000 genes compared to the species that provided the EST
> alignments.  You say their is good evidence that these genes exist from
> the alignments and I assume by this that you mean the EST/protein
> alignments that Maker produced.
> 
> 1) Is the closely related fungus annotated and if so have you included
> it's proteins in the evidence set that you provided to Maker.  If you
> haven't provided these proteins as evidence to maker then you should do
> this.  You can re-run maker passing your original models back through
> like this:
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
> 
> #-----Protein Homology Evidence (for best results provide a file for at
> least one) protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
> 
> 2) If you've already included those closely related species proteins
> but still didn't get the 1,000 genes, then take your
> nonoverlaping_abinits.fasta and blast them directly against your
> closely related proteins.  Presumably they don't hit too well because
> if they did they should have been promoted to predictions by Maker the
> first time, but here you can decide yourself what thresholds to allow
> to keep the abinit predictions that hit the closely related species
> proteins.  If you filter you blast hits the way you want and keep the
> names of the abinit predictions that pass your filter, then use the
> script Carson attached it it will generate a abinit precidtion GFF file
> with only the predictions you selected.  You can then pass those
> predictions back to Maker and force it to keep them and Maker will turn
> them from predictions
> (match/match_part) into gene models.
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
> 
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
> 
> keep_preds=1
> 
> Barry
> 
> >> Thanks,
> >> Carson
> >>
> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
> >> To:  <maker-devel at yandell-lab.org>
> >> Subject:  [maker-devel] Use pass-through system to add missing genes
> >>
> >> Hi,
> >> I  have a set of predicted proteins from the genome of a fungus
> >> annotated by MAKER  using EST data from a closely related species
> and
> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
> >> trained directly on the assembly and augustus with a model from a
> >> less closely related species), along with a set of fungal proteins.
> I
> >> am missing ~ 1000 proteins when I compare to the species i used EST
> >> data from, and there is good evidence from alignments that these
> >> genes exist. The question is how to proceed from Blast hits to
> actual
> >> gene models here. The idea would be to add these genes to the
> >> existing dataset, rather than reannotate the genome. I believe that
> >> reannotating it without any further evidence such as RNA-seq from
> the
> >> species itself would not change much,and i d rather stick with
> actual
> >> predictions that i trust and have used in subsequent analyses. The
> >> 1000 genes I can accept to annotate with a less stringent and
> reliable way than MAKER, I just want to add them so that the difference
> in gene count gets corrected.
> >> I was reading the MAKER 2 paper and i was wondering if I can use the
> >> legacy annotations scheme to do it, by providing GFF3 of the
> >> alignments between the two species in the regions where genes were
> >> missed, but as i said, I would not like to reannotate the whole
> >> genome, and running MAKER2 might cause slight changes that i d like
> >> to avoid. Is this possible? First, is it possible to provide a Gff3
> >> file of specific locations and not the entire genome alignment? (I
> >> guess so..) Second, how can I tag the existing annotations as 'not
> to be changed' or alternatively, tag the new models only?
> >> How should I run maker2, with which predictors on and which off?
> >> Thanks,
> >> Anastasia
> >>
> >> Anastasia Gioti
> >> Post-doctoral Researcher
> >>
> >> anastasia.gioti at scilifelab.se
> >> anastasia.gioti at ebc.uu.se
> >>
> >>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
> >> /
> >>
> >>
> >>
> >> _______________________________________________ maker-devel mailing
> >> list
> >> maker-
> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
> >> tinfo/ma
> >> ker-devel_yandell-lab.org
> >> <gff3_select>
> >
> > Anastasia Gioti
> > Post-doctoral Researcher
> >
> > anastasia.gioti at scilifelab.se
> > anastasia.gioti at ebc.uu.se
> >
> >
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> >
> >
> >
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.or
> > g
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
> 
> 
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> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
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> 
> 
> End of maker-devel Digest, Vol 47, Issue 14
> *******************************************



From carsonhh at gmail.com  Fri Apr 27 11:18:23 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 13:18:23 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>
Message-ID: <CBC04C5D.BF73%carsonhh@gmail.com>

Here you go.  This will also be part of the next MAKER release in some
form.

Thanks,
Carson



On 12-04-27 12:51 PM, "Collett, James R" <james.collett at pnnl.gov> wrote:

>Hi Carson,
>
>Could you please send me (or make available for download) the perl script
>that you mentioned in this previous post in this thread?
>
>>> Attached is a 
>>> script that would make selecting those easier.  It take the MAKER
>>> generated GFF3 and a list of predictions to keep (one name per line).
>>> These might be the results of a BLAST analysis for example.  It will
>>> then return the GFF3 entries for just those models selected.
>
>Thanks,
>
>Jim
>__________________________________________________
>James R. Collett, Ph.D.
>Senior Scientist
>Chemical and Biological Process Development Group
>Energy and Environment Directorate
>Pacific Northwest National Laboratory
>
>> -----Original Message-----
>> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
>> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
>> lab.org
>> Sent: Friday, April 27, 2012 6:48 AM
>> To: maker-devel at yandell-lab.org
>> Subject: maker-devel Digest, Vol 47, Issue 14
>> 
>> Send maker-devel mailing list submissions to
>> 	maker-devel at yandell-lab.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.org
>> 
>> or, via email, send a message with subject or body 'help' to
>> 	maker-devel-request at yandell-lab.org
>> 
>> You can reach the person managing the list at
>> 	maker-devel-owner at yandell-lab.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of maker-devel digest..."
>> 
>> 
>> Today's Topics:
>> 
>>    1. Re: Use pass-through system to add missing genes (Carson Holt)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Fri, 27 Apr 2012 09:27:24 -0400
>> From: Carson Holt <carsonhh at gmail.com>
>> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
>> 	<anastasia.gioti at scilifelab.se>
>> Cc: maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] Use pass-through system to add missing
>> 	genes
>> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> 
>> The only way you should be able to get BLASTX overlap and still not get
>> a model for the region is if 1.  The protein alignment in in a
>> different reading frame then your models for every single base pair of
>> the alignment (in which case it's not true overlap).  2. The BLASTX
>> HSPs are stacked on each other again and again in weird rearranged
>> overlaps to produce a very deep alignment which would mean this is a
>> repetitive region and is not really a significant alignment.  Otherwise
>> this should not happen unless you have the AED_threshold set to some
>> value where MAKER will ignore genes unless they have a minimum amount
>> of support (by default this option is always off).  The other two
>> possibilities can be tested by just looking at the alignments manually
>> in Apollo.  Also take a look at the AED and eAED values for your
>> missing genes.  Anything below 1 should always be kept by MAKER by
>> default because it has at least some evidence supported.
>> 
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> 
>> If they are already in your current run ignore this.
>> 
>> Barry provided detailed instructions on how to configure MAKER, for
>> your particular case.  So just follow his excellent instructions.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Barry Moore <barry.moore at genetics.utah.edu>
>> Date:  Friday, 27 April, 2012 7:57 AM
>> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
>> Subject:  Re: [maker-devel] Use pass-through system to add missing
>> genes
>> 
>> Hi Anastasia,
>> 
>> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
>> 
>> > Hi Carlson,
>> > Thanks for your help!
>> >
>> >> The way you proceed depends on why the genes are not there to begin
>> with.
>> >> Are they not there because of a lack of evidence?
>> >
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> >
>> 
>> This doesn't sound right.  If there are predicted models and blastx
>> protein evidence overlapping them you should get a model retained.  I
>> know for the EST evidence that it has to support a splice site before
>> it will be promoted and I can't remember if protein evidence is the
>> same but certainly if you pass back those protein2genome predictions
>> and the original proteins as evidence then they will be retained as
>> models.
>> 
>> >> If that's the case just adding the new fasta file should do the
>> trick.
>> >
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> >
>> 
>> Yes using the protein fasta from the closely related species as
>> evidence.  I think you said you've already done that right?
>> 
>> 
>> >> Or are they not there because an assembly error makes it impossible
>> >> to get a logical model for the region (I.e reading frame breaks).
>> >
>> > This is not the case in general.
>> >
>> >> Are there ab initio models already called in those regions that
>> could
>> >> just be promoted to the annotation tier?  You can test that one by
>> >> blasting against the nonoverlaping_abinits.fasta files.
>> >
>> > I have not done this, will do!
>> >
>> >>
>> >> For any of the cases described, you can provide the existing
>> >> annotation set as the input in GFF3 format, and previous models will
>> >> be maintained preferentially.
>> >
>> > You mean in a new maker run? is this possible with the old maker as
>> > well, not maker2, right?
>> >
>> 
>> Yes, the original MAKER will do this.
>> 
>> 
>> >> If you know which ab initio predictions you want to add (I.e. the ab
>> >> initio promoting scenario I descibed), you can provide those
>> >> predictions to the use the pred_gff option and then set keep_preds=1
>> >> and they will be maintained even without evidence.  Attached is a
>> >> script that would make selecting those easier.  It take the MAKER
>> >> generated GFF3 and a list of predictions to keep (one name per
>> line).
>> >> These might be the results of a BLAST analysis for example.  It will
>> >> then return the GFF3 entries for just those models selected.
>> >
>> > The thing is, for the few cases I have looked at, I cannot really
>> > decide which model is the best, and the 3 models from the ab initio
>> > predictors do not agree on the exact intron-exon junctions or the
>> start and stop codons.
>> >>
>> >> If the situation is more complex, just provide more detail, and I am
>> >> sure we can help you come up with a plan.
>> >>
>> > What i was thinking to do was to provide a gff file of alignments (eg
>> > by
>> > exonerate) to the proteins of the closely related species that i am
>> > missing, and somehow keep the previous annotations and get the extra
>> > ones by this gff file. But how exactly maker should be run to do this
>> > I am not sure. if I want to keep the previous annotations I  need the
>> > gff file of the last maker run as input, but then how do I
>> > discriminate with the exonerate gff file? And which mode of rediction
>> > should be on, and with which parameters? You mention
>> > keep_preds=1  for the existing annotations, but how do i also promote
>> > evidence from alignments on the same way in the same run?
>> > Looks feasible though. Thanks again,
>> > Anastasia
>> >
>> 
>> Let me just restate what you've said so that I can be sure that I am
>> correct about what you've already done.  You have run Maker with SNAP,
>> Genemark and Augustus using EST from a closely related species (passed
>> to altest) and protein evidence from other fungi.  You are missing
>> about 1,000 genes compared to the species that provided the EST
>> alignments.  You say their is good evidence that these genes exist from
>> the alignments and I assume by this that you mean the EST/protein
>> alignments that Maker produced.
>> 
>> 1) Is the closely related fungus annotated and if so have you included
>> it's proteins in the evidence set that you provided to Maker.  If you
>> haven't provided these proteins as evidence to maker then you should do
>> this.  You can re-run maker passing your original models back through
>> like this:
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=1
>> other_pass=1
>> 
>> #-----Protein Homology Evidence (for best results provide a file for at
>> least one) protein=proteins_from_closely_related.fasta
>> ## OR it sounds like you've already aligned these with exonerate?
>> protein_gff=proteins_from_closely_related_already_aligned.gff
>> 
>> 2) If you've already included those closely related species proteins
>> but still didn't get the 1,000 genes, then take your
>> nonoverlaping_abinits.fasta and blast them directly against your
>> closely related proteins.  Presumably they don't hit too well because
>> if they did they should have been promoted to predictions by Maker the
>> first time, but here you can decide yourself what thresholds to allow
>> to keep the abinit predictions that hit the closely related species
>> proteins.  If you filter you blast hits the way you want and keep the
>> names of the abinit predictions that pass your filter, then use the
>> script Carson attached it it will generate a abinit precidtion GFF file
>> with only the predictions you selected.  You can then pass those
>> predictions back to Maker and force it to keep them and Maker will turn
>> them from predictions
>> (match/match_part) into gene models.
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=0
>> other_pass=1
>> 
>> #-----Gene Prediction
>> snaphmm=
>> gmhmm=
>> augustus_species=
>> fgenesh_par_file=
>> pred_gff=ab_init_predictions_rescued_by_blast.gff
>> 
>> keep_preds=1
>> 
>> Barry
>> 
>> >> Thanks,
>> >> Carson
>> >>
>> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> >> To:  <maker-devel at yandell-lab.org>
>> >> Subject:  [maker-devel] Use pass-through system to add missing genes
>> >>
>> >> Hi,
>> >> I  have a set of predicted proteins from the genome of a fungus
>> >> annotated by MAKER  using EST data from a closely related species
>> and
>> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
>> >> trained directly on the assembly and augustus with a model from a
>> >> less closely related species), along with a set of fungal proteins.
>> I
>> >> am missing ~ 1000 proteins when I compare to the species i used EST
>> >> data from, and there is good evidence from alignments that these
>> >> genes exist. The question is how to proceed from Blast hits to
>> actual
>> >> gene models here. The idea would be to add these genes to the
>> >> existing dataset, rather than reannotate the genome. I believe that
>> >> reannotating it without any further evidence such as RNA-seq from
>> the
>> >> species itself would not change much,and i d rather stick with
>> actual
>> >> predictions that i trust and have used in subsequent analyses. The
>> >> 1000 genes I can accept to annotate with a less stringent and
>> reliable way than MAKER, I just want to add them so that the difference
>> in gene count gets corrected.
>> >> I was reading the MAKER 2 paper and i was wondering if I can use the
>> >> legacy annotations scheme to do it, by providing GFF3 of the
>> >> alignments between the two species in the regions where genes were
>> >> missed, but as i said, I would not like to reannotate the whole
>> >> genome, and running MAKER2 might cause slight changes that i d like
>> >> to avoid. Is this possible? First, is it possible to provide a Gff3
>> >> file of specific locations and not the entire genome alignment? (I
>> >> guess so..) Second, how can I tag the existing annotations as 'not
>> to be changed' or alternatively, tag the new models only?
>> >> How should I run maker2, with which predictors on and which off?
>> >> Thanks,
>> >> Anastasia
>> >>
>> >> Anastasia Gioti
>> >> Post-doctoral Researcher
>> >>
>> >> anastasia.gioti at scilifelab.se
>> >> anastasia.gioti at ebc.uu.se
>> >>
>> >>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
>> >> /
>> >>
>> >>
>> >>
>> >> _______________________________________________ maker-devel mailing
>> >> list
>> >> maker-
>> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
>> >> tinfo/ma
>> >> ker-devel_yandell-lab.org
>> >> <gff3_select>
>> >
>> > Anastasia Gioti
>> > Post-doctoral Researcher
>> >
>> > anastasia.gioti at scilifelab.se
>> > anastasia.gioti at ebc.uu.se
>> >
>> >
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> >
>> >
>> >
>> > _______________________________________________
>> > maker-devel mailing list
>> > maker-devel at box290.bluehost.com
>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.or
>> > g
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
>> ------------------------------
>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> End of maker-devel Digest, Vol 47, Issue 14
>> *******************************************
>
>_______________________________________________
>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 weckalba at asu.edu  Tue Apr  3 17:28:28 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 3 Apr 2012 16:28:28 -0700
Subject: [maker-devel] gff3_preds2models usage question
Message-ID: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a
few issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
 I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
chado yet, and it does not appear trivial.

Thanks for the help,

Walter
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From ranjani at uga.edu  Tue Apr  3 20:24:49 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Wed, 4 Apr 2012 02:24:49 +0000
Subject: [maker-devel] mRNA-seq data
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>

Hi,



I am using to MAKER to annotate a genome and I would like a couple of clarifications.



In the previous version of MAKER, under EST_evidence in maker_opts. ctl the user could input est and est_reads- the mRNAseq reads (although this was not fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation quality.

I have assembled transcriptome data from Sanger,454 and Illumina



Do I just provide all this data in a fasta file format to the 'est' option? Is this is the best way to provide the mRNA-seq evidence?Will this assure the mRNA-seq data is used to improve the annotations?



Thanks!



Ranjani
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From carsonhh at gmail.com  Tue Apr  3 20:39:02 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 03 Apr 2012 22:39:02 -0400
Subject: [maker-devel] mRNA-seq data
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>
Message-ID: <CBA12B6C.AA4A%carsonhh@gmail.com>

Yes.  If you have them in fasta format, just provide them to the est= option
and let MAEKR align them with exonerate.  If you used something like
cufflinks or trinity, to process them you can provide them to the est_gff
option (MAKER comes with a cufflinks2gff3 converter to make that easy).

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Wed, 4 Apr 2012 02:24:49 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mRNA-seq data

Hi,

 

I am using to MAKER to annotate a genome and I would like a couple of
clarifications.

 

In the previous version of MAKER, under EST_evidence in maker_opts. ctl the
user could input est and est_reads- the mRNAseq reads (although this was not
fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation
quality.

I have assembled transcriptome data from Sanger,454 and Illumina

 

Do I just provide all this data in a fasta file format to the 'est' option?
Is this is the best way to provide the mRNA-seq evidence?Will this assure
the mRNA-seq data is used to improve the annotations?

 

Thanks!

 

Ranjani
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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 pingouinandsheep at gmail.com  Thu Apr  5 08:14:39 2012
From: pingouinandsheep at gmail.com (pingouinandsheep at gmail.com)
Date: Thu, 5 Apr 2012 07:14:39 -0700 (PDT)
Subject: [maker-devel] Huge memory usage
Message-ID: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>

Hello,

When I try to run the test provided with maker2, maker start to use a
huge amount of memory. I stoped it after it reach ~100go of memory
used. I believe the test should not use that amount of memory.

In an other message someone suggest that the bioperl version installed
could be the cause of the problem, but the bioperl installed on my
cluster is already at version 1.6.

perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006901

Unfortunately I don't have an error message to provide, that could
clarify my problem.

But maybe it is a recurrent problem and you know a few things I should
check.

Thanks,

Ismael



From carsonhh at gmail.com  Thu Apr  5 08:26:17 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 05 Apr 2012 10:26:17 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>
Message-ID: <CBA321AA.AB7A%carsonhh@gmail.com>

The test should not use up more then a few megabytes of RAM.  Even on very
large datasets you should never really use more that 1 or 2 gig of RAM
perl MAKER instance

It's possible that their may be other perl modules that are broken need to
be reinstalled on your system.  This can happen when perl gets updated,
but you are pointing to modules built for a different perl version with
the PERL5LIB environmental variable.  Make sure you you have the latest
version of MAKER and run with --debug set.  Collect that output and send
it to me (the --debug option does some dependancy checking).

I know there is an issue on Macs with updating perl's DB_File module that
causes it to gobble up big sections of the hard drive (it will eventually
fill the drive if you let it).  It's not a memory issue but just one
example of how broken modules can cause weird behavior.

Thanks,
Carson




On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
<pingouinandsheep at gmail.com> wrote:

>Hello,
>
>When I try to run the test provided with maker2, maker start to use a
>huge amount of memory. I stoped it after it reach ~100go of memory
>used. I believe the test should not use that amount of memory.
>
>In an other message someone suggest that the bioperl version installed
>could be the cause of the problem, but the bioperl installed on my
>cluster is already at version 1.6.
>
>perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>1.006901
>
>Unfortunately I don't have an error message to provide, that could
>clarify my problem.
>
>But maybe it is a recurrent problem and you know a few things I should
>check.
>
>Thanks,
>
>Ismael
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From eernst at cshl.edu  Sun Apr  8 16:09:22 2012
From: eernst at cshl.edu (Evan Ernst)
Date: Sun, 8 Apr 2012 18:09:22 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log under
	openMPI
Message-ID: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker
instances, each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no
actual processing is required apart from marking the scaffolds FINISHED.
Comparing the result to a single, non-MPI maker instance running on the
same completed hierarchy reveals that many entries aren't being written to
the log at all when running under MPI. The single process instance runs
just fine, generating a complete log that can be used for the downstream
scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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From carsonhh at gmail.com  Tue Apr 10 08:26:40 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 10 Apr 2012 10:26:40 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log
 under openMPI
In-Reply-To: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>
Message-ID: <CBA9B62E.AE4E%carsonhh@gmail.com>

Depending on if your using NFS and other architecture design you can get
race conditions with the datastore log file.  This primarily happens when
you have multiple instances of MAKER running at the same time or thousands
of short contigs running in parallel so many finish at the same time.  In a
future release, I plan on having the last MAKER job to exit just rebuild the
log at the end of a run to ensure it is complete. For now though, just run
'maker -dsindex' at the end of a run when it happens.  It will rebbuild the
log and only takes a few seconds.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Sun, 8 Apr 2012 18:09:22 -0400
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Incomplete/Missing lines in datastore index log
under openMPI

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker instances,
each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no actual
processing is required apart from marking the scaffolds FINISHED. Comparing
the result to a single, non-MPI maker instance running on the same completed
hierarchy reveals that many entries aren't being written to the log at all
when running under MPI. The single process instance runs just fine,
generating a complete log that can be used for the downstream scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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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 smg283 at gmail.com  Fri Apr 13 13:00:29 2012
From: smg283 at gmail.com (Scott Geib)
Date: Fri, 13 Apr 2012 09:00:29 -1000
Subject: [maker-devel] mpi issue on computing cluster
Message-ID: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>

Hi,
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first,

Thanks
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From sbrubaker at solazyme.com  Fri Apr 13 14:12:24 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 20:12:24 +0000
Subject: [maker-devel] Functional annotation pipeline
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>

Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane



From joseph.fass at gmail.com  Fri Apr 13 14:42:51 2012
From: joseph.fass at gmail.com (Joseph Fass)
Date: Fri, 13 Apr 2012 13:42:51 -0700
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
References: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
Message-ID: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:

> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
>
> Thanks,
> Shane
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)
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From carsonhh at gmail.com  Fri Apr 13 13:51:38 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 15:51:38 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <CADNSSgBwH1-wbqpC3_EC+92yzLoi-f5CVwMVaewV=xCK3qkPaA@mail.gmail.com>
Message-ID: <CBADFB12.B16B%carsonhh@gmail.com>

You can pre-mask the genome, convert the RepaetMasker results to GFF3 and
pass them in, or just run the ./configure script in the RepeatMasker
directory to configure wublast to be the default.

You can also let MAKER install it's own separate installation of
RepeatMasker using rmblast.  Just go to the maker/src/ directory and run
this command --> ./Build repeatmasker

MAKER will use that installation preferentially if you let it install that.

Thanks,
Carson

From:  padioleau isma?l <ismpadioleau at gmail.com>
Date:  Fri, 13 Apr 2012 17:42:20 +0200
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Huge memory usage

Dear Carson,

I have a problem with RepeatMasker on my cluster. It work with wublast but
not with Crossmatch. As maker try to run RepeatMasker with default I can not
successfully run maker.

I wanted to know if I can provide to maker the genome already masked (if I
run with wublast externally), I though it was possible but I can't found in
the configuration files where I should provide it i.e : In maker_opts.ctl,
should I provide the result from RepeatMasker to 'genome_gff:' and set
'rm_pass' to 1, or set rm_gff in the 'Repeat Masking' part of the file?
Or maybe I should provide directly the masked fasta as genome reference.

An other solution could be to ask maker to run RepeatMasker with the option
'-e wublast'.

Is it possible to use one of these solutions?

Thanks,

Ismael

2012/4/5 padioleau isma?l <ismpadioleau at gmail.com>
> Dear Carson,
> 
> Thank you for your very quick answering.
> 
> I realised that I missed some error messages and the problem seems to be
> linked to the DB_file package as you suggested. The person in charge of
> installation told me that he will recover the configuration.
> 
> I will test it after the Easter weekend and come back to you if we have other
> issues.
> 
> Have a nice Easter weekend,
> 
> Ismael
> 
> Here Is the error message:
> Use of uninitialized value $DB_File::db_version in numeric ge (>=) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 276.
> Use of uninitialized value $DB_File::db_version in numeric gt (>) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 280.
> Deep recursion on subroutine "DB_File::AUTOLOAD" at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 235.
> 
> 
> 
> 2012/4/5 Carson Holt <carsonhh at gmail.com>
>> The test should not use up more then a few megabytes of RAM.  Even on very
>> large datasets you should never really use more that 1 or 2 gig of RAM
>> perl MAKER instance
>> 
>> It's possible that their may be other perl modules that are broken need to
>> be reinstalled on your system.  This can happen when perl gets updated,
>> but you are pointing to modules built for a different perl version with
>> the PERL5LIB environmental variable.  Make sure you you have the latest
>> version of MAKER and run with --debug set.  Collect that output and send
>> it to me (the --debug option does some dependancy checking).
>> 
>> I know there is an issue on Macs with updating perl's DB_File module that
>> causes it to gobble up big sections of the hard drive (it will eventually
>> fill the drive if you let it).  It's not a memory issue but just one
>> example of how broken modules can cause weird behavior.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> 
>> On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
>> <pingouinandsheep at gmail.com> wrote:
>> 
>>> >Hello,
>>> >
>>> >When I try to run the test provided with maker2, maker start to use a
>>> >huge amount of memory. I stoped it after it reach ~100go of memory
>>> >used. I believe the test should not use that amount of memory.
>>> >
>>> >In an other message someone suggest that the bioperl version installed
>>> >could be the cause of the problem, but the bioperl installed on my
>>> >cluster is already at version 1.6.
>>> >
>>> >perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>>> >1.006901
>>> >
>>> >Unfortunately I don't have an error message to provide, that could
>>> >clarify my problem.
>>> >
>>> >But maybe it is a recurrent problem and you know a few things I should
>>> >check.
>>> >
>>> >Thanks,
>>> >
>>> >Ismael
>>> >
>>> >_______________________________________________
>>> >maker-devel mailing list
>>> >maker-devel at box290.bluehost.com
>>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> 
> -- 
> Isma?l Padioleau
> Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
> Emmanouil Dermitzakis Group
> Dpt de M?decine G?n?tique et D?veloppement
> Universit? de Gen?ve - Facult? de M?decine
> CMU -  Rue Michel-Servet 1
> CH 1211 Gen?ve 4
> Tel: 0041 22 379 59 74
> ismael.padioleau at unige.ch
> 
> --
> Tel. 0041 78 77 69 561
> ismpadioleau at gmail.com



-- 
Isma?l Padioleau
Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
Emmanouil Dermitzakis Group
Dpt de M?decine G?n?tique et D?veloppement
Universit? de Gen?ve - Facult? de M?decine
CMU -  Rue Michel-Servet 1
CH 1211 Gen?ve 4
Tel: 0041 22 379 59 74
ismael.padioleau at unige.ch

--
Tel. 0041 78 77 69 561
ismpadioleau at gmail.com


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From carsonhh at gmail.com  Fri Apr 13 15:02:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 17:02:51 -0400
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
Message-ID: <CBAE0B9F.B1D2%carsonhh@gmail.com>

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
integrate interproscan results in the GFF3 files.  There are also a couple
of scripts maker_functional_gff and maker_functional_fasta that can do
putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From:  Joseph Fass <joseph.fass at gmail.com>
Date:  Fri, 13 Apr 2012 13:42:51 -0700
To:  Shane Brubaker <sbrubaker at solazyme.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>
wrote:
> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
> 
> Thanks,
> Shane
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com <http://gmail.com>  (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ 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 sbrubaker at solazyme.com  Fri Apr 13 15:18:10 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 21:18:10 +0000
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065BBA@EXCHANGE-05.internal.solazyme.com>

Great thank you ... I will take a look at those.

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Friday, April 13, 2012 2:03 PM
To: Joseph Fass; Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Functional annotation pipeline

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files.  There are also a couple of scripts maker_functional_gff and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From: Joseph Fass <joseph.fass at gmail.com<mailto:joseph.fass at gmail.com>>
Date: Fri, 13 Apr 2012 13:42:51 -0700
To: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>> wrote:
Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane

_______________________________________________
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



--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com<http://gmail.com> (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From dsth at ebi.ac.uk  Fri Apr 13 15:22:37 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:22:37 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>

Careful of interproscan atm.. I believe the executable is still in beta and
they definitely aren't recommending it for production use yet. If you do
use it be sure to check output file if using the lookup service as when i
used it recently it would sometimes exit normally despite lookup failures
(the lookup problems may have had something to do with running ~800 in
parallel - they're looking into the issue atm.).

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Carson Holt <carsonhh at gmail.com>

> I would agree blast2go.
>
> You can also try interproscan fro the EBI
>
> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
> integrate interproscan results in the GFF3 files.  There are also a couple
> of scripts maker_functional_gff and maker_functional_fasta that can do
> putative functional annotation using uniprot/swiss-prot.
>
> Thanks,
> Carson
>
>
>
> From: Joseph Fass <joseph.fass at gmail.com>
> Date: Fri, 13 Apr 2012 13:42:51 -0700
> To: Shane Brubaker <sbrubaker at solazyme.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Functional annotation pipeline
>
> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
> HTH,
> ~Joe
>
> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>
>> Hi, can you recommend any open source functional annotation pipelines -
>> to assign function, GO terms, pathways, etc. to gene models?
>>
>> Thanks,
>> Shane
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
> --
> Joseph Fass
> Lead Data Analyst
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From dsth at ebi.ac.uk  Fri Apr 13 15:37:06 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:37:06 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
	<CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
Message-ID: <CAP8X9uKOcovWFAetQTaGgQ6Mpb-rg_8PB5RCkfrhsev6Mx03bQ@mail.gmail.com>

sorry, that's the new version of course.

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Daniel Hughes <dsth at ebi.ac.uk>

> Careful of interproscan atm.. I believe the executable is still in beta
> and they definitely aren't recommending it for production use yet. If you
> do use it be sure to check output file if using the lookup service as when
> i used it recently it would sometimes exit normally despite lookup failures
> (the lookup problems may have had something to do with running ~800 in
> parallel - they're looking into the issue atm.).
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
>
> 2012/4/13 Carson Holt <carsonhh at gmail.com>
>
>> I would agree blast2go.
>>
>> You can also try interproscan fro the EBI
>>
>> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
>> integrate interproscan results in the GFF3 files.  There are also a couple
>> of scripts maker_functional_gff and maker_functional_fasta that can do
>> putative functional annotation using uniprot/swiss-prot.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: Joseph Fass <joseph.fass at gmail.com>
>> Date: Fri, 13 Apr 2012 13:42:51 -0700
>> To: Shane Brubaker <sbrubaker at solazyme.com>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] Functional annotation pipeline
>>
>> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
>> HTH,
>> ~Joe
>>
>> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>>
>>> Hi, can you recommend any open source functional annotation pipelines -
>>> to assign function, GO terms, pathways, etc. to gene models?
>>>
>>> Thanks,
>>> Shane
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>>
>>
>> --
>> Joseph Fass
>> Lead Data Analyst
>> UC Davis Bioinformatics Core
>> joseph.fass -at- gmail.com (professional)
>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
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From kd7gwt at exchange.usfood.com  Sat Apr 14 00:50:28 2012
From: kd7gwt at exchange.usfood.com (Liz Douglas)
Date: Sat, 14 Apr 2012 14:50:28 +0800
Subject: [maker-devel] Incredible effect on your possibilities in bed
Message-ID: <002801cd1a0b$727fe840$5047c36a@SAMrc6umq>

http://sten-stil.dk/require.html Do you wish to satisfy your babe tonight?




From ranjani at uga.edu  Tue Apr 17 10:46:40 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Tue, 17 Apr 2012 16:46:40 +0000
Subject: [maker-devel] MAKER2.23 output
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>

Hi,

I tried running the latest version of Maker 2.23 with my dataset but with out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2 /usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further details

I was able run the previous version of Maker 2.10 successfully with my dataset.

Thanks,
Ranjani


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From carsonhh at gmail.com  Tue Apr 17 10:56:11 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 12:56:11 -0400
Subject: [maker-devel] MAKER2.23 output
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>
Message-ID: <CBB31716.B317%carsonhh@gmail.com>

Segmentation fault means there was a failure with C code.  It was likely in
one of the modules being used.

These are all potential culprits

Inline::C
Proc::ProcessTable
DB_file
forks

Based on when the error occurred.  I would lean more toward DB_File.  Is it
possible that BerkleyDB has been updated on your system, perhaps as part of
another installation or a system update?  That sometimes breaks this module
(which is part of the perl core).

You can try reinstalling that module from CPAN.  Also if you run MAKER
version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug')
to get more information just before the error occurs.  You can then capture
the error log send that to me.

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tue, 17 Apr 2012 16:46:40 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER2.23 output

Hi, 

I tried running the latest version of Maker 2.23 with my dataset but with
out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output
files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2
/usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further
details

I was able run the previous version of Maker 2.10 successfully with my
dataset.

Thanks,
Ranjani


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From carsonhh at gmail.com  Tue Apr 17 11:09:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 13:09:32 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>
Message-ID: <CBB31953.B329%carsonhh@gmail.com>

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    }

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

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

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From carsonhh at gmail.com  Tue Apr 17 14:25:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 16:25:51 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CBB31953.B329%carsonhh@gmail.com>
Message-ID: <CBB349BE.B364%carsonhh@gmail.com>

Sorry missed the ';' at the end of the eval block.

Should be this -->

    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


--Carson

From:  Carson Holt <carsonhh at gmail.com>
Date:  Tue, 17 Apr 2012 13:09:32 -0400
To:  Scott Geib <smg283 at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] mpi issue on computing cluster

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

Thanks
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From elzedliu at gmail.com  Tue Apr 17 17:22:53 2012
From: elzedliu at gmail.com (Huanle)
Date: Tue, 17 Apr 2012 16:22:53 -0700 (PDT)
Subject: [maker-devel] gene predictors in MARKER
Message-ID: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>

I am using MAKER to annotate a recently assembled plant genome.
Hi There,

I am using MAKER to annotate a recently assembled plant genome.

I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial

The denovo gene predictors i included in the maker_exe.ctl file are
#-----Ab-initio Gene Prediction Algorithms
snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
augustus executable

However, I am not sure whether they were really used.

During the running, i could see repeatmasker, exonerate and wublast
were called. But i did see any information popped up for those gene
predictors.

So i am wondering if they were actually used.

Could you please let me know how to know if all or one of those gene
predictors were called by marker?

Kind Regards,
Huanle



From carsonhh at gmail.com  Mon Apr 23 15:04:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 23 Apr 2012 17:04:16 -0400
Subject: [maker-devel] gene predictors in MARKER
In-Reply-To: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>
Message-ID: <CBBB3AB1.BC17%carsonhh@gmail.com>

The gene predictors have to be trained first, and when they are trained
they produce an HMM file that can be supplied to MAKER.  You can either
use MAKER's protein2genome option or est2genome option to produce rough
models to train with, or you can try one of the models that come
prepackaged with those algorithms.

SNAP models will be in --> /sw/maker/2.10/bin/../exe/snap/HMM
Augustus --> run this to see species in augustus -->
/sw/maker/2.10/bin/../exe/augustus/bin/augustus --species=help
GeneMark is self training.  Run it one directly on your genome fasta or
for speed just a chromosome or two of the assembly and it will produce a
file called es.mod as part of it's results.  That is the file you need.

If you have any questions or issues with training just let us know.

Thanks,
Carson



On 12-04-17 7:22 PM, "Huanle" <elzedliu at gmail.com> wrote:

>I am using MAKER to annotate a recently assembled plant genome.
>Hi There,
>
>I am using MAKER to annotate a recently assembled plant genome.
>
>I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial
>
>The denovo gene predictors i included in the maker_exe.ctl file are
>#-----Ab-initio Gene Prediction Algorithms
>snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
>gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
>genemark executable
>gmhmmp= #location of prokaryotic genemark executable
>augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
>augustus executable
>
>However, I am not sure whether they were really used.
>
>During the running, i could see repeatmasker, exonerate and wublast
>were called. But i did see any information popped up for those gene
>predictors.
>
>So i am wondering if they were actually used.
>
>Could you please let me know how to know if all or one of those gene
>predictors were called by marker?
>
>Kind Regards,
>Huanle
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From anastasia.gioti at scilifelab.se  Wed Apr 25 03:09:36 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:09:36 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
Message-ID: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:22:03 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:22:03 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>

For cross-species comparisons you might have be better off including the
actual peptide sequences of the other fungi too in the annotation run - I'd
be very surprised if you really did get the same result.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> I  have a set of predicted proteins from the genome of a fungus annotated
> by MAKER  using EST data from a closely related species and 3 ab initio
> predictors  (snap iterativelly trained 3 times, genemark trained directly
> on the assembly and augustus with a model from a less closely related
> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
> when I compare to the species i used EST data from, and there is good
> evidence from alignments that these genes exist. The question is how to
> proceed from Blast hits to actual gene models here. The idea would be to
> add these genes to the existing dataset, rather than reannotate the genome.
> I believe that reannotating it without any further evidence such as RNA-seq
> from the species itself would not change much,and i d rather stick with
> actual predictions that i trust and have used in subsequent analyses. The
> 1000 genes I can accept to annotate with a less stringent and reliable way
> than MAKER, I just want to add them so that the difference in gene count
> gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the
> legacy annotations scheme to do it, by providing GFF3 of the alignments
> between the two species in the regions where genes were missed, but as i
> said, I would not like to reannotate the whole genome, and running MAKER2
> might cause slight changes that i d like to avoid. Is this possible? First,
> is it possible to provide a Gff3 file of specific locations and not the
> entire genome alignment? (I guess so..) Second, how can I tag the existing
> annotations as 'not to be changed' or alternatively, tag the new models
> only? How should I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
> _______________________________________________
> 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 anastasia.gioti at scilifelab.se  Wed Apr 25 03:29:30 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:29:30 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
Message-ID: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>

Hi, 
Do you mean that I should have not include the proteins of the closely related species in my fungal protein fasta file that I used as evidence in MAKER? i do not see why... What I have been trying to do now is further 'bias' the annotations in favor of this species, so as to get the missing genes. Can you explain a bit more whta you mean?
Thanks, 
Anastasia
On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:

> For cross-species comparisons you might have be better off including the actual peptide sequences of the other fungi too in the annotation run - I'd be very surprised if you really did get the same result.
> 
> dan.
> 
> 
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
> 
> 
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Hi, 
> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
> Thanks, 
> Anastasia
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:39:49 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:39:49 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
	<A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
Message-ID: <CAP8X9u+BvAG8xRqd_DHwdoiFAbWu0nZ0Get-UNkbGrU_qOEHXA@mail.gmail.com>

sorry my bad, i missed the part about you having already included the
fungal proteins as fasta ;/ - too early for me.

in that case have you viewed the full gff output for specific instances of
such missing proteins in something like apollo to try and work out why
maker hasn't made a call at those loci (aed score...)?

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> Do you mean that I should have not include the proteins of the closely
> related species in my fungal protein fasta file that I used as evidence in
> MAKER? i do not see why... What I have been trying to do now is further
> 'bias' the annotations in favor of this species, so as to get the missing
> genes. Can you explain a bit more whta you mean?
> Thanks,
> Anastasia
>
> On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:
>
> For cross-species comparisons you might have be better off including the
> actual peptide sequences of the other fungi too in the annotation run - I'd
> be very surprised if you really did get the same result.
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
>
>> Hi,
>> I  have a set of predicted proteins from the genome of a fungus annotated
>> by MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly
>> on the assembly and augustus with a model from a less closely related
>> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
>> when I compare to the species i used EST data from, and there is good
>> evidence from alignments that these genes exist. The question is how to
>> proceed from Blast hits to actual gene models here. The idea would be to
>> add these genes to the existing dataset, rather than reannotate the genome.
>> I believe that reannotating it without any further evidence such as RNA-seq
>> from the species itself would not change much,and i d rather stick with
>> actual predictions that i trust and have used in subsequent analyses. The
>> 1000 genes I can accept to annotate with a less stringent and reliable way
>> than MAKER, I just want to add them so that the difference in gene count
>> gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the
>> legacy annotations scheme to do it, by providing GFF3 of the alignments
>> between the two species in the regions where genes were missed, but as i
>> said, I would not like to reannotate the whole genome, and running MAKER2
>> might cause slight changes that i d like to avoid. Is this possible? First,
>> is it possible to provide a Gff3 file of specific locations and not the
>> entire genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models
>> only? How should I run maker2, with which predictors on and which off?
>> Thanks,
>> Anastasia
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
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From carsonhh at gmail.com  Wed Apr 25 08:29:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Apr 2012 10:29:01 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CBBD7372.BD57%carsonhh@gmail.com>

The way you proceed depends on why the genes are not there to begin with.
Are they not there because of a lack of evidence?  If that's the case just
adding the new fasta file should do the trick.  Or are they not there
because an assembly error makes it impossible to get a logical model for the
region (I.e reading frame breaks).  Are there ab initio models already
called in those regions that could just be promoted to the annotation tier?
You can test that one by blasting against the nonoverlaping_abinits.fasta
files.

For any of the cases described, you can provide the existing annotation set
as the input in GFF3 format, and previous models will be maintained
preferentially.  If you know which ab initio predictions you want to add
(I.e. the ab initio promoting scenario I descibed), you can provide those
predictions to the use the pred_gff option and then set keep_preds=1 and
they will be maintained even without evidence.  Attached is a script that
would make selecting those easier.  It take the MAKER generated GFF3 and a
list of predictions to keep (one name per line).  These might be the results
of a BLAST analysis for example.  It will then return the GFF3 entries for
just those models selected.

If the situation is more complex, just provide more detail, and I am sure we
can help you come up with a plan.

Thanks,
Carson

From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Date:  Wed, 25 Apr 2012 11:09:36 +0200
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Use pass-through system to add missing genes

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by
MAKER  using EST data from a closely related species and 3 ab initio
predictors  (snap iterativelly trained 3 times, genemark trained directly on
the assembly and augustus with a model from a less closely related species),
along with a set of fungal proteins. I am missing ~ 1000 proteins when I
compare to the species i used EST data from, and there is good evidence from
alignments that these genes exist. The question is how to proceed from Blast
hits to actual gene models here. The idea would be to add these genes to the
existing dataset, rather than reannotate the genome. I believe that
reannotating it without any further evidence such as RNA-seq from the
species itself would not change much,and i d rather stick with actual
predictions that i trust and have used in subsequent analyses. The 1000
genes I can accept to annotate with a less stringent and reliable way than
MAKER, I just want to add them so that the difference in gene count gets
corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy
annotations scheme to do it, by providing GFF3 of the alignments between the
two species in the regions where genes were missed, but as i said, I would
not like to reannotate the whole genome, and running MAKER2 might cause
slight changes that i d like to avoid. Is this possible? First, is it
possible to provide a Gff3 file of specific locations and not the entire
genome alignment? (I guess so..) Second, how can I tag the existing
annotations as 'not to be changed' or alternatively, tag the new models
only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



_______________________________________________ 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 anastasia.gioti at scilifelab.se  Fri Apr 27 02:43:14 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Fri, 27 Apr 2012 10:43:14 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CBBD7372.BD57%carsonhh@gmail.com>
References: <CBBD7372.BD57%carsonhh@gmail.com>
Message-ID: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>

Hi Carlson,
Thanks for your help!

> The way you proceed depends on why the genes are not there to begin  
> with.  Are they not there because of a lack of evidence?

It is a mixture of cases, and I can only look at some examples to say  
that. There are cases where all 3 used ab initio predictors provide  
models, there are blastx hits, or both blastx and protein2 genome, but  
no EST evidence, thus  no model is retained. i guess my default  
parameters could be responsible for these cases at least.

> If that's the case just adding the new fasta file should do the trick.

which fasta do you refer to? The proteins file I use as evidence  
contains all proteins i can actually use.

> Or are they not there because an assembly error makes it impossible  
> to get a logical model for the region (I.e reading frame breaks).

This is not the case in general.

> Are there ab initio models already called in those regions that  
> could just be promoted to the annotation tier?  You can test that  
> one by blasting against the nonoverlaping_abinits.fasta files.

I have not done this, will do!

>
> For any of the cases described, you can provide the existing  
> annotation set as the input in GFF3 format, and previous models will  
> be maintained preferentially.

You mean in a new maker run? is this possible with the old maker as  
well, not maker2, right?

> If you know which ab initio predictions you want to add (I.e. the ab  
> initio promoting scenario I descibed), you can provide those  
> predictions to the use the pred_gff option and then set keep_preds=1  
> and they will be maintained even without evidence.  Attached is a  
> script that would make selecting those easier.  It take the MAKER  
> generated GFF3 and a list of predictions to keep (one name per  
> line).  These might be the results of a BLAST analysis for example.   
> It will then return the GFF3 entries for just those models selected.

The thing is, for the few cases I have looked at, I cannot really  
decide which model is the best, and the 3 models from the ab initio  
predictors do not agree on the exact intron-exon junctions or the  
start and stop codons.
>
> If the situation is more complex, just provide more detail, and I am  
> sure we can help you come up with a plan.
>
What i was thinking to do was to provide a gff file of alignments (eg  
by exonerate) to the proteins of the closely related species that i  
am  missing, and somehow keep the previous annotations and get the  
extra ones by this gff file. But how exactly maker should be run to do  
this I am not sure. if I want to keep the previous annotations I  need  
the gff file of the last maker run as input, but then how do I  
discriminate with the exonerate gff file? And which mode of rediction  
should be on, and with which parameters? You mention keep_preds=1  for  
the existing annotations, but how do i also promote evidence from  
alignments on the same way in the same run?
Looks feasible though. Thanks again,
Anastasia

> Thanks,
> Carson
>
> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Date: Wed, 25 Apr 2012 11:09:36 +0200
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Use pass-through system to add missing genes
>
> Hi,
> I  have a set of predicted proteins from the genome of a fungus  
> annotated by MAKER  using EST data from a closely related species  
> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
> genemark trained directly on the assembly and augustus with a model  
> from a less closely related species), along with a set of fungal  
> proteins. I am missing ~ 1000 proteins when I compare to the species  
> i used EST data from, and there is good evidence from alignments  
> that these genes exist. The question is how to proceed from Blast  
> hits to actual gene models here. The idea would be to add these  
> genes to the existing dataset, rather than reannotate the genome. I  
> believe that reannotating it without any further evidence such as  
> RNA-seq from the species itself would not change much,and i d rather  
> stick with actual predictions that i trust and have used in  
> subsequent analyses. The 1000 genes I can accept to annotate with a  
> less stringent and reliable way than MAKER, I just want to add them  
> so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the  
> legacy annotations scheme to do it, by providing GFF3 of the  
> alignments between the two species in the regions where genes were  
> missed, but as i said, I would not like to reannotate the whole  
> genome, and running MAKER2 might cause slight changes that i d like  
> to avoid. Is this possible? First, is it possible to provide a Gff3  
> file of specific locations and not the entire genome alignment? (I  
> guess so..) Second, how can I tag the existing annotations as 'not  
> to be changed' or alternatively, tag the new models only? How should  
> I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
> _______________________________________________ maker-devel mailing  
> list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> <gff3_select>

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From barry.moore at genetics.utah.edu  Fri Apr 27 05:57:01 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 27 Apr 2012 05:57:01 -0600
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
Message-ID: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.  Are they not there because of a lack of evidence?  
> 
> It is a mixture of cases, and I can only look at some examples to say that. There are cases where all 3 used ab initio predictors provide models, there are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus  no model is retained. i guess my default parameters could be responsible for these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein evidence overlapping them you should get a model retained.  I know for the EST evidence that it has to support a splice site before it will be promoted and I can't remember if protein evidence is the same but certainly if you pass back those protein2genome predictions and the original proteins as evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.  
> 
> which fasta do you refer to? The proteins file I use as evidence contains all proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a logical model for the region (I.e reading frame breaks).  
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be promoted to the annotation tier?  You can test that one by blasting against the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set as the input in GFF3 format, and previous models will be maintained preferentially.  
> 
> You mean in a new maker run? is this possible with the old maker as well, not maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which model is the best, and the 3 models from the ab initio predictors do not agree on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by exonerate) to the proteins of the closely related species that i am  missing, and somehow keep the previous annotations and get the extra ones by this gff file. But how exactly maker should be run to do this I am not sure. if I want to keep the previous annotations I  need the gff file of the last maker run as input, but then how do I discriminate with the exonerate gff file? And which mode of rediction should be on, and with which parameters? You mention keep_preds=1  for the existing annotations, but how do i also promote evidence from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct about what you've already done.  You have run Maker with SNAP, Genemark and Augustus using EST from a closely related species (passed to altest) and protein evidence from other fungi.  You are missing about 1,000 genes compared to the species that provided the EST alignments.  You say their is good evidence that these genes exist from the alignments and I assume by this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's proteins in the evidence set that you provided to Maker.  If you haven't provided these proteins as evidence to maker then you should do this.  You can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta and blast them directly against your closely related proteins.  Presumably they don't hit too well because if they did they should have been promoted to predictions by Maker the first time, but here you can decide yourself what thresholds to allow to keep the abinit predictions that hit the closely related species proteins.  If you filter you blast hits the way you want and keep the names of the abinit predictions that pass your filter, then use the script Carson attached it it will generate a abinit precidtion GFF file with only the predictions you selected.  You can then pass those predictions back to Maker and force it to keep them and Maker will turn them from predictions (match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Fri Apr 27 07:27:24 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 09:27:24 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <CBC01559.BF45%carsonhh@gmail.com>

> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.

The only way you should be able to get BLASTX overlap and still not get a
model for the region is if 1.  The protein alignment in in a different
reading frame then your models for every single base pair of the alignment
(in which case it's not true overlap).  2. The BLASTX HSPs are stacked on
each other again and again in weird rearranged overlaps to produce a very
deep alignment which would mean this is a repetitive region and is not
really a significant alignment.  Otherwise this should not happen unless you
have the AED_threshold set to some value where MAKER will ignore genes
unless they have a minimum amount of support (by default this option is
always off).  The other two possibilities can be tested by just looking at
the alignments manually in Apollo.  Also take a look at the AED and eAED
values for your missing genes.  Anything below 1 should always be kept by
MAKER by default because it has at least some evidence supported.

> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.

If they are already in your current run ignore this.

Barry provided detailed instructions on how to configure MAKER, for your
particular case.  So just follow his excellent instructions.

Thanks,
Carson



From:  Barry Moore <barry.moore at genetics.utah.edu>
Date:  Friday, 27 April, 2012 7:57 AM
To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Use pass-through system to add missing genes

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.
>> Are they not there because of a lack of evidence?
> 
> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein
evidence overlapping them you should get a model retained.  I know for the
EST evidence that it has to support a splice site before it will be promoted
and I can't remember if protein evidence is the same but certainly if you
pass back those protein2genome predictions and the original proteins as
evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.
> 
> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I
think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a
>> logical model for the region (I.e reading frame breaks).
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be
>> promoted to the annotation tier?  You can test that one by blasting against
>> the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set
>> as the input in GFF3 format, and previous models will be maintained
>> preferentially. 
> 
> You mean in a new maker run? is this possible with the old maker as well, not
> maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio
>> promoting scenario I descibed), you can provide those predictions to the use
>> the pred_gff option and then set keep_preds=1 and they will be maintained
>> even without evidence.  Attached is a script that would make selecting those
>> easier.  It take the MAKER generated GFF3 and a list of predictions to keep
>> (one name per line).  These might be the results of a BLAST analysis for
>> example.  It will then return the GFF3 entries for just those models
>> selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which
> model is the best, and the 3 models from the ab initio predictors do not agree
> on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we
>> can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by
> exonerate) to the proteins of the closely related species that i am  missing,
> and somehow keep the previous annotations and get the extra ones by this gff
> file. But how exactly maker should be run to do this I am not sure. if I want
> to keep the previous annotations I  need the gff file of the last maker run as
> input, but then how do I discriminate with the exonerate gff file? And which
> mode of rediction should be on, and with which parameters? You mention
> keep_preds=1  for the existing annotations, but how do i also promote evidence
> from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct
about what you've already done.  You have run Maker with SNAP, Genemark and
Augustus using EST from a closely related species (passed to altest) and
protein evidence from other fungi.  You are missing about 1,000 genes
compared to the species that provided the EST alignments.  You say their is
good evidence that these genes exist from the alignments and I assume by
this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's
proteins in the evidence set that you provided to Maker.  If you haven't
provided these proteins as evidence to maker then you should do this.  You
can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but
still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta
and blast them directly against your closely related proteins.  Presumably
they don't hit too well because if they did they should have been promoted
to predictions by Maker the first time, but here you can decide yourself
what thresholds to allow to keep the abinit predictions that hit the closely
related species proteins.  If you filter you blast hits the way you want and
keep the names of the abinit predictions that pass your filter, then use the
script Carson attached it it will generate a abinit precidtion GFF file with
only the predictions you selected.  You can then pass those predictions back
to Maker and force it to keep them and Maker will turn them from predictions
(match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> To:  <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by
>> MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly on
>> the assembly and augustus with a model from a less closely related species),
>> along with a set of fungal proteins. I am missing ~ 1000 proteins when I
>> compare to the species i used EST data from, and there is good evidence from
>> alignments that these genes exist. The question is how to proceed from Blast
>> hits to actual gene models here. The idea would be to add these genes to the
>> existing dataset, rather than reannotate the genome. I believe that
>> reannotating it without any further evidence such as RNA-seq from the species
>> itself would not change much,and i d rather stick with actual predictions
>> that i trust and have used in subsequent analyses. The 1000 genes I can
>> accept to annotate with a less stringent and reliable way than MAKER, I just
>> want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy
>> annotations scheme to do it, by providing GFF3 of the alignments between the
>> two species in the regions where genes were missed, but as i said, I would
>> not like to reannotate the whole genome, and running MAKER2 might cause
>> slight changes that i d like to avoid. Is this possible? First, is it
>> possible to provide a Gff3 file of specific locations and not the entire
>> genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models only?
>> How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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






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From james.collett at pnnl.gov  Fri Apr 27 10:51:05 2012
From: james.collett at pnnl.gov (Collett, James R)
Date: Fri, 27 Apr 2012 09:51:05 -0700
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>

Hi Carson,

Could you please send me (or make available for download) the perl script that you mentioned in this previous post in this thread?

>> Attached is a 
>> script that would make selecting those easier.  It take the MAKER 
>> generated GFF3 and a list of predictions to keep (one name per line).  
>> These might be the results of a BLAST analysis for example.  It will 
>> then return the GFF3 entries for just those models selected.

Thanks,

Jim
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory

> -----Original Message-----
> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
> lab.org
> Sent: Friday, April 27, 2012 6:48 AM
> To: maker-devel at yandell-lab.org
> Subject: maker-devel Digest, Vol 47, Issue 14
> 
> Send maker-devel mailing list submissions to
> 	maker-devel at yandell-lab.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.org
> 
> or, via email, send a message with subject or body 'help' to
> 	maker-devel-request at yandell-lab.org
> 
> You can reach the person managing the list at
> 	maker-devel-owner at yandell-lab.org
> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of maker-devel digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Use pass-through system to add missing genes (Carson Holt)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 27 Apr 2012 09:27:24 -0400
> From: Carson Holt <carsonhh at gmail.com>
> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
> 	<anastasia.gioti at scilifelab.se>
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] Use pass-through system to add missing
> 	genes
> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> 
> The only way you should be able to get BLASTX overlap and still not get
> a model for the region is if 1.  The protein alignment in in a
> different reading frame then your models for every single base pair of
> the alignment (in which case it's not true overlap).  2. The BLASTX
> HSPs are stacked on each other again and again in weird rearranged
> overlaps to produce a very deep alignment which would mean this is a
> repetitive region and is not really a significant alignment.  Otherwise
> this should not happen unless you have the AED_threshold set to some
> value where MAKER will ignore genes unless they have a minimum amount
> of support (by default this option is always off).  The other two
> possibilities can be tested by just looking at the alignments manually
> in Apollo.  Also take a look at the AED and eAED values for your
> missing genes.  Anything below 1 should always be kept by MAKER by
> default because it has at least some evidence supported.
> 
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> 
> If they are already in your current run ignore this.
> 
> Barry provided detailed instructions on how to configure MAKER, for
> your particular case.  So just follow his excellent instructions.
> 
> Thanks,
> Carson
> 
> 
> 
> From:  Barry Moore <barry.moore at genetics.utah.edu>
> Date:  Friday, 27 April, 2012 7:57 AM
> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Use pass-through system to add missing
> genes
> 
> Hi Anastasia,
> 
> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
> 
> > Hi Carlson,
> > Thanks for your help!
> >
> >> The way you proceed depends on why the genes are not there to begin
> with.
> >> Are they not there because of a lack of evidence?
> >
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> >
> 
> This doesn't sound right.  If there are predicted models and blastx
> protein evidence overlapping them you should get a model retained.  I
> know for the EST evidence that it has to support a splice site before
> it will be promoted and I can't remember if protein evidence is the
> same but certainly if you pass back those protein2genome predictions
> and the original proteins as evidence then they will be retained as
> models.
> 
> >> If that's the case just adding the new fasta file should do the
> trick.
> >
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> >
> 
> Yes using the protein fasta from the closely related species as
> evidence.  I think you said you've already done that right?
> 
> 
> >> Or are they not there because an assembly error makes it impossible
> >> to get a logical model for the region (I.e reading frame breaks).
> >
> > This is not the case in general.
> >
> >> Are there ab initio models already called in those regions that
> could
> >> just be promoted to the annotation tier?  You can test that one by
> >> blasting against the nonoverlaping_abinits.fasta files.
> >
> > I have not done this, will do!
> >
> >>
> >> For any of the cases described, you can provide the existing
> >> annotation set as the input in GFF3 format, and previous models will
> >> be maintained preferentially.
> >
> > You mean in a new maker run? is this possible with the old maker as
> > well, not maker2, right?
> >
> 
> Yes, the original MAKER will do this.
> 
> 
> >> If you know which ab initio predictions you want to add (I.e. the ab
> >> initio promoting scenario I descibed), you can provide those
> >> predictions to the use the pred_gff option and then set keep_preds=1
> >> and they will be maintained even without evidence.  Attached is a
> >> script that would make selecting those easier.  It take the MAKER
> >> generated GFF3 and a list of predictions to keep (one name per
> line).
> >> These might be the results of a BLAST analysis for example.  It will
> >> then return the GFF3 entries for just those models selected.
> >
> > The thing is, for the few cases I have looked at, I cannot really
> > decide which model is the best, and the 3 models from the ab initio
> > predictors do not agree on the exact intron-exon junctions or the
> start and stop codons.
> >>
> >> If the situation is more complex, just provide more detail, and I am
> >> sure we can help you come up with a plan.
> >>
> > What i was thinking to do was to provide a gff file of alignments (eg
> > by
> > exonerate) to the proteins of the closely related species that i am
> > missing, and somehow keep the previous annotations and get the extra
> > ones by this gff file. But how exactly maker should be run to do this
> > I am not sure. if I want to keep the previous annotations I  need the
> > gff file of the last maker run as input, but then how do I
> > discriminate with the exonerate gff file? And which mode of rediction
> > should be on, and with which parameters? You mention
> > keep_preds=1  for the existing annotations, but how do i also promote
> > evidence from alignments on the same way in the same run?
> > Looks feasible though. Thanks again,
> > Anastasia
> >
> 
> Let me just restate what you've said so that I can be sure that I am
> correct about what you've already done.  You have run Maker with SNAP,
> Genemark and Augustus using EST from a closely related species (passed
> to altest) and protein evidence from other fungi.  You are missing
> about 1,000 genes compared to the species that provided the EST
> alignments.  You say their is good evidence that these genes exist from
> the alignments and I assume by this that you mean the EST/protein
> alignments that Maker produced.
> 
> 1) Is the closely related fungus annotated and if so have you included
> it's proteins in the evidence set that you provided to Maker.  If you
> haven't provided these proteins as evidence to maker then you should do
> this.  You can re-run maker passing your original models back through
> like this:
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
> 
> #-----Protein Homology Evidence (for best results provide a file for at
> least one) protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
> 
> 2) If you've already included those closely related species proteins
> but still didn't get the 1,000 genes, then take your
> nonoverlaping_abinits.fasta and blast them directly against your
> closely related proteins.  Presumably they don't hit too well because
> if they did they should have been promoted to predictions by Maker the
> first time, but here you can decide yourself what thresholds to allow
> to keep the abinit predictions that hit the closely related species
> proteins.  If you filter you blast hits the way you want and keep the
> names of the abinit predictions that pass your filter, then use the
> script Carson attached it it will generate a abinit precidtion GFF file
> with only the predictions you selected.  You can then pass those
> predictions back to Maker and force it to keep them and Maker will turn
> them from predictions
> (match/match_part) into gene models.
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
> 
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
> 
> keep_preds=1
> 
> Barry
> 
> >> Thanks,
> >> Carson
> >>
> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
> >> To:  <maker-devel at yandell-lab.org>
> >> Subject:  [maker-devel] Use pass-through system to add missing genes
> >>
> >> Hi,
> >> I  have a set of predicted proteins from the genome of a fungus
> >> annotated by MAKER  using EST data from a closely related species
> and
> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
> >> trained directly on the assembly and augustus with a model from a
> >> less closely related species), along with a set of fungal proteins.
> I
> >> am missing ~ 1000 proteins when I compare to the species i used EST
> >> data from, and there is good evidence from alignments that these
> >> genes exist. The question is how to proceed from Blast hits to
> actual
> >> gene models here. The idea would be to add these genes to the
> >> existing dataset, rather than reannotate the genome. I believe that
> >> reannotating it without any further evidence such as RNA-seq from
> the
> >> species itself would not change much,and i d rather stick with
> actual
> >> predictions that i trust and have used in subsequent analyses. The
> >> 1000 genes I can accept to annotate with a less stringent and
> reliable way than MAKER, I just want to add them so that the difference
> in gene count gets corrected.
> >> I was reading the MAKER 2 paper and i was wondering if I can use the
> >> legacy annotations scheme to do it, by providing GFF3 of the
> >> alignments between the two species in the regions where genes were
> >> missed, but as i said, I would not like to reannotate the whole
> >> genome, and running MAKER2 might cause slight changes that i d like
> >> to avoid. Is this possible? First, is it possible to provide a Gff3
> >> file of specific locations and not the entire genome alignment? (I
> >> guess so..) Second, how can I tag the existing annotations as 'not
> to be changed' or alternatively, tag the new models only?
> >> How should I run maker2, with which predictors on and which off?
> >> Thanks,
> >> Anastasia
> >>
> >> Anastasia Gioti
> >> Post-doctoral Researcher
> >>
> >> anastasia.gioti at scilifelab.se
> >> anastasia.gioti at ebc.uu.se
> >>
> >>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
> >> /
> >>
> >>
> >>
> >> _______________________________________________ maker-devel mailing
> >> list
> >> maker-
> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
> >> tinfo/ma
> >> ker-devel_yandell-lab.org
> >> <gff3_select>
> >
> > Anastasia Gioti
> > Post-doctoral Researcher
> >
> > anastasia.gioti at scilifelab.se
> > anastasia.gioti at ebc.uu.se
> >
> >
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> >
> >
> >
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.or
> > g
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
> 
> 
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> 
> _______________________________________________
> maker-devel mailing list
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> 
> 
> End of maker-devel Digest, Vol 47, Issue 14
> *******************************************



From carsonhh at gmail.com  Fri Apr 27 11:18:23 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 13:18:23 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>
Message-ID: <CBC04C5D.BF73%carsonhh@gmail.com>

Here you go.  This will also be part of the next MAKER release in some
form.

Thanks,
Carson



On 12-04-27 12:51 PM, "Collett, James R" <james.collett at pnnl.gov> wrote:

>Hi Carson,
>
>Could you please send me (or make available for download) the perl script
>that you mentioned in this previous post in this thread?
>
>>> Attached is a 
>>> script that would make selecting those easier.  It take the MAKER
>>> generated GFF3 and a list of predictions to keep (one name per line).
>>> These might be the results of a BLAST analysis for example.  It will
>>> then return the GFF3 entries for just those models selected.
>
>Thanks,
>
>Jim
>__________________________________________________
>James R. Collett, Ph.D.
>Senior Scientist
>Chemical and Biological Process Development Group
>Energy and Environment Directorate
>Pacific Northwest National Laboratory
>
>> -----Original Message-----
>> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
>> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
>> lab.org
>> Sent: Friday, April 27, 2012 6:48 AM
>> To: maker-devel at yandell-lab.org
>> Subject: maker-devel Digest, Vol 47, Issue 14
>> 
>> Send maker-devel mailing list submissions to
>> 	maker-devel at yandell-lab.org
>> 
>> To subscribe or unsubscribe via the World Wide Web, visit
>> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.org
>> 
>> or, via email, send a message with subject or body 'help' to
>> 	maker-devel-request at yandell-lab.org
>> 
>> You can reach the person managing the list at
>> 	maker-devel-owner at yandell-lab.org
>> 
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of maker-devel digest..."
>> 
>> 
>> Today's Topics:
>> 
>>    1. Re: Use pass-through system to add missing genes (Carson Holt)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Fri, 27 Apr 2012 09:27:24 -0400
>> From: Carson Holt <carsonhh at gmail.com>
>> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
>> 	<anastasia.gioti at scilifelab.se>
>> Cc: maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] Use pass-through system to add missing
>> 	genes
>> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> 
>> The only way you should be able to get BLASTX overlap and still not get
>> a model for the region is if 1.  The protein alignment in in a
>> different reading frame then your models for every single base pair of
>> the alignment (in which case it's not true overlap).  2. The BLASTX
>> HSPs are stacked on each other again and again in weird rearranged
>> overlaps to produce a very deep alignment which would mean this is a
>> repetitive region and is not really a significant alignment.  Otherwise
>> this should not happen unless you have the AED_threshold set to some
>> value where MAKER will ignore genes unless they have a minimum amount
>> of support (by default this option is always off).  The other two
>> possibilities can be tested by just looking at the alignments manually
>> in Apollo.  Also take a look at the AED and eAED values for your
>> missing genes.  Anything below 1 should always be kept by MAKER by
>> default because it has at least some evidence supported.
>> 
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> 
>> If they are already in your current run ignore this.
>> 
>> Barry provided detailed instructions on how to configure MAKER, for
>> your particular case.  So just follow his excellent instructions.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Barry Moore <barry.moore at genetics.utah.edu>
>> Date:  Friday, 27 April, 2012 7:57 AM
>> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
>> Subject:  Re: [maker-devel] Use pass-through system to add missing
>> genes
>> 
>> Hi Anastasia,
>> 
>> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
>> 
>> > Hi Carlson,
>> > Thanks for your help!
>> >
>> >> The way you proceed depends on why the genes are not there to begin
>> with.
>> >> Are they not there because of a lack of evidence?
>> >
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> >
>> 
>> This doesn't sound right.  If there are predicted models and blastx
>> protein evidence overlapping them you should get a model retained.  I
>> know for the EST evidence that it has to support a splice site before
>> it will be promoted and I can't remember if protein evidence is the
>> same but certainly if you pass back those protein2genome predictions
>> and the original proteins as evidence then they will be retained as
>> models.
>> 
>> >> If that's the case just adding the new fasta file should do the
>> trick.
>> >
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> >
>> 
>> Yes using the protein fasta from the closely related species as
>> evidence.  I think you said you've already done that right?
>> 
>> 
>> >> Or are they not there because an assembly error makes it impossible
>> >> to get a logical model for the region (I.e reading frame breaks).
>> >
>> > This is not the case in general.
>> >
>> >> Are there ab initio models already called in those regions that
>> could
>> >> just be promoted to the annotation tier?  You can test that one by
>> >> blasting against the nonoverlaping_abinits.fasta files.
>> >
>> > I have not done this, will do!
>> >
>> >>
>> >> For any of the cases described, you can provide the existing
>> >> annotation set as the input in GFF3 format, and previous models will
>> >> be maintained preferentially.
>> >
>> > You mean in a new maker run? is this possible with the old maker as
>> > well, not maker2, right?
>> >
>> 
>> Yes, the original MAKER will do this.
>> 
>> 
>> >> If you know which ab initio predictions you want to add (I.e. the ab
>> >> initio promoting scenario I descibed), you can provide those
>> >> predictions to the use the pred_gff option and then set keep_preds=1
>> >> and they will be maintained even without evidence.  Attached is a
>> >> script that would make selecting those easier.  It take the MAKER
>> >> generated GFF3 and a list of predictions to keep (one name per
>> line).
>> >> These might be the results of a BLAST analysis for example.  It will
>> >> then return the GFF3 entries for just those models selected.
>> >
>> > The thing is, for the few cases I have looked at, I cannot really
>> > decide which model is the best, and the 3 models from the ab initio
>> > predictors do not agree on the exact intron-exon junctions or the
>> start and stop codons.
>> >>
>> >> If the situation is more complex, just provide more detail, and I am
>> >> sure we can help you come up with a plan.
>> >>
>> > What i was thinking to do was to provide a gff file of alignments (eg
>> > by
>> > exonerate) to the proteins of the closely related species that i am
>> > missing, and somehow keep the previous annotations and get the extra
>> > ones by this gff file. But how exactly maker should be run to do this
>> > I am not sure. if I want to keep the previous annotations I  need the
>> > gff file of the last maker run as input, but then how do I
>> > discriminate with the exonerate gff file? And which mode of rediction
>> > should be on, and with which parameters? You mention
>> > keep_preds=1  for the existing annotations, but how do i also promote
>> > evidence from alignments on the same way in the same run?
>> > Looks feasible though. Thanks again,
>> > Anastasia
>> >
>> 
>> Let me just restate what you've said so that I can be sure that I am
>> correct about what you've already done.  You have run Maker with SNAP,
>> Genemark and Augustus using EST from a closely related species (passed
>> to altest) and protein evidence from other fungi.  You are missing
>> about 1,000 genes compared to the species that provided the EST
>> alignments.  You say their is good evidence that these genes exist from
>> the alignments and I assume by this that you mean the EST/protein
>> alignments that Maker produced.
>> 
>> 1) Is the closely related fungus annotated and if so have you included
>> it's proteins in the evidence set that you provided to Maker.  If you
>> haven't provided these proteins as evidence to maker then you should do
>> this.  You can re-run maker passing your original models back through
>> like this:
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=1
>> other_pass=1
>> 
>> #-----Protein Homology Evidence (for best results provide a file for at
>> least one) protein=proteins_from_closely_related.fasta
>> ## OR it sounds like you've already aligned these with exonerate?
>> protein_gff=proteins_from_closely_related_already_aligned.gff
>> 
>> 2) If you've already included those closely related species proteins
>> but still didn't get the 1,000 genes, then take your
>> nonoverlaping_abinits.fasta and blast them directly against your
>> closely related proteins.  Presumably they don't hit too well because
>> if they did they should have been promoted to predictions by Maker the
>> first time, but here you can decide yourself what thresholds to allow
>> to keep the abinit predictions that hit the closely related species
>> proteins.  If you filter you blast hits the way you want and keep the
>> names of the abinit predictions that pass your filter, then use the
>> script Carson attached it it will generate a abinit precidtion GFF file
>> with only the predictions you selected.  You can then pass those
>> predictions back to Maker and force it to keep them and Maker will turn
>> them from predictions
>> (match/match_part) into gene models.
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=0
>> other_pass=1
>> 
>> #-----Gene Prediction
>> snaphmm=
>> gmhmm=
>> augustus_species=
>> fgenesh_par_file=
>> pred_gff=ab_init_predictions_rescued_by_blast.gff
>> 
>> keep_preds=1
>> 
>> Barry
>> 
>> >> Thanks,
>> >> Carson
>> >>
>> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> >> To:  <maker-devel at yandell-lab.org>
>> >> Subject:  [maker-devel] Use pass-through system to add missing genes
>> >>
>> >> Hi,
>> >> I  have a set of predicted proteins from the genome of a fungus
>> >> annotated by MAKER  using EST data from a closely related species
>> and
>> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
>> >> trained directly on the assembly and augustus with a model from a
>> >> less closely related species), along with a set of fungal proteins.
>> I
>> >> am missing ~ 1000 proteins when I compare to the species i used EST
>> >> data from, and there is good evidence from alignments that these
>> >> genes exist. The question is how to proceed from Blast hits to
>> actual
>> >> gene models here. The idea would be to add these genes to the
>> >> existing dataset, rather than reannotate the genome. I believe that
>> >> reannotating it without any further evidence such as RNA-seq from
>> the
>> >> species itself would not change much,and i d rather stick with
>> actual
>> >> predictions that i trust and have used in subsequent analyses. The
>> >> 1000 genes I can accept to annotate with a less stringent and
>> reliable way than MAKER, I just want to add them so that the difference
>> in gene count gets corrected.
>> >> I was reading the MAKER 2 paper and i was wondering if I can use the
>> >> legacy annotations scheme to do it, by providing GFF3 of the
>> >> alignments between the two species in the regions where genes were
>> >> missed, but as i said, I would not like to reannotate the whole
>> >> genome, and running MAKER2 might cause slight changes that i d like
>> >> to avoid. Is this possible? First, is it possible to provide a Gff3
>> >> file of specific locations and not the entire genome alignment? (I
>> >> guess so..) Second, how can I tag the existing annotations as 'not
>> to be changed' or alternatively, tag the new models only?
>> >> How should I run maker2, with which predictors on and which off?
>> >> Thanks,
>> >> Anastasia
>> >>
>> >> Anastasia Gioti
>> >> Post-doctoral Researcher
>> >>
>> >> anastasia.gioti at scilifelab.se
>> >> anastasia.gioti at ebc.uu.se
>> >>
>> >>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
>> >> /
>> >>
>> >>
>> >>
>> >> _______________________________________________ maker-devel mailing
>> >> list
>> >> maker-
>> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
>> >> tinfo/ma
>> >> ker-devel_yandell-lab.org
>> >> <gff3_select>
>> >
>> > Anastasia Gioti
>> > Post-doctoral Researcher
>> >
>> > anastasia.gioti at scilifelab.se
>> > anastasia.gioti at ebc.uu.se
>> >
>> >
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> >
>> >
>> >
>> > _______________________________________________
>> > maker-devel mailing list
>> > maker-devel at box290.bluehost.com
>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.or
>> > g
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
>> 
>> 
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>> 
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
>> End of maker-devel Digest, Vol 47, Issue 14
>> *******************************************
>
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From weckalba at asu.edu  Tue Apr  3 17:28:28 2012
From: weckalba at asu.edu (Walter Eckalbar)
Date: Tue, 3 Apr 2012 16:28:28 -0700
Subject: [maker-devel] gff3_preds2models usage question
Message-ID: <CANRPJSdHUx_BmAzb+OBLFab02dDtugM9Jf3zsXqjThrKauX29g@mail.gmail.com>

Hello maker developers and users,

I am attempting to use the gff3_preds2models scripts, but running into a
few issues.

Initially, I hit errors that seemed to be fixed by installing CGI and its
dependancies.  However, that during that installation a few tests did fail.
 I can provide error logs if that would be helpful, however, I went on to
install and attempt gff3_preds2models anyway.

What I am currently doing is running gff3_merge first, to gather the maker
outputs.  I am doing so with both the -n option on and off.  When providing
the gff3 file with the sequence I get the following error from
gff3_preds2models:

Undefined subroutine &maker::auto_annotator::annotate called at
/Users/Walter/Bioinformatics/Tools/maker/bin/gff3_preds2models line 97,
<GEN16> line 992291.

This seemed to be the same error as that of what someone else saw on these
boards, but I did not see a later email resolving the issue.

I also tried giving it just the gff3 without the sequences at the bottom of
the file and then I get this error:

ERROR: There was a problem in the writing the fasta entry
Either no sequence was given, or there was an error in writing

This leads me to believe I should be using the one with the sequence, but I
am not certain of that.

I see it might be possible to go from maker outputs to chado database then
to gene->mRNA->exon gff3s, but I have not set up my machine for XML or
chado yet, and it does not appear trivial.

Thanks for the help,

Walter
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From ranjani at uga.edu  Tue Apr  3 20:24:49 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Wed, 4 Apr 2012 02:24:49 +0000
Subject: [maker-devel] mRNA-seq data
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>

Hi,



I am using to MAKER to annotate a genome and I would like a couple of clarifications.



In the previous version of MAKER, under EST_evidence in maker_opts. ctl the user could input est and est_reads- the mRNAseq reads (although this was not fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation quality.

I have assembled transcriptome data from Sanger,454 and Illumina



Do I just provide all this data in a fasta file format to the 'est' option? Is this is the best way to provide the mRNA-seq evidence?Will this assure the mRNA-seq data is used to improve the annotations?



Thanks!



Ranjani
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From carsonhh at gmail.com  Tue Apr  3 20:39:02 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 03 Apr 2012 22:39:02 -0400
Subject: [maker-devel] mRNA-seq data
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF3454CA257@SN2PRD0202MB117.namprd02.prod.outlook.com>
Message-ID: <CBA12B6C.AA4A%carsonhh@gmail.com>

Yes.  If you have them in fasta format, just provide them to the est= option
and let MAEKR align them with exonerate.  If you used something like
cufflinks or trinity, to process them you can provide them to the est_gff
option (MAKER comes with a cufflinks2gff3 converter to make that easy).

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Wed, 4 Apr 2012 02:24:49 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mRNA-seq data

Hi,

 

I am using to MAKER to annotate a genome and I would like a couple of
clarifications.

 

In the previous version of MAKER, under EST_evidence in maker_opts. ctl the
user could input est and est_reads- the mRNAseq reads (although this was not
fully implemented).

The latest version of MAKER uses mRNA-seq data to improve annotation
quality.

I have assembled transcriptome data from Sanger,454 and Illumina

 

Do I just provide all this data in a fasta file format to the 'est' option?
Is this is the best way to provide the mRNA-seq evidence?Will this assure
the mRNA-seq data is used to improve the annotations?

 

Thanks!

 

Ranjani
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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 pingouinandsheep at gmail.com  Thu Apr  5 08:14:39 2012
From: pingouinandsheep at gmail.com (pingouinandsheep at gmail.com)
Date: Thu, 5 Apr 2012 07:14:39 -0700 (PDT)
Subject: [maker-devel] Huge memory usage
Message-ID: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>

Hello,

When I try to run the test provided with maker2, maker start to use a
huge amount of memory. I stoped it after it reach ~100go of memory
used. I believe the test should not use that amount of memory.

In an other message someone suggest that the bioperl version installed
could be the cause of the problem, but the bioperl installed on my
cluster is already at version 1.6.

perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
1.006901

Unfortunately I don't have an error message to provide, that could
clarify my problem.

But maybe it is a recurrent problem and you know a few things I should
check.

Thanks,

Ismael



From carsonhh at gmail.com  Thu Apr  5 08:26:17 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Thu, 05 Apr 2012 10:26:17 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <5338ad1d-dc04-4150-b5ee-a88da7c42549@h5g2000vbx.googlegroups.com>
Message-ID: <CBA321AA.AB7A%carsonhh@gmail.com>

The test should not use up more then a few megabytes of RAM.  Even on very
large datasets you should never really use more that 1 or 2 gig of RAM
perl MAKER instance

It's possible that their may be other perl modules that are broken need to
be reinstalled on your system.  This can happen when perl gets updated,
but you are pointing to modules built for a different perl version with
the PERL5LIB environmental variable.  Make sure you you have the latest
version of MAKER and run with --debug set.  Collect that output and send
it to me (the --debug option does some dependancy checking).

I know there is an issue on Macs with updating perl's DB_File module that
causes it to gobble up big sections of the hard drive (it will eventually
fill the drive if you let it).  It's not a memory issue but just one
example of how broken modules can cause weird behavior.

Thanks,
Carson




On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
<pingouinandsheep at gmail.com> wrote:

>Hello,
>
>When I try to run the test provided with maker2, maker start to use a
>huge amount of memory. I stoped it after it reach ~100go of memory
>used. I believe the test should not use that amount of memory.
>
>In an other message someone suggest that the bioperl version installed
>could be the cause of the problem, but the bioperl installed on my
>cluster is already at version 1.6.
>
>perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>1.006901
>
>Unfortunately I don't have an error message to provide, that could
>clarify my problem.
>
>But maybe it is a recurrent problem and you know a few things I should
>check.
>
>Thanks,
>
>Ismael
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From eernst at cshl.edu  Sun Apr  8 16:09:22 2012
From: eernst at cshl.edu (Evan Ernst)
Date: Sun, 8 Apr 2012 18:09:22 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log under
	openMPI
Message-ID: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker
instances, each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no
actual processing is required apart from marking the scaffolds FINISHED.
Comparing the result to a single, non-MPI maker instance running on the
same completed hierarchy reveals that many entries aren't being written to
the log at all when running under MPI. The single process instance runs
just fine, generating a complete log that can be used for the downstream
scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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From carsonhh at gmail.com  Tue Apr 10 08:26:40 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 10 Apr 2012 10:26:40 -0400
Subject: [maker-devel] Incomplete/Missing lines in datastore index log
 under openMPI
In-Reply-To: <CAOqGFX_YfpikUCMfDwS0iHiYT-v8KMCHRwEFcLwZ9Vypm4Pxow@mail.gmail.com>
Message-ID: <CBA9B62E.AE4E%carsonhh@gmail.com>

Depending on if your using NFS and other architecture design you can get
race conditions with the datastore log file.  This primarily happens when
you have multiple instances of MAKER running at the same time or thousands
of short contigs running in parallel so many finish at the same time.  In a
future release, I plan on having the last MAKER job to exit just rebuild the
log at the end of a run to ensure it is complete. For now though, just run
'maker -dsindex' at the end of a run when it happens.  It will rebbuild the
log and only takes a few seconds.

Thanks,
Carson




From:  Evan Ernst <eernst at cshl.edu>
Date:  Sun, 8 Apr 2012 18:09:22 -0400
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Incomplete/Missing lines in datastore index log
under openMPI

Hi Carson,

It looks like there may be a locking issue with the datastore index log in
MAKER 2.25/openmpi 1.4.5. I noticed this when running 8 MPI maker instances,
each with 32 nodes. Examples from the log:

scaffold1001.1  genome_datastore/93/A6/scaffold1001.1/  FINISHED
scaffold1002.1  genome_datastore/72/43/scaffold1002.1/  FINISHED

scaffold1003.1  genome_datastore/B8/05/scaffold1003.1/  FINISHED

...

scaffold10085.1 genome_datastore/1C/7E/scaffold10085.1/ FINISHED
scaffold8265.1  genome_datastore/01/E4/scaffold8265.1/  FINISHED
D
scaffold8295.1  genome_datastore/63/13/scaffold8295.1/  FINISHED

...

scaffold8351.1  genome_datastore/27/52/scaffold8351.1/  FINISHED
scaffold8343.1  genome_datastore/BF/31/scaffold8343.1/  FINISHED
scaffold10167.1 genome_datastore/0B/9A/scaffold10167.1/
FINISHEscaffold10170.1  genome_datastore/F4/FF/scaffold10170.1/ FINISHED
scaffold10209.1 genome_datastore/2D/AA/scaffold10209.1/
FINISHEscaffold10072.1  genome_datastore/E0/A5/scaffold10072.1/ FINISHED
scaffold10113.1 genome_datastore/00/23/scaffold10113.1/ FINISHED

I see this even when running a single MPI instance, 32 nodes, when no actual
processing is required apart from marking the scaffolds FINISHED. Comparing
the result to a single, non-MPI maker instance running on the same completed
hierarchy reveals that many entries aren't being written to the log at all
when running under MPI. The single process instance runs just fine,
generating a complete log that can be used for the downstream scripts.

Between runs, I execute a

find genome.maker.output/ -name .NFSLock* -type f -print0 | xargs -0 rm &

to be sure lingering lock files from badly exiting processes weren't
interfering.

This looks like the sort of thing that may be difficult to track down, and
there's a clear workaround, but I'm happy to provide more information if
you'd like to debug it.

Thanks,
Evan
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http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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From smg283 at gmail.com  Fri Apr 13 13:00:29 2012
From: smg283 at gmail.com (Scott Geib)
Date: Fri, 13 Apr 2012 09:00:29 -1000
Subject: [maker-devel] mpi issue on computing cluster
Message-ID: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>

Hi,
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first,

Thanks
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From sbrubaker at solazyme.com  Fri Apr 13 14:12:24 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 20:12:24 +0000
Subject: [maker-devel] Functional annotation pipeline
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>

Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane



From joseph.fass at gmail.com  Fri Apr 13 14:42:51 2012
From: joseph.fass at gmail.com (Joseph Fass)
Date: Fri, 13 Apr 2012 13:42:51 -0700
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
References: <61D01ACB70C1E141A150BA9F586D5BFA065AD9@EXCHANGE-05.internal.solazyme.com>
Message-ID: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:

> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
>
> Thanks,
> Shane
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com (professional)
970.227.5928 (c)  ||  530.752.2698 (w)
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From carsonhh at gmail.com  Fri Apr 13 13:51:38 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 15:51:38 -0400
Subject: [maker-devel] Huge memory usage
In-Reply-To: <CADNSSgBwH1-wbqpC3_EC+92yzLoi-f5CVwMVaewV=xCK3qkPaA@mail.gmail.com>
Message-ID: <CBADFB12.B16B%carsonhh@gmail.com>

You can pre-mask the genome, convert the RepaetMasker results to GFF3 and
pass them in, or just run the ./configure script in the RepeatMasker
directory to configure wublast to be the default.

You can also let MAKER install it's own separate installation of
RepeatMasker using rmblast.  Just go to the maker/src/ directory and run
this command --> ./Build repeatmasker

MAKER will use that installation preferentially if you let it install that.

Thanks,
Carson

From:  padioleau isma?l <ismpadioleau at gmail.com>
Date:  Fri, 13 Apr 2012 17:42:20 +0200
To:  Carson Holt <carsonhh at gmail.com>
Subject:  Re: [maker-devel] Huge memory usage

Dear Carson,

I have a problem with RepeatMasker on my cluster. It work with wublast but
not with Crossmatch. As maker try to run RepeatMasker with default I can not
successfully run maker.

I wanted to know if I can provide to maker the genome already masked (if I
run with wublast externally), I though it was possible but I can't found in
the configuration files where I should provide it i.e : In maker_opts.ctl,
should I provide the result from RepeatMasker to 'genome_gff:' and set
'rm_pass' to 1, or set rm_gff in the 'Repeat Masking' part of the file?
Or maybe I should provide directly the masked fasta as genome reference.

An other solution could be to ask maker to run RepeatMasker with the option
'-e wublast'.

Is it possible to use one of these solutions?

Thanks,

Ismael

2012/4/5 padioleau isma?l <ismpadioleau at gmail.com>
> Dear Carson,
> 
> Thank you for your very quick answering.
> 
> I realised that I missed some error messages and the problem seems to be
> linked to the DB_file package as you suggested. The person in charge of
> installation told me that he will recover the configuration.
> 
> I will test it after the Easter weekend and come back to you if we have other
> issues.
> 
> Have a nice Easter weekend,
> 
> Ismael
> 
> Here Is the error message:
> Use of uninitialized value $DB_File::db_version in numeric ge (>=) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 276.
> Use of uninitialized value $DB_File::db_version in numeric gt (>) at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 280.
> Deep recursion on subroutine "DB_File::AUTOLOAD" at
> /mnt/common/DevTools/install/Linux/x86_64/perl/perl-5.10.1/lib/5.10.1/x86_64-l
> inux-thread-multi/DB_File.pm line 235.
> 
> 
> 
> 2012/4/5 Carson Holt <carsonhh at gmail.com>
>> The test should not use up more then a few megabytes of RAM.  Even on very
>> large datasets you should never really use more that 1 or 2 gig of RAM
>> perl MAKER instance
>> 
>> It's possible that their may be other perl modules that are broken need to
>> be reinstalled on your system.  This can happen when perl gets updated,
>> but you are pointing to modules built for a different perl version with
>> the PERL5LIB environmental variable.  Make sure you you have the latest
>> version of MAKER and run with --debug set.  Collect that output and send
>> it to me (the --debug option does some dependancy checking).
>> 
>> I know there is an issue on Macs with updating perl's DB_File module that
>> causes it to gobble up big sections of the hard drive (it will eventually
>> fill the drive if you let it).  It's not a memory issue but just one
>> example of how broken modules can cause weird behavior.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> 
>> On 12-04-05 10:14 AM, "pingouinandsheep at gmail.com"
>> <pingouinandsheep at gmail.com> wrote:
>> 
>>> >Hello,
>>> >
>>> >When I try to run the test provided with maker2, maker start to use a
>>> >huge amount of memory. I stoped it after it reach ~100go of memory
>>> >used. I believe the test should not use that amount of memory.
>>> >
>>> >In an other message someone suggest that the bioperl version installed
>>> >could be the cause of the problem, but the bioperl installed on my
>>> >cluster is already at version 1.6.
>>> >
>>> >perl -MBio::Root::Version -e 'print $Bio::Root::Version::VERSION,"\n"'
>>> >1.006901
>>> >
>>> >Unfortunately I don't have an error message to provide, that could
>>> >clarify my problem.
>>> >
>>> >But maybe it is a recurrent problem and you know a few things I should
>>> >check.
>>> >
>>> >Thanks,
>>> >
>>> >Ismael
>>> >
>>> >_______________________________________________
>>> >maker-devel mailing list
>>> >maker-devel at box290.bluehost.com
>>> >http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> 
>> 
> 
> 
> 
> -- 
> Isma?l Padioleau
> Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
> Emmanouil Dermitzakis Group
> Dpt de M?decine G?n?tique et D?veloppement
> Universit? de Gen?ve - Facult? de M?decine
> CMU -  Rue Michel-Servet 1
> CH 1211 Gen?ve 4
> Tel: 0041 22 379 59 74
> ismael.padioleau at unige.ch
> 
> --
> Tel. 0041 78 77 69 561
> ismpadioleau at gmail.com



-- 
Isma?l Padioleau
Evgeny Zdobnov Group (Computational Evolutionary Genomics Group)
Emmanouil Dermitzakis Group
Dpt de M?decine G?n?tique et D?veloppement
Universit? de Gen?ve - Facult? de M?decine
CMU -  Rue Michel-Servet 1
CH 1211 Gen?ve 4
Tel: 0041 22 379 59 74
ismael.padioleau at unige.ch

--
Tel. 0041 78 77 69 561
ismpadioleau at gmail.com


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From carsonhh at gmail.com  Fri Apr 13 15:02:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 13 Apr 2012 17:02:51 -0400
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
Message-ID: <CBAE0B9F.B1D2%carsonhh@gmail.com>

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
integrate interproscan results in the GFF3 files.  There are also a couple
of scripts maker_functional_gff and maker_functional_fasta that can do
putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From:  Joseph Fass <joseph.fass at gmail.com>
Date:  Fri, 13 Apr 2012 13:42:51 -0700
To:  Shane Brubaker <sbrubaker at solazyme.com>
Cc:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>
wrote:
> Hi, can you recommend any open source functional annotation pipelines - to
> assign function, GO terms, pathways, etc. to gene models?
> 
> Thanks,
> Shane
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org



-- 
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com <http://gmail.com>  (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ 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 sbrubaker at solazyme.com  Fri Apr 13 15:18:10 2012
From: sbrubaker at solazyme.com (Shane Brubaker)
Date: Fri, 13 Apr 2012 21:18:10 +0000
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <61D01ACB70C1E141A150BA9F586D5BFA065BBA@EXCHANGE-05.internal.solazyme.com>

Great thank you ... I will take a look at those.

From: Carson Holt [mailto:carsonhh at gmail.com]
Sent: Friday, April 13, 2012 2:03 PM
To: Joseph Fass; Shane Brubaker
Cc: maker-devel at yandell-lab.org
Subject: Re: [maker-devel] Functional annotation pipeline

I would agree blast2go.

You can also try interproscan fro the EBI

MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help integrate interproscan results in the GFF3 files.  There are also a couple of scripts maker_functional_gff and maker_functional_fasta that can do putative functional annotation using uniprot/swiss-prot.

Thanks,
Carson



From: Joseph Fass <joseph.fass at gmail.com<mailto:joseph.fass at gmail.com>>
Date: Fri, 13 Apr 2012 13:42:51 -0700
To: Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>>
Cc: "maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>" <maker-devel at yandell-lab.org<mailto:maker-devel at yandell-lab.org>>
Subject: Re: [maker-devel] Functional annotation pipeline

Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
HTH,
~Joe

On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com<mailto:sbrubaker at solazyme.com>> wrote:
Hi, can you recommend any open source functional annotation pipelines - to assign function, GO terms, pathways, etc. to gene models?

Thanks,
Shane

_______________________________________________
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



--
Joseph Fass
Lead Data Analyst
UC Davis Bioinformatics Core
joseph.fass -at- gmail.com<http://gmail.com> (professional)
970.227.5928 (c)  ||  530.752.2698 (w)

_______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com<mailto:maker-devel at box290.bluehost.com> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
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From dsth at ebi.ac.uk  Fri Apr 13 15:22:37 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:22:37 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CBAE0B9F.B1D2%carsonhh@gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
Message-ID: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>

Careful of interproscan atm.. I believe the executable is still in beta and
they definitely aren't recommending it for production use yet. If you do
use it be sure to check output file if using the lookup service as when i
used it recently it would sometimes exit normally despite lookup failures
(the lookup problems may have had something to do with running ~800 in
parallel - they're looking into the issue atm.).

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Carson Holt <carsonhh at gmail.com>

> I would agree blast2go.
>
> You can also try interproscan fro the EBI
>
> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
> integrate interproscan results in the GFF3 files.  There are also a couple
> of scripts maker_functional_gff and maker_functional_fasta that can do
> putative functional annotation using uniprot/swiss-prot.
>
> Thanks,
> Carson
>
>
>
> From: Joseph Fass <joseph.fass at gmail.com>
> Date: Fri, 13 Apr 2012 13:42:51 -0700
> To: Shane Brubaker <sbrubaker at solazyme.com>
> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
> Subject: Re: [maker-devel] Functional annotation pipeline
>
> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
> HTH,
> ~Joe
>
> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>
>> Hi, can you recommend any open source functional annotation pipelines -
>> to assign function, GO terms, pathways, etc. to gene models?
>>
>> Thanks,
>> Shane
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>
>
>
> --
> Joseph Fass
> Lead Data Analyst
> UC Davis Bioinformatics Core
> joseph.fass -at- gmail.com (professional)
> 970.227.5928 (c)  ||  530.752.2698 (w)
>
> _______________________________________________ maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>
>
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From dsth at ebi.ac.uk  Fri Apr 13 15:37:06 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Fri, 13 Apr 2012 22:37:06 +0100
Subject: [maker-devel] Functional annotation pipeline
In-Reply-To: <CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
References: <CAKAActaA+0Jbw7hO65FaAv-Q_7jgsYZ4O99qvTTFfEc3YDOTBQ@mail.gmail.com>
	<CBAE0B9F.B1D2%carsonhh@gmail.com>
	<CAP8X9uKgoQfpqRe4y4Jz0wSAXLc11VtQQUqzzPsmjFPZQ5=EUA@mail.gmail.com>
Message-ID: <CAP8X9uKOcovWFAetQTaGgQ6Mpb-rg_8PB5RCkfrhsev6Mx03bQ@mail.gmail.com>

sorry, that's the new version of course.

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/13 Daniel Hughes <dsth at ebi.ac.uk>

> Careful of interproscan atm.. I believe the executable is still in beta
> and they definitely aren't recommending it for production use yet. If you
> do use it be sure to check output file if using the lookup service as when
> i used it recently it would sometimes exit normally despite lookup failures
> (the lookup problems may have had something to do with running ~800 in
> parallel - they're looking into the issue atm.).
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
>
> 2012/4/13 Carson Holt <carsonhh at gmail.com>
>
>> I would agree blast2go.
>>
>> You can also try interproscan fro the EBI
>>
>> MAKER comes with two scripts ipr_update_gff and iprscan2gff3 that help
>> integrate interproscan results in the GFF3 files.  There are also a couple
>> of scripts maker_functional_gff and maker_functional_fasta that can do
>> putative functional annotation using uniprot/swiss-prot.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> From: Joseph Fass <joseph.fass at gmail.com>
>> Date: Fri, 13 Apr 2012 13:42:51 -0700
>> To: Shane Brubaker <sbrubaker at solazyme.com>
>> Cc: "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] Functional annotation pipeline
>>
>> Would http://blast2go.de/b2ghome be the kind of thing you're looking for?
>> HTH,
>> ~Joe
>>
>> On Fri, Apr 13, 2012 at 1:12 PM, Shane Brubaker <sbrubaker at solazyme.com>wrote:
>>
>>> Hi, can you recommend any open source functional annotation pipelines -
>>> to assign function, GO terms, pathways, etc. to gene models?
>>>
>>> Thanks,
>>> Shane
>>>
>>> _______________________________________________
>>> maker-devel mailing list
>>> maker-devel at box290.bluehost.com
>>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>>
>>
>>
>>
>> --
>> Joseph Fass
>> Lead Data Analyst
>> UC Davis Bioinformatics Core
>> joseph.fass -at- gmail.com (professional)
>> 970.227.5928 (c)  ||  530.752.2698 (w)
>>
>> _______________________________________________ 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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>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
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From kd7gwt at exchange.usfood.com  Sat Apr 14 00:50:28 2012
From: kd7gwt at exchange.usfood.com (Liz Douglas)
Date: Sat, 14 Apr 2012 14:50:28 +0800
Subject: [maker-devel] Incredible effect on your possibilities in bed
Message-ID: <002801cd1a0b$727fe840$5047c36a@SAMrc6umq>

http://sten-stil.dk/require.html Do you wish to satisfy your babe tonight?




From ranjani at uga.edu  Tue Apr 17 10:46:40 2012
From: ranjani at uga.edu (Sivaranjani Namasivayam)
Date: Tue, 17 Apr 2012 16:46:40 +0000
Subject: [maker-devel] MAKER2.23 output
Message-ID: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>

Hi,

I tried running the latest version of Maker 2.23 with my dataset but with out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2 /usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further details

I was able run the previous version of Maker 2.10 successfully with my dataset.

Thanks,
Ranjani


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From carsonhh at gmail.com  Tue Apr 17 10:56:11 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 12:56:11 -0400
Subject: [maker-devel] MAKER2.23 output
In-Reply-To: <A21F03FBB429334EB4D450CC75E8CBF345939803@SN2PRD0202MB118.namprd02.prod.outlook.com>
Message-ID: <CBB31716.B317%carsonhh@gmail.com>

Segmentation fault means there was a failure with C code.  It was likely in
one of the modules being used.

These are all potential culprits

Inline::C
Proc::ProcessTable
DB_file
forks

Based on when the error occurred.  I would lean more toward DB_File.  Is it
possible that BerkleyDB has been updated on your system, perhaps as part of
another installation or a system update?  That sometimes breaks this module
(which is part of the perl core).

You can try reinstalling that module from CPAN.  Also if you run MAKER
version 2.25 (latest version), you can run with -debug (i.e. 'maker -debug')
to get more information just before the error occurs.  You can then capture
the error log send that to me.

Thanks,
Carson

From:  Sivaranjani Namasivayam <ranjani at uga.edu>
Date:  Tue, 17 Apr 2012 16:46:40 +0000
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] MAKER2.23 output

Hi, 

I tried running the latest version of Maker 2.23 with my dataset but with
out much success.

When I run it without the mpi option I exits with a segmentation fault

STATUS: Processing and indexing input FASTA files...
Segmentation fault

So, I tried it with mpi, the run does start but I don't see any output
files. I ran it with 20 cpus for close to 10 hrs

I tested this with the sample data in maker's data folder.

Input in maker_opts.ctl file

genome=/usr/local/maker/2.23/data/dpp_contig.fasta
est= /usr/local/maker/2.23/data/dpp_est.fasta
protein= /usr/local/maker/2.23/data/dpp_protein.fasta
est2genome=1

This was the command I executed

usr/local/mpich2/1.4.1p1/gcc_4.5.3/bin/mpirun -np 2
/usr/local/maker/2.23/bin/maker maker_opts.ctl maker_bopts.ctl maker_exe.ctl

The following folder with the protein sequence file gets created

dpp_contig.maker.output

But I can't see any progress after that.

Can you please tell me if I might be doing something wrong or need further
details

I was able run the previous version of Maker 2.10 successfully with my
dataset.

Thanks,
Ranjani


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

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From carsonhh at gmail.com  Tue Apr 17 11:09:32 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 13:09:32 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CAH221bveim-ANrybVrQeKKEqDB6u5Hgca1iN6-27+jqX3XO74g@mail.gmail.com>
Message-ID: <CBB31953.B329%carsonhh@gmail.com>

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    }

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

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

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From carsonhh at gmail.com  Tue Apr 17 14:25:51 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Tue, 17 Apr 2012 16:25:51 -0400
Subject: [maker-devel] mpi issue on computing cluster
In-Reply-To: <CBB31953.B329%carsonhh@gmail.com>
Message-ID: <CBB349BE.B364%carsonhh@gmail.com>

Sorry missed the ';' at the end of the eval block.

Should be this -->

    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


--Carson

From:  Carson Holt <carsonhh at gmail.com>
Date:  Tue, 17 Apr 2012 13:09:32 -0400
To:  Scott Geib <smg283 at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] mpi issue on computing cluster

If it's a sharedlibs issue then 'maker -help' would cause the same error.
Try that.


Are you sure that  you are not worried about Signal.pm causing the error?
Try changing 
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm lines
136-143 from this -->


    require Proc::ProcessTable;
    my $obj = new Proc::ProcessTable;
    foreach my $p (@{$obj->table}) {
        #now check for the id
        return $p if ($p->pid == $id);
    }

    return undef;



To this -->


    my $select;
    eval{
        require Proc::ProcessTable;
        my $obj = new Proc::ProcessTable;
        foreach my $p (@{$obj->table}) {
    #now check for the id
            if ($p->pid == $id){
$select = $p;
last;
            }
        }
    };

    return $select;


If it works, I can generate a cleaner workaround, but I'd like to know If
that is the root of the problem.

Thanks,
Carson


From:  Scott Geib <smg283 at gmail.com>
Date:  Fri, 13 Apr 2012 09:00:29 -1000
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] mpi issue on computing cluster

Hi, 
I am trying to run maker 2.24 on a compute cluster and get the following
error (not worried about Signal.pm error):

an into unknown state (hex char: 29) at
/mnt/work/scratch/scottge/maker-2.24/maker/bin/../lib/Proc/Signal.pm line
138.
Fatal error in MPI_Init: Other MPI error, error stack:
MPIR_Init_thread(388)........:
MPID_Init(139)...............: channel initialization failed
MPIDI_CH3_Init(49)...........: progress_init failed
MPIDI_CH3I_Progress_init(808): This version of MPICH requires the SIGUSR1
signal, but the application has already installed a handler
[proxy:0:0 at r01n11.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:0 at r01n11.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:0 at r01n11.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:1 at r01n13.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:1 at r01n13.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:1 at r01n13.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[proxy:0:3 at r07n27.local] HYD_pmcd_pmip_control_cmd_cb
(./pm/pmiserv/pmip_cb.c:868): assert (!closed) failed
[proxy:0:3 at r07n27.local] HYDT_dmxu_poll_wait_for_event
(./tools/demux/demux_poll.c:77): callback returned error status
[proxy:0:3 at r07n27.local] main (./pm/pmiserv/pmip.c:208): demux engine error
waiting for event
[mpiexec at r01n11.local] HYDT_bscu_wait_for_completion
(./tools/bootstrap/utils/bscu_wait.c:70): one of the processes terminated
badly; aborting
[mpiexec at r01n11.local] HYDT_bsci_wait_for_completion
(./tools/bootstrap/src/bsci_wait.c:18): launcher returned error waiting for
completion
[mpiexec at r01n11.local] HYD_pmci_wait_for_completion
(./pm/pmiserv/pmiserv_pmci.c:216): launcher returned error waiting for
completion
[mpiexec at r01n11.local] main (./ui/mpich/mpiexec.c:404): process manager
error waiting for completion

I do not know how mpich2 was compiled, I feel this may be a
--enable-sharedlibs issue?

I may need to contact my cluster support, but I thought I would try here
first, 

Thanks
_______________________________________________ maker-devel mailing list
maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/m
aker-devel_yandell-lab.org


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From elzedliu at gmail.com  Tue Apr 17 17:22:53 2012
From: elzedliu at gmail.com (Huanle)
Date: Tue, 17 Apr 2012 16:22:53 -0700 (PDT)
Subject: [maker-devel] gene predictors in MARKER
Message-ID: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>

I am using MAKER to annotate a recently assembled plant genome.
Hi There,

I am using MAKER to annotate a recently assembled plant genome.

I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial

The denovo gene predictors i included in the maker_exe.ctl file are
#-----Ab-initio Gene Prediction Algorithms
snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
genemark executable
gmhmmp= #location of prokaryotic genemark executable
augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
augustus executable

However, I am not sure whether they were really used.

During the running, i could see repeatmasker, exonerate and wublast
were called. But i did see any information popped up for those gene
predictors.

So i am wondering if they were actually used.

Could you please let me know how to know if all or one of those gene
predictors were called by marker?

Kind Regards,
Huanle



From carsonhh at gmail.com  Mon Apr 23 15:04:16 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Mon, 23 Apr 2012 17:04:16 -0400
Subject: [maker-devel] gene predictors in MARKER
In-Reply-To: <aa46c1e2-2f9f-4151-9622-e10e9db59d59@t7g2000pbp.googlegroups.com>
Message-ID: <CBBB3AB1.BC17%carsonhh@gmail.com>

The gene predictors have to be trained first, and when they are trained
they produce an HMM file that can be supplied to MAKER.  You can either
use MAKER's protein2genome option or est2genome option to produce rough
models to train with, or you can try one of the models that come
prepackaged with those algorithms.

SNAP models will be in --> /sw/maker/2.10/bin/../exe/snap/HMM
Augustus --> run this to see species in augustus -->
/sw/maker/2.10/bin/../exe/augustus/bin/augustus --species=help
GeneMark is self training.  Run it one directly on your genome fasta or
for speed just a chromosome or two of the assembly and it will produce a
file called es.mod as part of it's results.  That is the file you need.

If you have any questions or issues with training just let us know.

Thanks,
Carson



On 12-04-17 7:22 PM, "Huanle" <elzedliu at gmail.com> wrote:

>I am using MAKER to annotate a recently assembled plant genome.
>Hi There,
>
>I am using MAKER to annotate a recently assembled plant genome.
>
>I followed the tutorial here: http://gmod.org/wiki/MAKER_Tutorial
>
>The denovo gene predictors i included in the maker_exe.ctl file are
>#-----Ab-initio Gene Prediction Algorithms
>snap=/sw/maker/2.10/bin/../exe/snap/snap #location of snap executable
>gmhmme3=/sw/GeneMark/20120203/bin/gmhmme3 #location of eukaryotic
>genemark executable
>gmhmmp= #location of prokaryotic genemark executable
>augustus=/sw/maker/2.10/bin/../exe/augustus/bin/augustus #location of
>augustus executable
>
>However, I am not sure whether they were really used.
>
>During the running, i could see repeatmasker, exonerate and wublast
>were called. But i did see any information popped up for those gene
>predictors.
>
>So i am wondering if they were actually used.
>
>Could you please let me know how to know if all or one of those gene
>predictors were called by marker?
>
>Kind Regards,
>Huanle
>
>_______________________________________________
>maker-devel mailing list
>maker-devel at box290.bluehost.com
>http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org





From anastasia.gioti at scilifelab.se  Wed Apr 25 03:09:36 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:09:36 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
Message-ID: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:22:03 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:22:03 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>

For cross-species comparisons you might have be better off including the
actual peptide sequences of the other fungi too in the annotation run - I'd
be very surprised if you really did get the same result.

dan.


Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> I  have a set of predicted proteins from the genome of a fungus annotated
> by MAKER  using EST data from a closely related species and 3 ab initio
> predictors  (snap iterativelly trained 3 times, genemark trained directly
> on the assembly and augustus with a model from a less closely related
> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
> when I compare to the species i used EST data from, and there is good
> evidence from alignments that these genes exist. The question is how to
> proceed from Blast hits to actual gene models here. The idea would be to
> add these genes to the existing dataset, rather than reannotate the genome.
> I believe that reannotating it without any further evidence such as RNA-seq
> from the species itself would not change much,and i d rather stick with
> actual predictions that i trust and have used in subsequent analyses. The
> 1000 genes I can accept to annotate with a less stringent and reliable way
> than MAKER, I just want to add them so that the difference in gene count
> gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the
> legacy annotations scheme to do it, by providing GFF3 of the alignments
> between the two species in the regions where genes were missed, but as i
> said, I would not like to reannotate the whole genome, and running MAKER2
> might cause slight changes that i d like to avoid. Is this possible? First,
> is it possible to provide a Gff3 file of specific locations and not the
> entire genome alignment? (I guess so..) Second, how can I tag the existing
> annotations as 'not to be changed' or alternatively, tag the new models
> only? How should I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
> _______________________________________________
> 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 anastasia.gioti at scilifelab.se  Wed Apr 25 03:29:30 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Wed, 25 Apr 2012 11:29:30 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
Message-ID: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>

Hi, 
Do you mean that I should have not include the proteins of the closely related species in my fungal protein fasta file that I used as evidence in MAKER? i do not see why... What I have been trying to do now is further 'bias' the annotations in favor of this species, so as to get the missing genes. Can you explain a bit more whta you mean?
Thanks, 
Anastasia
On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:

> For cross-species comparisons you might have be better off including the actual peptide sequences of the other fungi too in the annotation run - I'd be very surprised if you really did get the same result.
> 
> dan.
> 
> 
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
> 
> 
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Hi, 
> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
> Thanks, 
> Anastasia
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> 
> 

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From dsth at ebi.ac.uk  Wed Apr 25 03:39:49 2012
From: dsth at ebi.ac.uk (Daniel Hughes)
Date: Wed, 25 Apr 2012 10:39:49 +0100
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
References: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
	<CAP8X9uLAV_Pr+c4463SaYMR3WfuVjy2Oy2HiBf8XGOesQduXYw@mail.gmail.com>
	<A00EFBF8-5D8D-4109-96E4-1528213787E4@scilifelab.se>
Message-ID: <CAP8X9u+BvAG8xRqd_DHwdoiFAbWu0nZ0Get-UNkbGrU_qOEHXA@mail.gmail.com>

sorry my bad, i missed the part about you having already included the
fungal proteins as fasta ;/ - too early for me.

in that case have you viewed the full gff output for specific instances of
such missing proteins in something like apollo to try and work out why
maker hasn't made a call at those loci (aed score...)?

dan.

Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
-------------------------------------------------------------------------------------
dsth at cantab.net
dsth at cpan.org


2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>

> Hi,
> Do you mean that I should have not include the proteins of the closely
> related species in my fungal protein fasta file that I used as evidence in
> MAKER? i do not see why... What I have been trying to do now is further
> 'bias' the annotations in favor of this species, so as to get the missing
> genes. Can you explain a bit more whta you mean?
> Thanks,
> Anastasia
>
> On Apr 25, 2012, at 11:22 AM, Daniel Hughes wrote:
>
> For cross-species comparisons you might have be better off including the
> actual peptide sequences of the other fungi too in the annotation run - I'd
> be very surprised if you really did get the same result.
>
> dan.
>
>
> Daniel S. T. Hughes M.Biochem (Hons; Oxford), Ph.D (Cambridge)
>
> -------------------------------------------------------------------------------------
> dsth at cantab.net
> dsth at cpan.org
>
>
> 2012/4/25 Anastasia Gioti <anastasia.gioti at scilifelab.se>
>
>> Hi,
>> I  have a set of predicted proteins from the genome of a fungus annotated
>> by MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly
>> on the assembly and augustus with a model from a less closely related
>> species), along with a set of fungal proteins. I am missing ~ 1000 proteins
>> when I compare to the species i used EST data from, and there is good
>> evidence from alignments that these genes exist. The question is how to
>> proceed from Blast hits to actual gene models here. The idea would be to
>> add these genes to the existing dataset, rather than reannotate the genome.
>> I believe that reannotating it without any further evidence such as RNA-seq
>> from the species itself would not change much,and i d rather stick with
>> actual predictions that i trust and have used in subsequent analyses. The
>> 1000 genes I can accept to annotate with a less stringent and reliable way
>> than MAKER, I just want to add them so that the difference in gene count
>> gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the
>> legacy annotations scheme to do it, by providing GFF3 of the alignments
>> between the two species in the regions where genes were missed, but as i
>> said, I would not like to reannotate the whole genome, and running MAKER2
>> might cause slight changes that i d like to avoid. Is this possible? First,
>> is it possible to provide a Gff3 file of specific locations and not the
>> entire genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models
>> only? How should I run maker2, with which predictors on and which off?
>> Thanks,
>> Anastasia
>>
>> Anastasia Gioti
>> Post-doctoral Researcher
>>
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>>
>>
>>
>>
>> _______________________________________________
>> maker-devel mailing list
>> maker-devel at box290.bluehost.com
>> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>>
>>
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
>
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From carsonhh at gmail.com  Wed Apr 25 08:29:01 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Wed, 25 Apr 2012 10:29:01 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <EE2180AE-B3D3-4181-B03C-C57F440760C9@scilifelab.se>
Message-ID: <CBBD7372.BD57%carsonhh@gmail.com>

The way you proceed depends on why the genes are not there to begin with.
Are they not there because of a lack of evidence?  If that's the case just
adding the new fasta file should do the trick.  Or are they not there
because an assembly error makes it impossible to get a logical model for the
region (I.e reading frame breaks).  Are there ab initio models already
called in those regions that could just be promoted to the annotation tier?
You can test that one by blasting against the nonoverlaping_abinits.fasta
files.

For any of the cases described, you can provide the existing annotation set
as the input in GFF3 format, and previous models will be maintained
preferentially.  If you know which ab initio predictions you want to add
(I.e. the ab initio promoting scenario I descibed), you can provide those
predictions to the use the pred_gff option and then set keep_preds=1 and
they will be maintained even without evidence.  Attached is a script that
would make selecting those easier.  It take the MAKER generated GFF3 and a
list of predictions to keep (one name per line).  These might be the results
of a BLAST analysis for example.  It will then return the GFF3 entries for
just those models selected.

If the situation is more complex, just provide more detail, and I am sure we
can help you come up with a plan.

Thanks,
Carson

From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Date:  Wed, 25 Apr 2012 11:09:36 +0200
To:  <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Use pass-through system to add missing genes

Hi, 
I  have a set of predicted proteins from the genome of a fungus annotated by
MAKER  using EST data from a closely related species and 3 ab initio
predictors  (snap iterativelly trained 3 times, genemark trained directly on
the assembly and augustus with a model from a less closely related species),
along with a set of fungal proteins. I am missing ~ 1000 proteins when I
compare to the species i used EST data from, and there is good evidence from
alignments that these genes exist. The question is how to proceed from Blast
hits to actual gene models here. The idea would be to add these genes to the
existing dataset, rather than reannotate the genome. I believe that
reannotating it without any further evidence such as RNA-seq from the
species itself would not change much,and i d rather stick with actual
predictions that i trust and have used in subsequent analyses. The 1000
genes I can accept to annotate with a less stringent and reliable way than
MAKER, I just want to add them so that the difference in gene count gets
corrected.
I was reading the MAKER 2 paper and i was wondering if I can use the legacy
annotations scheme to do it, by providing GFF3 of the alignments between the
two species in the regions where genes were missed, but as i said, I would
not like to reannotate the whole genome, and running MAKER2 might cause
slight changes that i d like to avoid. Is this possible? First, is it
possible to provide a Gff3 file of specific locations and not the entire
genome alignment? (I guess so..) Second, how can I tag the existing
annotations as 'not to be changed' or alternatively, tag the new models
only? How should I run maker2, with which predictors on and which off?
Thanks, 
Anastasia

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



_______________________________________________ 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 anastasia.gioti at scilifelab.se  Fri Apr 27 02:43:14 2012
From: anastasia.gioti at scilifelab.se (Anastasia Gioti)
Date: Fri, 27 Apr 2012 10:43:14 +0200
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <CBBD7372.BD57%carsonhh@gmail.com>
References: <CBBD7372.BD57%carsonhh@gmail.com>
Message-ID: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>

Hi Carlson,
Thanks for your help!

> The way you proceed depends on why the genes are not there to begin  
> with.  Are they not there because of a lack of evidence?

It is a mixture of cases, and I can only look at some examples to say  
that. There are cases where all 3 used ab initio predictors provide  
models, there are blastx hits, or both blastx and protein2 genome, but  
no EST evidence, thus  no model is retained. i guess my default  
parameters could be responsible for these cases at least.

> If that's the case just adding the new fasta file should do the trick.

which fasta do you refer to? The proteins file I use as evidence  
contains all proteins i can actually use.

> Or are they not there because an assembly error makes it impossible  
> to get a logical model for the region (I.e reading frame breaks).

This is not the case in general.

> Are there ab initio models already called in those regions that  
> could just be promoted to the annotation tier?  You can test that  
> one by blasting against the nonoverlaping_abinits.fasta files.

I have not done this, will do!

>
> For any of the cases described, you can provide the existing  
> annotation set as the input in GFF3 format, and previous models will  
> be maintained preferentially.

You mean in a new maker run? is this possible with the old maker as  
well, not maker2, right?

> If you know which ab initio predictions you want to add (I.e. the ab  
> initio promoting scenario I descibed), you can provide those  
> predictions to the use the pred_gff option and then set keep_preds=1  
> and they will be maintained even without evidence.  Attached is a  
> script that would make selecting those easier.  It take the MAKER  
> generated GFF3 and a list of predictions to keep (one name per  
> line).  These might be the results of a BLAST analysis for example.   
> It will then return the GFF3 entries for just those models selected.

The thing is, for the few cases I have looked at, I cannot really  
decide which model is the best, and the 3 models from the ab initio  
predictors do not agree on the exact intron-exon junctions or the  
start and stop codons.
>
> If the situation is more complex, just provide more detail, and I am  
> sure we can help you come up with a plan.
>
What i was thinking to do was to provide a gff file of alignments (eg  
by exonerate) to the proteins of the closely related species that i  
am  missing, and somehow keep the previous annotations and get the  
extra ones by this gff file. But how exactly maker should be run to do  
this I am not sure. if I want to keep the previous annotations I  need  
the gff file of the last maker run as input, but then how do I  
discriminate with the exonerate gff file? And which mode of rediction  
should be on, and with which parameters? You mention keep_preds=1  for  
the existing annotations, but how do i also promote evidence from  
alignments on the same way in the same run?
Looks feasible though. Thanks again,
Anastasia

> Thanks,
> Carson
>
> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Date: Wed, 25 Apr 2012 11:09:36 +0200
> To: <maker-devel at yandell-lab.org>
> Subject: [maker-devel] Use pass-through system to add missing genes
>
> Hi,
> I  have a set of predicted proteins from the genome of a fungus  
> annotated by MAKER  using EST data from a closely related species  
> and 3 ab initio predictors  (snap iterativelly trained 3 times,  
> genemark trained directly on the assembly and augustus with a model  
> from a less closely related species), along with a set of fungal  
> proteins. I am missing ~ 1000 proteins when I compare to the species  
> i used EST data from, and there is good evidence from alignments  
> that these genes exist. The question is how to proceed from Blast  
> hits to actual gene models here. The idea would be to add these  
> genes to the existing dataset, rather than reannotate the genome. I  
> believe that reannotating it without any further evidence such as  
> RNA-seq from the species itself would not change much,and i d rather  
> stick with actual predictions that i trust and have used in  
> subsequent analyses. The 1000 genes I can accept to annotate with a  
> less stringent and reliable way than MAKER, I just want to add them  
> so that the difference in gene count gets corrected.
> I was reading the MAKER 2 paper and i was wondering if I can use the  
> legacy annotations scheme to do it, by providing GFF3 of the  
> alignments between the two species in the regions where genes were  
> missed, but as i said, I would not like to reannotate the whole  
> genome, and running MAKER2 might cause slight changes that i d like  
> to avoid. Is this possible? First, is it possible to provide a Gff3  
> file of specific locations and not the entire genome alignment? (I  
> guess so..) Second, how can I tag the existing annotations as 'not  
> to be changed' or alternatively, tag the new models only? How should  
> I run maker2, with which predictors on and which off?
> Thanks,
> Anastasia
>
> Anastasia Gioti
> Post-doctoral Researcher
>
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>
>
>
> _______________________________________________ maker-devel mailing  
> list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
> <gff3_select>

Anastasia Gioti
Post-doctoral Researcher

anastasia.gioti at scilifelab.se
anastasia.gioti at ebc.uu.se

http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/



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From barry.moore at genetics.utah.edu  Fri Apr 27 05:57:01 2012
From: barry.moore at genetics.utah.edu (Barry Moore)
Date: Fri, 27 Apr 2012 05:57:01 -0600
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
References: <CBBD7372.BD57%carsonhh@gmail.com>
	<4FE7CD5B-FC1C-43E7-AC41-A05823348B99@scilifelab.se>
Message-ID: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.  Are they not there because of a lack of evidence?  
> 
> It is a mixture of cases, and I can only look at some examples to say that. There are cases where all 3 used ab initio predictors provide models, there are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus  no model is retained. i guess my default parameters could be responsible for these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein evidence overlapping them you should get a model retained.  I know for the EST evidence that it has to support a splice site before it will be promoted and I can't remember if protein evidence is the same but certainly if you pass back those protein2genome predictions and the original proteins as evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.  
> 
> which fasta do you refer to? The proteins file I use as evidence contains all proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a logical model for the region (I.e reading frame breaks).  
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be promoted to the annotation tier?  You can test that one by blasting against the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set as the input in GFF3 format, and previous models will be maintained preferentially.  
> 
> You mean in a new maker run? is this possible with the old maker as well, not maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio promoting scenario I descibed), you can provide those predictions to the use the pred_gff option and then set keep_preds=1 and they will be maintained even without evidence.  Attached is a script that would make selecting those easier.  It take the MAKER generated GFF3 and a list of predictions to keep (one name per line).  These might be the results of a BLAST analysis for example.  It will then return the GFF3 entries for just those models selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which model is the best, and the 3 models from the ab initio predictors do not agree on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by exonerate) to the proteins of the closely related species that i am  missing, and somehow keep the previous annotations and get the extra ones by this gff file. But how exactly maker should be run to do this I am not sure. if I want to keep the previous annotations I  need the gff file of the last maker run as input, but then how do I discriminate with the exonerate gff file? And which mode of rediction should be on, and with which parameters? You mention keep_preds=1  for the existing annotations, but how do i also promote evidence from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct about what you've already done.  You have run Maker with SNAP, Genemark and Augustus using EST from a closely related species (passed to altest) and protein evidence from other fungi.  You are missing about 1,000 genes compared to the species that provided the EST alignments.  You say their is good evidence that these genes exist from the alignments and I assume by this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's proteins in the evidence set that you provided to Maker.  If you haven't provided these proteins as evidence to maker then you should do this.  You can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta and blast them directly against your closely related proteins.  Presumably they don't hit too well because if they did they should have been promoted to predictions by Maker the first time, but here you can decide yourself what thresholds to allow to keep the abinit predictions that hit the closely related species proteins.  If you filter you blast hits the way you want and keep the names of the abinit predictions that pass your filter, then use the script Carson attached it it will generate a abinit precidtion GFF file with only the predictions you selected.  You can then pass those predictions back to Maker and force it to keep them and Maker will turn them from predictions (match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From: Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date: Wed, 25 Apr 2012 11:09:36 +0200
>> To: <maker-devel at yandell-lab.org>
>> Subject: [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by MAKER  using EST data from a closely related species and 3 ab initio predictors  (snap iterativelly trained 3 times, genemark trained directly on the assembly and augustus with a model from a less closely related species), along with a set of fungal proteins. I am missing ~ 1000 proteins when I compare to the species i used EST data from, and there is good evidence from alignments that these genes exist. The question is how to proceed from Blast hits to actual gene models here. The idea would be to add these genes to the existing dataset, rather than reannotate the genome. I believe that reannotating it without any further evidence such as RNA-seq from the species itself would not change much,and i d rather stick with actual predictions that i trust and have used in subsequent analyses. The 1000 genes I can accept to annotate with a less stringent and reliable way than MAKER, I just want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy annotations scheme to do it, by providing GFF3 of the alignments between the two species in the regions where genes were missed, but as i said, I would not like to reannotate the whole genome, and running MAKER2 might cause slight changes that i d like to avoid. Is this possible? First, is it possible to provide a Gff3 file of specific locations and not the entire genome alignment? (I guess so..) Second, how can I tag the existing annotations as 'not to be changed' or alternatively, tag the new models only? How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list maker-devel at box290.bluehost.com http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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




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From carsonhh at gmail.com  Fri Apr 27 07:27:24 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 09:27:24 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <03439C8F-75B0-42FE-894C-CC564AEB73E9@genetics.utah.edu>
Message-ID: <CBC01559.BF45%carsonhh@gmail.com>

> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.

The only way you should be able to get BLASTX overlap and still not get a
model for the region is if 1.  The protein alignment in in a different
reading frame then your models for every single base pair of the alignment
(in which case it's not true overlap).  2. The BLASTX HSPs are stacked on
each other again and again in weird rearranged overlaps to produce a very
deep alignment which would mean this is a repetitive region and is not
really a significant alignment.  Otherwise this should not happen unless you
have the AED_threshold set to some value where MAKER will ignore genes
unless they have a minimum amount of support (by default this option is
always off).  The other two possibilities can be tested by just looking at
the alignments manually in Apollo.  Also take a look at the AED and eAED
values for your missing genes.  Anything below 1 should always be kept by
MAKER by default because it has at least some evidence supported.

> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.

If they are already in your current run ignore this.

Barry provided detailed instructions on how to configure MAKER, for your
particular case.  So just follow his excellent instructions.

Thanks,
Carson



From:  Barry Moore <barry.moore at genetics.utah.edu>
Date:  Friday, 27 April, 2012 7:57 AM
To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
Subject:  Re: [maker-devel] Use pass-through system to add missing genes

Hi Anastasia,

On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:

> Hi Carlson, 
> Thanks for your help!
> 
>> The way you proceed depends on why the genes are not there to begin with.
>> Are they not there because of a lack of evidence?
> 
> It is a mixture of cases, and I can only look at some examples to say that.
> There are cases where all 3 used ab initio predictors provide models, there
> are blastx hits, or both blastx and protein2 genome, but no EST evidence, thus
> no model is retained. i guess my default parameters could be responsible for
> these cases at least.
> 

This doesn't sound right.  If there are predicted models and blastx protein
evidence overlapping them you should get a model retained.  I know for the
EST evidence that it has to support a splice site before it will be promoted
and I can't remember if protein evidence is the same but certainly if you
pass back those protein2genome predictions and the original proteins as
evidence then they will be retained as models.

>> If that's the case just adding the new fasta file should do the trick.
> 
> which fasta do you refer to? The proteins file I use as evidence contains all
> proteins i can actually use.
> 

Yes using the protein fasta from the closely related species as evidence.  I
think you said you've already done that right?


>> Or are they not there because an assembly error makes it impossible to get a
>> logical model for the region (I.e reading frame breaks).
> 
> This is not the case in general.
> 
>> Are there ab initio models already called in those regions that could just be
>> promoted to the annotation tier?  You can test that one by blasting against
>> the nonoverlaping_abinits.fasta files.
> 
> I have not done this, will do!
> 
>> 
>> For any of the cases described, you can provide the existing annotation set
>> as the input in GFF3 format, and previous models will be maintained
>> preferentially. 
> 
> You mean in a new maker run? is this possible with the old maker as well, not
> maker2, right?
> 

Yes, the original MAKER will do this.


>> If you know which ab initio predictions you want to add (I.e. the ab initio
>> promoting scenario I descibed), you can provide those predictions to the use
>> the pred_gff option and then set keep_preds=1 and they will be maintained
>> even without evidence.  Attached is a script that would make selecting those
>> easier.  It take the MAKER generated GFF3 and a list of predictions to keep
>> (one name per line).  These might be the results of a BLAST analysis for
>> example.  It will then return the GFF3 entries for just those models
>> selected.
> 
> The thing is, for the few cases I have looked at, I cannot really decide which
> model is the best, and the 3 models from the ab initio predictors do not agree
> on the exact intron-exon junctions or the start and stop codons.
>> 
>> If the situation is more complex, just provide more detail, and I am sure we
>> can help you come up with a plan.
>> 
> What i was thinking to do was to provide a gff file of alignments (eg by
> exonerate) to the proteins of the closely related species that i am  missing,
> and somehow keep the previous annotations and get the extra ones by this gff
> file. But how exactly maker should be run to do this I am not sure. if I want
> to keep the previous annotations I  need the gff file of the last maker run as
> input, but then how do I discriminate with the exonerate gff file? And which
> mode of rediction should be on, and with which parameters? You mention
> keep_preds=1  for the existing annotations, but how do i also promote evidence
> from alignments on the same way in the same run?
> Looks feasible though. Thanks again,
> Anastasia
> 

Let me just restate what you've said so that I can be sure that I am correct
about what you've already done.  You have run Maker with SNAP, Genemark and
Augustus using EST from a closely related species (passed to altest) and
protein evidence from other fungi.  You are missing about 1,000 genes
compared to the species that provided the EST alignments.  You say their is
good evidence that these genes exist from the alignments and I assume by
this that you mean the EST/protein alignments that Maker produced.

1) Is the closely related fungus annotated and if so have you included it's
proteins in the evidence set that you provided to Maker.  If you haven't
provided these proteins as evidence to maker then you should do this.  You
can re-run maker passing your original models back through like this:

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=1
other_pass=1

#-----Protein Homology Evidence (for best results provide a file for at
least one)
protein=proteins_from_closely_related.fasta
## OR it sounds like you've already aligned these with exonerate?
protein_gff=proteins_from_closely_related_already_aligned.gff

2) If you've already included those closely related species proteins but
still didn't get the 1,000 genes, then take your nonoverlaping_abinits.fasta
and blast them directly against your closely related proteins.  Presumably
they don't hit too well because if they did they should have been promoted
to predictions by Maker the first time, but here you can decide yourself
what thresholds to allow to keep the abinit predictions that hit the closely
related species proteins.  If you filter you blast hits the way you want and
keep the names of the abinit predictions that pass your filter, then use the
script Carson attached it it will generate a abinit precidtion GFF file with
only the predictions you selected.  You can then pass those predictions back
to Maker and force it to keep them and Maker will turn them from predictions
(match/match_part) into gene models.

#-----Re-annotation Using MAKER Derived GFF3
genome_gff=original_maker_annotations.gff3
est_pass=1
altest_pass=1
protein_pass=1
rm_pass=1
model_pass=1
pred_pass=0
other_pass=1

#-----Gene Prediction
snaphmm=
gmhmm=
augustus_species=
fgenesh_par_file=
pred_gff=ab_init_predictions_rescued_by_blast.gff

keep_preds=1

Barry

>> Thanks,
>> Carson
>> 
>> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> To:  <maker-devel at yandell-lab.org>
>> Subject:  [maker-devel] Use pass-through system to add missing genes
>> 
>> Hi, 
>> I  have a set of predicted proteins from the genome of a fungus annotated by
>> MAKER  using EST data from a closely related species and 3 ab initio
>> predictors  (snap iterativelly trained 3 times, genemark trained directly on
>> the assembly and augustus with a model from a less closely related species),
>> along with a set of fungal proteins. I am missing ~ 1000 proteins when I
>> compare to the species i used EST data from, and there is good evidence from
>> alignments that these genes exist. The question is how to proceed from Blast
>> hits to actual gene models here. The idea would be to add these genes to the
>> existing dataset, rather than reannotate the genome. I believe that
>> reannotating it without any further evidence such as RNA-seq from the species
>> itself would not change much,and i d rather stick with actual predictions
>> that i trust and have used in subsequent analyses. The 1000 genes I can
>> accept to annotate with a less stringent and reliable way than MAKER, I just
>> want to add them so that the difference in gene count gets corrected.
>> I was reading the MAKER 2 paper and i was wondering if I can use the legacy
>> annotations scheme to do it, by providing GFF3 of the alignments between the
>> two species in the regions where genes were missed, but as i said, I would
>> not like to reannotate the whole genome, and running MAKER2 might cause
>> slight changes that i d like to avoid. Is this possible? First, is it
>> possible to provide a Gff3 file of specific locations and not the entire
>> genome alignment? (I guess so..) Second, how can I tag the existing
>> annotations as 'not to be changed' or alternatively, tag the new models only?
>> How should I run maker2, with which predictors on and which off?
>> Thanks, 
>> Anastasia
>> 
>> Anastasia Gioti
>> Post-doctoral Researcher
>> 
>> anastasia.gioti at scilifelab.se
>> anastasia.gioti at ebc.uu.se
>> 
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> 
>> 
>> 
>> _______________________________________________ maker-devel mailing list
>> maker-devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/listinfo/ma
>> ker-devel_yandell-lab.org
>> <gff3_select>
> 
> Anastasia Gioti
> Post-doctoral Researcher
> 
> anastasia.gioti at scilifelab.se
> anastasia.gioti at ebc.uu.se
> 
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> 
> 
> 
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org

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






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From james.collett at pnnl.gov  Fri Apr 27 10:51:05 2012
From: james.collett at pnnl.gov (Collett, James R)
Date: Fri, 27 Apr 2012 09:51:05 -0700
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
References: <mailman.81.1335534450.2580.maker-devel_yandell-lab.org@box290.bluehost.com>
Message-ID: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>

Hi Carson,

Could you please send me (or make available for download) the perl script that you mentioned in this previous post in this thread?

>> Attached is a 
>> script that would make selecting those easier.  It take the MAKER 
>> generated GFF3 and a list of predictions to keep (one name per line).  
>> These might be the results of a BLAST analysis for example.  It will 
>> then return the GFF3 entries for just those models selected.

Thanks,

Jim
__________________________________________________
James R. Collett, Ph.D.
Senior Scientist
Chemical and Biological Process Development Group
Energy and Environment Directorate
Pacific Northwest National Laboratory

> -----Original Message-----
> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
> lab.org
> Sent: Friday, April 27, 2012 6:48 AM
> To: maker-devel at yandell-lab.org
> Subject: maker-devel Digest, Vol 47, Issue 14
> 
> Send maker-devel mailing list submissions to
> 	maker-devel at yandell-lab.org
> 
> To subscribe or unsubscribe via the World Wide Web, visit
> 	http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.org
> 
> or, via email, send a message with subject or body 'help' to
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> 
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> 
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of maker-devel digest..."
> 
> 
> Today's Topics:
> 
>    1. Re: Use pass-through system to add missing genes (Carson Holt)
> 
> 
> ----------------------------------------------------------------------
> 
> Message: 1
> Date: Fri, 27 Apr 2012 09:27:24 -0400
> From: Carson Holt <carsonhh at gmail.com>
> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
> 	<anastasia.gioti at scilifelab.se>
> Cc: maker-devel at yandell-lab.org
> Subject: Re: [maker-devel] Use pass-through system to add missing
> 	genes
> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
> Content-Type: text/plain; charset="us-ascii"
> 
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> 
> The only way you should be able to get BLASTX overlap and still not get
> a model for the region is if 1.  The protein alignment in in a
> different reading frame then your models for every single base pair of
> the alignment (in which case it's not true overlap).  2. The BLASTX
> HSPs are stacked on each other again and again in weird rearranged
> overlaps to produce a very deep alignment which would mean this is a
> repetitive region and is not really a significant alignment.  Otherwise
> this should not happen unless you have the AED_threshold set to some
> value where MAKER will ignore genes unless they have a minimum amount
> of support (by default this option is always off).  The other two
> possibilities can be tested by just looking at the alignments manually
> in Apollo.  Also take a look at the AED and eAED values for your
> missing genes.  Anything below 1 should always be kept by MAKER by
> default because it has at least some evidence supported.
> 
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> 
> If they are already in your current run ignore this.
> 
> Barry provided detailed instructions on how to configure MAKER, for
> your particular case.  So just follow his excellent instructions.
> 
> Thanks,
> Carson
> 
> 
> 
> From:  Barry Moore <barry.moore at genetics.utah.edu>
> Date:  Friday, 27 April, 2012 7:57 AM
> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
> Subject:  Re: [maker-devel] Use pass-through system to add missing
> genes
> 
> Hi Anastasia,
> 
> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
> 
> > Hi Carlson,
> > Thanks for your help!
> >
> >> The way you proceed depends on why the genes are not there to begin
> with.
> >> Are they not there because of a lack of evidence?
> >
> > It is a mixture of cases, and I can only look at some examples to say
> that.
> > There are cases where all 3 used ab initio predictors provide models,
> > there are blastx hits, or both blastx and protein2 genome, but no EST
> > evidence, thus no model is retained. i guess my default parameters
> > could be responsible for these cases at least.
> >
> 
> This doesn't sound right.  If there are predicted models and blastx
> protein evidence overlapping them you should get a model retained.  I
> know for the EST evidence that it has to support a splice site before
> it will be promoted and I can't remember if protein evidence is the
> same but certainly if you pass back those protein2genome predictions
> and the original proteins as evidence then they will be retained as
> models.
> 
> >> If that's the case just adding the new fasta file should do the
> trick.
> >
> > which fasta do you refer to? The proteins file I use as evidence
> > contains all proteins i can actually use.
> >
> 
> Yes using the protein fasta from the closely related species as
> evidence.  I think you said you've already done that right?
> 
> 
> >> Or are they not there because an assembly error makes it impossible
> >> to get a logical model for the region (I.e reading frame breaks).
> >
> > This is not the case in general.
> >
> >> Are there ab initio models already called in those regions that
> could
> >> just be promoted to the annotation tier?  You can test that one by
> >> blasting against the nonoverlaping_abinits.fasta files.
> >
> > I have not done this, will do!
> >
> >>
> >> For any of the cases described, you can provide the existing
> >> annotation set as the input in GFF3 format, and previous models will
> >> be maintained preferentially.
> >
> > You mean in a new maker run? is this possible with the old maker as
> > well, not maker2, right?
> >
> 
> Yes, the original MAKER will do this.
> 
> 
> >> If you know which ab initio predictions you want to add (I.e. the ab
> >> initio promoting scenario I descibed), you can provide those
> >> predictions to the use the pred_gff option and then set keep_preds=1
> >> and they will be maintained even without evidence.  Attached is a
> >> script that would make selecting those easier.  It take the MAKER
> >> generated GFF3 and a list of predictions to keep (one name per
> line).
> >> These might be the results of a BLAST analysis for example.  It will
> >> then return the GFF3 entries for just those models selected.
> >
> > The thing is, for the few cases I have looked at, I cannot really
> > decide which model is the best, and the 3 models from the ab initio
> > predictors do not agree on the exact intron-exon junctions or the
> start and stop codons.
> >>
> >> If the situation is more complex, just provide more detail, and I am
> >> sure we can help you come up with a plan.
> >>
> > What i was thinking to do was to provide a gff file of alignments (eg
> > by
> > exonerate) to the proteins of the closely related species that i am
> > missing, and somehow keep the previous annotations and get the extra
> > ones by this gff file. But how exactly maker should be run to do this
> > I am not sure. if I want to keep the previous annotations I  need the
> > gff file of the last maker run as input, but then how do I
> > discriminate with the exonerate gff file? And which mode of rediction
> > should be on, and with which parameters? You mention
> > keep_preds=1  for the existing annotations, but how do i also promote
> > evidence from alignments on the same way in the same run?
> > Looks feasible though. Thanks again,
> > Anastasia
> >
> 
> Let me just restate what you've said so that I can be sure that I am
> correct about what you've already done.  You have run Maker with SNAP,
> Genemark and Augustus using EST from a closely related species (passed
> to altest) and protein evidence from other fungi.  You are missing
> about 1,000 genes compared to the species that provided the EST
> alignments.  You say their is good evidence that these genes exist from
> the alignments and I assume by this that you mean the EST/protein
> alignments that Maker produced.
> 
> 1) Is the closely related fungus annotated and if so have you included
> it's proteins in the evidence set that you provided to Maker.  If you
> haven't provided these proteins as evidence to maker then you should do
> this.  You can re-run maker passing your original models back through
> like this:
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=1
> other_pass=1
> 
> #-----Protein Homology Evidence (for best results provide a file for at
> least one) protein=proteins_from_closely_related.fasta
> ## OR it sounds like you've already aligned these with exonerate?
> protein_gff=proteins_from_closely_related_already_aligned.gff
> 
> 2) If you've already included those closely related species proteins
> but still didn't get the 1,000 genes, then take your
> nonoverlaping_abinits.fasta and blast them directly against your
> closely related proteins.  Presumably they don't hit too well because
> if they did they should have been promoted to predictions by Maker the
> first time, but here you can decide yourself what thresholds to allow
> to keep the abinit predictions that hit the closely related species
> proteins.  If you filter you blast hits the way you want and keep the
> names of the abinit predictions that pass your filter, then use the
> script Carson attached it it will generate a abinit precidtion GFF file
> with only the predictions you selected.  You can then pass those
> predictions back to Maker and force it to keep them and Maker will turn
> them from predictions
> (match/match_part) into gene models.
> 
> #-----Re-annotation Using MAKER Derived GFF3
> genome_gff=original_maker_annotations.gff3
> est_pass=1
> altest_pass=1
> protein_pass=1
> rm_pass=1
> model_pass=1
> pred_pass=0
> other_pass=1
> 
> #-----Gene Prediction
> snaphmm=
> gmhmm=
> augustus_species=
> fgenesh_par_file=
> pred_gff=ab_init_predictions_rescued_by_blast.gff
> 
> keep_preds=1
> 
> Barry
> 
> >> Thanks,
> >> Carson
> >>
> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
> >> To:  <maker-devel at yandell-lab.org>
> >> Subject:  [maker-devel] Use pass-through system to add missing genes
> >>
> >> Hi,
> >> I  have a set of predicted proteins from the genome of a fungus
> >> annotated by MAKER  using EST data from a closely related species
> and
> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
> >> trained directly on the assembly and augustus with a model from a
> >> less closely related species), along with a set of fungal proteins.
> I
> >> am missing ~ 1000 proteins when I compare to the species i used EST
> >> data from, and there is good evidence from alignments that these
> >> genes exist. The question is how to proceed from Blast hits to
> actual
> >> gene models here. The idea would be to add these genes to the
> >> existing dataset, rather than reannotate the genome. I believe that
> >> reannotating it without any further evidence such as RNA-seq from
> the
> >> species itself would not change much,and i d rather stick with
> actual
> >> predictions that i trust and have used in subsequent analyses. The
> >> 1000 genes I can accept to annotate with a less stringent and
> reliable way than MAKER, I just want to add them so that the difference
> in gene count gets corrected.
> >> I was reading the MAKER 2 paper and i was wondering if I can use the
> >> legacy annotations scheme to do it, by providing GFF3 of the
> >> alignments between the two species in the regions where genes were
> >> missed, but as i said, I would not like to reannotate the whole
> >> genome, and running MAKER2 might cause slight changes that i d like
> >> to avoid. Is this possible? First, is it possible to provide a Gff3
> >> file of specific locations and not the entire genome alignment? (I
> >> guess so..) Second, how can I tag the existing annotations as 'not
> to be changed' or alternatively, tag the new models only?
> >> How should I run maker2, with which predictors on and which off?
> >> Thanks,
> >> Anastasia
> >>
> >> Anastasia Gioti
> >> Post-doctoral Researcher
> >>
> >> anastasia.gioti at scilifelab.se
> >> anastasia.gioti at ebc.uu.se
> >>
> >>
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
> >> /
> >>
> >>
> >>
> >> _______________________________________________ maker-devel mailing
> >> list
> >> maker-
> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
> >> tinfo/ma
> >> ker-devel_yandell-lab.org
> >> <gff3_select>
> >
> > Anastasia Gioti
> > Post-doctoral Researcher
> >
> > anastasia.gioti at scilifelab.se
> > anastasia.gioti at ebc.uu.se
> >
> >
> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
> >
> >
> >
> > _______________________________________________
> > maker-devel mailing list
> > maker-devel at box290.bluehost.com
> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
> lab.or
> > g
> 
> Barry Moore
> Research Scientist
> Dept. of Human Genetics
> University of Utah
> Salt Lake City, UT 84112
> --------------------------------------------
> (801) 585-3543
> 
> 
> 
> 
> 
> 
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> 
> End of maker-devel Digest, Vol 47, Issue 14
> *******************************************



From carsonhh at gmail.com  Fri Apr 27 11:18:23 2012
From: carsonhh at gmail.com (Carson Holt)
Date: Fri, 27 Apr 2012 13:18:23 -0400
Subject: [maker-devel] Use pass-through system to add missing genes
In-Reply-To: <F0F90F8B4D282340A6D984CE8FA7A0A7012BABB39B33@EMAIL05.pnl.gov>
Message-ID: <CBC04C5D.BF73%carsonhh@gmail.com>

Here you go.  This will also be part of the next MAKER release in some
form.

Thanks,
Carson



On 12-04-27 12:51 PM, "Collett, James R" <james.collett at pnnl.gov> wrote:

>Hi Carson,
>
>Could you please send me (or make available for download) the perl script
>that you mentioned in this previous post in this thread?
>
>>> Attached is a 
>>> script that would make selecting those easier.  It take the MAKER
>>> generated GFF3 and a list of predictions to keep (one name per line).
>>> These might be the results of a BLAST analysis for example.  It will
>>> then return the GFF3 entries for just those models selected.
>
>Thanks,
>
>Jim
>__________________________________________________
>James R. Collett, Ph.D.
>Senior Scientist
>Chemical and Biological Process Development Group
>Energy and Environment Directorate
>Pacific Northwest National Laboratory
>
>> -----Original Message-----
>> From: maker-devel-bounces at yandell-lab.org [mailto:maker-devel-
>> bounces at yandell-lab.org] On Behalf Of maker-devel-request at yandell-
>> lab.org
>> Sent: Friday, April 27, 2012 6:48 AM
>> To: maker-devel at yandell-lab.org
>> Subject: maker-devel Digest, Vol 47, Issue 14
>> 
>> Send maker-devel mailing list submissions to
>> 	maker-devel at yandell-lab.org
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>> or, via email, send a message with subject or body 'help' to
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>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of maker-devel digest..."
>> 
>> 
>> Today's Topics:
>> 
>>    1. Re: Use pass-through system to add missing genes (Carson Holt)
>> 
>> 
>> ----------------------------------------------------------------------
>> 
>> Message: 1
>> Date: Fri, 27 Apr 2012 09:27:24 -0400
>> From: Carson Holt <carsonhh at gmail.com>
>> To: Barry Moore <barry.moore at genetics.utah.edu>,	Anastasia Gioti
>> 	<anastasia.gioti at scilifelab.se>
>> Cc: maker-devel at yandell-lab.org
>> Subject: Re: [maker-devel] Use pass-through system to add missing
>> 	genes
>> Message-ID: <CBC01559.BF45%carsonhh at gmail.com>
>> Content-Type: text/plain; charset="us-ascii"
>> 
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> 
>> The only way you should be able to get BLASTX overlap and still not get
>> a model for the region is if 1.  The protein alignment in in a
>> different reading frame then your models for every single base pair of
>> the alignment (in which case it's not true overlap).  2. The BLASTX
>> HSPs are stacked on each other again and again in weird rearranged
>> overlaps to produce a very deep alignment which would mean this is a
>> repetitive region and is not really a significant alignment.  Otherwise
>> this should not happen unless you have the AED_threshold set to some
>> value where MAKER will ignore genes unless they have a minimum amount
>> of support (by default this option is always off).  The other two
>> possibilities can be tested by just looking at the alignments manually
>> in Apollo.  Also take a look at the AED and eAED values for your
>> missing genes.  Anything below 1 should always be kept by MAKER by
>> default because it has at least some evidence supported.
>> 
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> 
>> If they are already in your current run ignore this.
>> 
>> Barry provided detailed instructions on how to configure MAKER, for
>> your particular case.  So just follow his excellent instructions.
>> 
>> Thanks,
>> Carson
>> 
>> 
>> 
>> From:  Barry Moore <barry.moore at genetics.utah.edu>
>> Date:  Friday, 27 April, 2012 7:57 AM
>> To:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> Cc:  Carson Holt <carsonhh at gmail.com>, <maker-devel at yandell-lab.org>
>> Subject:  Re: [maker-devel] Use pass-through system to add missing
>> genes
>> 
>> Hi Anastasia,
>> 
>> On Apr 27, 2012, at 2:43 AM, Anastasia Gioti wrote:
>> 
>> > Hi Carlson,
>> > Thanks for your help!
>> >
>> >> The way you proceed depends on why the genes are not there to begin
>> with.
>> >> Are they not there because of a lack of evidence?
>> >
>> > It is a mixture of cases, and I can only look at some examples to say
>> that.
>> > There are cases where all 3 used ab initio predictors provide models,
>> > there are blastx hits, or both blastx and protein2 genome, but no EST
>> > evidence, thus no model is retained. i guess my default parameters
>> > could be responsible for these cases at least.
>> >
>> 
>> This doesn't sound right.  If there are predicted models and blastx
>> protein evidence overlapping them you should get a model retained.  I
>> know for the EST evidence that it has to support a splice site before
>> it will be promoted and I can't remember if protein evidence is the
>> same but certainly if you pass back those protein2genome predictions
>> and the original proteins as evidence then they will be retained as
>> models.
>> 
>> >> If that's the case just adding the new fasta file should do the
>> trick.
>> >
>> > which fasta do you refer to? The proteins file I use as evidence
>> > contains all proteins i can actually use.
>> >
>> 
>> Yes using the protein fasta from the closely related species as
>> evidence.  I think you said you've already done that right?
>> 
>> 
>> >> Or are they not there because an assembly error makes it impossible
>> >> to get a logical model for the region (I.e reading frame breaks).
>> >
>> > This is not the case in general.
>> >
>> >> Are there ab initio models already called in those regions that
>> could
>> >> just be promoted to the annotation tier?  You can test that one by
>> >> blasting against the nonoverlaping_abinits.fasta files.
>> >
>> > I have not done this, will do!
>> >
>> >>
>> >> For any of the cases described, you can provide the existing
>> >> annotation set as the input in GFF3 format, and previous models will
>> >> be maintained preferentially.
>> >
>> > You mean in a new maker run? is this possible with the old maker as
>> > well, not maker2, right?
>> >
>> 
>> Yes, the original MAKER will do this.
>> 
>> 
>> >> If you know which ab initio predictions you want to add (I.e. the ab
>> >> initio promoting scenario I descibed), you can provide those
>> >> predictions to the use the pred_gff option and then set keep_preds=1
>> >> and they will be maintained even without evidence.  Attached is a
>> >> script that would make selecting those easier.  It take the MAKER
>> >> generated GFF3 and a list of predictions to keep (one name per
>> line).
>> >> These might be the results of a BLAST analysis for example.  It will
>> >> then return the GFF3 entries for just those models selected.
>> >
>> > The thing is, for the few cases I have looked at, I cannot really
>> > decide which model is the best, and the 3 models from the ab initio
>> > predictors do not agree on the exact intron-exon junctions or the
>> start and stop codons.
>> >>
>> >> If the situation is more complex, just provide more detail, and I am
>> >> sure we can help you come up with a plan.
>> >>
>> > What i was thinking to do was to provide a gff file of alignments (eg
>> > by
>> > exonerate) to the proteins of the closely related species that i am
>> > missing, and somehow keep the previous annotations and get the extra
>> > ones by this gff file. But how exactly maker should be run to do this
>> > I am not sure. if I want to keep the previous annotations I  need the
>> > gff file of the last maker run as input, but then how do I
>> > discriminate with the exonerate gff file? And which mode of rediction
>> > should be on, and with which parameters? You mention
>> > keep_preds=1  for the existing annotations, but how do i also promote
>> > evidence from alignments on the same way in the same run?
>> > Looks feasible though. Thanks again,
>> > Anastasia
>> >
>> 
>> Let me just restate what you've said so that I can be sure that I am
>> correct about what you've already done.  You have run Maker with SNAP,
>> Genemark and Augustus using EST from a closely related species (passed
>> to altest) and protein evidence from other fungi.  You are missing
>> about 1,000 genes compared to the species that provided the EST
>> alignments.  You say their is good evidence that these genes exist from
>> the alignments and I assume by this that you mean the EST/protein
>> alignments that Maker produced.
>> 
>> 1) Is the closely related fungus annotated and if so have you included
>> it's proteins in the evidence set that you provided to Maker.  If you
>> haven't provided these proteins as evidence to maker then you should do
>> this.  You can re-run maker passing your original models back through
>> like this:
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=1
>> other_pass=1
>> 
>> #-----Protein Homology Evidence (for best results provide a file for at
>> least one) protein=proteins_from_closely_related.fasta
>> ## OR it sounds like you've already aligned these with exonerate?
>> protein_gff=proteins_from_closely_related_already_aligned.gff
>> 
>> 2) If you've already included those closely related species proteins
>> but still didn't get the 1,000 genes, then take your
>> nonoverlaping_abinits.fasta and blast them directly against your
>> closely related proteins.  Presumably they don't hit too well because
>> if they did they should have been promoted to predictions by Maker the
>> first time, but here you can decide yourself what thresholds to allow
>> to keep the abinit predictions that hit the closely related species
>> proteins.  If you filter you blast hits the way you want and keep the
>> names of the abinit predictions that pass your filter, then use the
>> script Carson attached it it will generate a abinit precidtion GFF file
>> with only the predictions you selected.  You can then pass those
>> predictions back to Maker and force it to keep them and Maker will turn
>> them from predictions
>> (match/match_part) into gene models.
>> 
>> #-----Re-annotation Using MAKER Derived GFF3
>> genome_gff=original_maker_annotations.gff3
>> est_pass=1
>> altest_pass=1
>> protein_pass=1
>> rm_pass=1
>> model_pass=1
>> pred_pass=0
>> other_pass=1
>> 
>> #-----Gene Prediction
>> snaphmm=
>> gmhmm=
>> augustus_species=
>> fgenesh_par_file=
>> pred_gff=ab_init_predictions_rescued_by_blast.gff
>> 
>> keep_preds=1
>> 
>> Barry
>> 
>> >> Thanks,
>> >> Carson
>> >>
>> >> From:  Anastasia Gioti <anastasia.gioti at scilifelab.se>
>> >> Date:  Wed, 25 Apr 2012 11:09:36 +0200
>> >> To:  <maker-devel at yandell-lab.org>
>> >> Subject:  [maker-devel] Use pass-through system to add missing genes
>> >>
>> >> Hi,
>> >> I  have a set of predicted proteins from the genome of a fungus
>> >> annotated by MAKER  using EST data from a closely related species
>> and
>> >> 3 ab initio predictors  (snap iterativelly trained 3 times, genemark
>> >> trained directly on the assembly and augustus with a model from a
>> >> less closely related species), along with a set of fungal proteins.
>> I
>> >> am missing ~ 1000 proteins when I compare to the species i used EST
>> >> data from, and there is good evidence from alignments that these
>> >> genes exist. The question is how to proceed from Blast hits to
>> actual
>> >> gene models here. The idea would be to add these genes to the
>> >> existing dataset, rather than reannotate the genome. I believe that
>> >> reannotating it without any further evidence such as RNA-seq from
>> the
>> >> species itself would not change much,and i d rather stick with
>> actual
>> >> predictions that i trust and have used in subsequent analyses. The
>> >> 1000 genes I can accept to annotate with a less stringent and
>> reliable way than MAKER, I just want to add them so that the difference
>> in gene count gets corrected.
>> >> I was reading the MAKER 2 paper and i was wondering if I can use the
>> >> legacy annotations scheme to do it, by providing GFF3 of the
>> >> alignments between the two species in the regions where genes were
>> >> missed, but as i said, I would not like to reannotate the whole
>> >> genome, and running MAKER2 might cause slight changes that i d like
>> >> to avoid. Is this possible? First, is it possible to provide a Gff3
>> >> file of specific locations and not the entire genome alignment? (I
>> >> guess so..) Second, how can I tag the existing annotations as 'not
>> to be changed' or alternatively, tag the new models only?
>> >> How should I run maker2, with which predictors on and which off?
>> >> Thanks,
>> >> Anastasia
>> >>
>> >> Anastasia Gioti
>> >> Post-doctoral Researcher
>> >>
>> >> anastasia.gioti at scilifelab.se
>> >> anastasia.gioti at ebc.uu.se
>> >>
>> >>
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia
>> >> /
>> >>
>> >>
>> >>
>> >> _______________________________________________ maker-devel mailing
>> >> list
>> >> maker-
>> devel at box290.bluehost.comhttp://box290.bluehost.com/mailman/lis
>> >> tinfo/ma
>> >> ker-devel_yandell-lab.org
>> >> <gff3_select>
>> >
>> > Anastasia Gioti
>> > Post-doctoral Researcher
>> >
>> > anastasia.gioti at scilifelab.se
>> > anastasia.gioti at ebc.uu.se
>> >
>> >
>> http://www.ebc.uu.se/Research/IEG/evbiol/people/pages/Gioti_Anastasia/
>> >
>> >
>> >
>> > _______________________________________________
>> > maker-devel mailing list
>> > maker-devel at box290.bluehost.com
>> > http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-
>> lab.or
>> > g
>> 
>> Barry Moore
>> Research Scientist
>> Dept. of Human Genetics
>> University of Utah
>> Salt Lake City, UT 84112
>> --------------------------------------------
>> (801) 585-3543
>> 
>> 
>> 
>> 
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