[maker-devel] Maker issues
Mark Yandell
myandell at genetics.utah.edu
Thu Nov 8 07:47:20 MST 2012
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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