[maker-devel] Maker issues

Carson Holt carsonhh at gmail.com
Mon Nov 12 08:02:21 MST 2012 

The first error is an IO error with your system.  I've added some more
detail to the errors in the development version if you do an 'svn update'.
Then you will know the system specific reason why close or opened failed.
For the other error, could you send me this file  -->
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.make
r.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold
_7.1869077-1869882.comp59027_c1_seq93.est_exonerate.0

This one --> 
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make
r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffo
ld_23.716125-721460.0.fasta

And this one --> 
/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.make
r.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58
983_c0_seq101.for.716125-721460.0.fasta

thanks,
Carson




From:  Daniel Standage <daniel.standage at gmail.com>
Date:  Thursday, 8 November, 2012 9:32 AM
To:  Carson Holt <carsonhh at gmail.com>
Cc:  Maker Mailing List <maker-devel at yandell-lab.org>
Subject:  Re: 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_2
> 3.716125-721460.0.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_2
> 3.716125-721460.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.1869
> 077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno
> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sca
> ffold_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/est2gen
> ome.pm:686 <http://est2genome.pm:686>
> STACK: Widget::exonerate::est2genome::parse
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2gen
> ome.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.p
> m:82 <http://est.pm:82>
> STACK: polisher::exonerate::est::polish
> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/est.p
> m: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> wrote:
> Thanks.  Typo now fixed on my end too ;-)
> 
> Thanks,
> Carson
> 
> 
> From:  Daniel Standage <daniel.standage at gmail.com>
> Date:  Wednesday, 7 November, 2012 11:43 AM
> 
> To:  Carson Holt <carsonhh at gmail.com>
> Cc:  Maker Mailing List <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>
> 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> 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>
>>> Date:  Monday, 5 November, 2012 10:14 AM
>>> To:  Carson Holt <carsonhh at gmail.com>
>>> Cc:  Maker Mailing List <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> 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>
>>>> Date:  Monday, 5 November, 2012 10:05 AM
>>>> To:  Carson Holt <carsonhh at gmail.com>, Maker Mailing List
>>>> <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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