[maker-devel] Maker issues

Daniel Standage daniel.standage at gmail.com
Thu Nov 8 07:32:59 MST 2012 

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
STACK: Widget::exonerate::est2genome::assemble
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/
est2genome.pm:686
STACK: Widget::exonerate::est2genome::parse
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/
est2genome.pm:961
STACK: polisher::exonerate::est::e_exonerate
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/
est.pm:82
STACK: polisher::exonerate::est::polish
/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/
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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