[maker-devel] Maker issues

Thu Nov 8 08:48:52 MST 2012

Based on Mark's suggestion, I took a look at the EST files. Luckily there
is no protein sequence contamination.

[dstandag at mason Transcriptome] grep -v '^>' Pdom.Trinity.Trimmomatic.fasta
| grep -o . | sort | uniq -c
79400764 A
39834991 C
40702954 G
77980105 T
[dstandag at mason Transcriptome] grep -v '^>' Pmet.Trinity.R.fasta | grep -o
. | sort | uniq -c
18294708 A
9108213 C
9449127 G
17756470 T

--
Daniel S. Standage
Ph.D. Candidate
Bioinformatics and Computational Biology Program
Department of Genetics, Development, and Cell Biology
Iowa State University

On Thu, Nov 8, 2012 at 9:47 AM, Mark Yandell <myandell at genetics.utah.edu>wrote:

> Hi Daniel,
>
> is it possible you have some proteins in your EST files?
>
> '------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Sequence is a protein. Cannot revcom
> STACK: Error::throw'
>
>
>
> Mark Yandell
> Professor of Human Genetics
> H.A. & Edna Benning Presidential Endowed Chair
> Eccles Institute of Human Genetics
> University of Utah
> 15 North 2030 East, Room 2100
> Salt Lake City, UT 84112-5330
> ph:801-587-7707
>
> ________________________________________
> From: maker-devel-bounces at yandell-lab.org [
> maker-devel-bounces at yandell-lab.org] on behalf of Daniel Standage [
> daniel.standage at gmail.com]
> Sent: Thursday, November 08, 2012 7:32 AM
> To: Carson Holt
> Cc: Maker Mailing List
> Subject: Re: [maker-devel] Maker issues
>
> Scaling up to whole-genome annotation, things seem to be going well.
> However, there are some intermittent issues. I've seen a couple occurrences
> of the following error...
>
> #-------------------------------#
> Calling out to FastaSeq::convert at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.
> running  est2genome search.
> #--------- command -------------#
> Widget::exonerate::est2genome:
> /N/hd01/dstandag/Mason/local/bin/exonerate  -q
> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta
> -t
> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta
> -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000
> --showcigar --percent 20 >
> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0
> #-------------------------------#
> Calling out to FastaSeq::convert at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.
> couldn't close
> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta
> at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line
> 60.
> --> rank=NA, hostname=c4
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:2
> FAILED CONTIG:scaffold_23
>
> ERROR: Chunk failed at level:5, tier_type:0
> FAILED CONTIG:scaffold_23
>
> examining contents of the fasta file and run log
> Calling Datastore::MD5::mkdir at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling uri_escape at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling File::Path::mkpath at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
>
>
> ...as well as one occurrence of this error.
>
> #-------------------------------#
> Calling out to FastaSeq::convert at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.
> running  est2genome search.
> #--------- command -------------#
> Widget::exonerate::est2genome:
> /N/hd01/dstandag/Mason/local/bin/exonerate  -q
> /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd
> om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta
> -t /N/dc/scratch/dstandag/PdomGenomic/Anno
>
> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta
> -Q dna -T dna --model est2genome  --minintron 20 --maxintron 10000
> --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/
>
> output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se
> q93.est_exonerate.0
> #-------------------------------#
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Sequence is a protein. Cannot revcom
> STACK: Error::throw
> STACK: Bio::Root::Root::throw
> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368
> STACK: Bio::PrimarySeqI::revcom
> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381
> STACK: Bio::LocatableSeq::revcom
> /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577
> STACK: exonerate::splice_info::needs_to_be_revcomped
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/
> splice_info.pm:86<http://splice_info.pm:86>
> STACK: Widget::exonerate::est2genome::assemble
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/
> est2genome.pm:686<http://est2genome.pm:686>
> STACK: Widget::exonerate::est2genome::parse
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/
> est2genome.pm:961<http://est2genome.pm:961>
> STACK: polisher::exonerate::est::e_exonerate
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/
> est.pm:82<http://est.pm:82>
> STACK: polisher::exonerate::est::polish
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/
> est.pm:44<http://est.pm:44>
> STACK: GI::to_polisher
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670
> STACK: GI::polish_exonerate
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517
> STACK: Process::MpiChunk::_go
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663
> STACK: Process::MpiChunk::run
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335
> STACK: Process::MpiChunk::run_all
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351
> STACK: Process::MpiTiers::run_all
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286
> STACK: Process::MpiTiers::run_all
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286
> STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644
> -----------------------------------------------------------
> --> rank=NA, hostname=c4
> ERROR: Failed while polishig ESTs
> ERROR: Chunk failed at level:2, tier_type:2
> FAILED CONTIG:scaffold_7
>
> ERROR: Chunk failed at level:5, tier_type:0
> FAILED CONTIG:scaffold_7
>
> examining contents of the fasta file and run log
> Calling Datastore::MD5::mkdir at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling uri_escape at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling File::Path::mkpath at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
>
> I'll let you know if I see anything else.
>
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
> On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt <carsonhh at gmail.com<mailto:
> carsonhh at gmail.com>> wrote:
> Thanks.  Typo now fixed on my end too ;-)
>
> Thanks,
> Carson
>
>
> From: Daniel Standage <daniel.standage at gmail.com<mailto:
> daniel.standage at gmail.com>>
> Date: Wednesday, 7 November, 2012 11:43 AM
>
> To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
> Cc: Maker Mailing List <maker-devel at yandell-lab.org<mailto:
> maker-devel at yandell-lab.org>>
> Subject: Re: Maker issues
>
> Looked good for a while, but came across this error.
>
> total clusters:20 now processing 0
> flattening EST clusters
> doing tblastx of alt-ESTs
> Undefined subroutine &GI::loalize_file called at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648.
> --> rank=NA, hostname=c4
> ERROR: Failed while doing tblastx of alt-ESTs
> ERROR: Chunk failed at level:4, tier_type:2
> FAILED CONTIG:scaffold_58
>
> ERROR: Chunk failed at level:5, tier_type:0
> FAILED CONTIG:scaffold_58
>
> examining contents of the fasta file and run log
> Calling Datastore::MD5::mkdir at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling uri_escape at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
> Calling File::Path::mkpath at
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm
> line 433.
>
>
>
> --Next Contig--
>
> It seems pretty clear that there is a typo in GI.pm. I changed loalize to
> localize and relaunched.
>
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
> On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage <daniel.standage at gmail.com
> <mailto:daniel.standage at gmail.com>> wrote:
> Done.
>
> Test job has successfully cleared the preliminary Fasta indexing steps and
> is repeat masking. I'll let you know if there are any problems. Thanks!
>
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
> On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt <carsonhh at gmail.com<mailto:
> carsonhh at gmail.com>> wrote:
> 1.006902        Bio::Root::Version
>  /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm
>
> One thing I noticed, in the debug output is that you are using Bioperl
> live (here -->  /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live).  It's
> fasta indexer is broken.  I have an open bug I am trying to resolve with
> the Bioperl developers, but for now use the CPAN version of Bioperl.
>
> Thanks,
> Carson
>
>
>
>
> From: Daniel Standage <daniel.standage at gmail.com<mailto:
> daniel.standage at gmail.com>>
> Date: Monday, 5 November, 2012 10:14 AM
> To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>
> Cc: Maker Mailing List <maker-devel at yandell-lab.org<mailto:
> maker-devel at yandell-lab.org>>
> Subject: Re: Maker issues
>
> Debug output attached (bzip2 compressed).
>
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
> On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt <carsonhh at gmail.com<mailto:
> carsonhh at gmail.com>> wrote:
> Thanks. Could you also run with the --debug flag set on the command line
> for a few minutes and send me that.
>
> --Carson
>
>
> From: Daniel Standage <daniel.standage at gmail.com<mailto:
> daniel.standage at gmail.com>>
> Date: Monday, 5 November, 2012 10:05 AM
> To: Carson Holt <carsonhh at gmail.com<mailto:carsonhh at gmail.com>>, Maker
> Mailing List <maker-devel at yandell-lab.org<mailto:
> maker-devel at yandell-lab.org>>
> Subject: Maker issues
>
> Carson,
>
> I updated to the latest development version, made sure the TMP directory
> is on native disk space, and relaunched. I have attached the output of the
> job that failed in <5 minutes. It looks pretty similar to the errors I got
> the last time I used the dev version.
>
> --
> Daniel S. Standage
> Ph.D. Candidate
> Bioinformatics and Computational Biology Program
> Department of Genetics, Development, and Cell Biology
> Iowa State University
>
>
>
>
>
>
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