[maker-devel] Maker issues
Carson Holt
carsonhh at gmail.com
Mon Nov 26 14:37:43 MST 2012
The sequence object is being created well down into BioPerl (outside of my
control), but I think I can explicitly set the alphabet to 'dna' by
modifying the existing object just before calling the revcomp method to
get around that.
Thanks,
Carson
On 12-11-26 4:32 PM, "Jason Stajich" <jason.stajich at gmail.com> wrote:
>right - you can explicitly set the alphabet to 'dna' when building a
>sequence object but I don't know if this down in MAKER code that is
>tripping up?
>
>Jason
>On Nov 25, 2012, at 9:33 PM, "Fields, Christopher J"
><cjfields at illinois.edu> wrote:
>
>> This is coming from BioPerl trying to guess the alphabet if one is not
>>provided. The specific spot:
>>
>> if( ($str =~ tr/ATUGCNatugcn//) / $total > 0.7 ) {
>> if ( $str =~ m/U/i ) {
>> $alphabet = 'rna';
>> } else {
>> $alphabet = 'dna';
>> }
>> } else {
>> $alphabet = 'protein';
>> }
>>
>> Easy enough to fix to allow for additional ambiguous nucleotides (just
>>committed, in fact). It's probably best to explicitly set this when
>>possible, though; it is a guess, after all.
>>
>> chris
>>
>> On Nov 25, 2012, at 10:56 PM, Mark Yandell <myandell at genetics.utah.edu>
>>wrote:
>>
>>> good detective work there Carson!
>>>
>>>
>>> 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 Carson Holt
>>>[carsonhh at gmail.com]
>>> Sent: Sunday, November 25, 2012 9:10 PM
>>> To: Daniel Standage
>>> Cc: Maker Mailing List
>>> Subject: Re: [maker-devel] Maker issues
>>>
>>> I think the problem is in the sequence of your scaffold. I pulled
>>>this out of the exonerate alignment -->
>>> WTGGGGCTATGAAAAAAAAAWTTKMGMMAAAAAWTTWTKRWMRATC
>>>
>>> Notice the letters W, K, R, M, etc. While these are technically legal
>>>nucleotides, many external programs, and in this case BioPerl doesn't
>>>handle them well.
>>> That is why you get -->
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: Sequence is a protein. Cannot revcom
>>>
>>> You might want to replace them in your input fasta with the letter 'N'
>>>so they are treated as masked. You will have to delete the mpi_blastdb
>>>directory to let maker rebuild the fasta indexes and you will probably
>>>have to set clean_try=1 in the control files so that MAKER deletes old
>>>result files that contain those characters on the retry. The other
>>>error may be just a snowball effect from the first error, so you should
>>>see of it still happens after fixing the input fasta file.
>>>
>>> Thanks,
>>> Carson
>>>
>>>
>>>
>>> From: Daniel Standage
>>><daniel.standage at gmail.com<mailto:daniel.standage at gmail.com>>
>>> Date: Friday, 23 November, 2012 3:06 PM
>>> 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
>>>
>>> Thanks for your reply, and sorry for my delayed response.
>>>
>>> I have attached the first file you requested, but the other two do not
>>>exist. I have attached a listing of the files in that directory. Let me
>>>know if you need anything else.
>>>
>>>
>>> --
>>> Daniel S. Standage
>>> Ph.D. Candidate
>>> Bioinformatics and Computational Biology Program
>>> Department of Genetics, Development, and Cell Biology
>>> Iowa State University
>>>
>>>
>>>
>>> On Mon, Nov 12, 2012 at 10:02 AM, Carson Holt
>>><carsonhh at gmail.com<mailto:carsonhh at gmail.com>> wrote:
>>> 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.
>>>maker.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.
>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2
>>>3/scaffold_23.716125-721460.0.fasta
>>>
>>> And this one -->
>>>/N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.
>>>maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_2
>>>3/comp58983_c0_seq101.for.716125-721460.0.fasta
>>>
>>> thanks,
>>> Carson
>>>
>>>
>>>
>>>
>>> From: Daniel Standage
>>><daniel.standage at gmail.com<mailto:daniel.standage at gmail.com>>
>>> Date: Thursday, 8 November, 2012 9:32 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
>>>
>>> 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_2
>>>3/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_2
>>>3/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_2
>>>3/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_2
>>>3/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.p
>>>m line 433.
>>> Calling uri_escape at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m line 433.
>>> Calling File::Path::mkpath at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m 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.fo
>>>r.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno
>>>
>>>tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datasto
>>>re/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/scaf
>>>fold_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_i
>>>nfo.pm:86<http://splice_info.pm:86>
>>> STACK: Widget::exonerate::est2genome::assemble
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e
>>>st2genome.pm:686<http://est2genome.pm:686>
>>> STACK: Widget::exonerate::est2genome::parse
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/e
>>>st2genome.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.p
>>>m:1663
>>> STACK: Process::MpiChunk::run
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m:335
>>> STACK: Process::MpiChunk::run_all
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m:351
>>> STACK: Process::MpiTiers::run_all
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p
>>>m:286
>>> STACK: Process::MpiTiers::run_all
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.p
>>>m: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.p
>>>m line 433.
>>> Calling uri_escape at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m line 433.
>>> Calling File::Path::mkpath at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m 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.p
>>>m line 433.
>>> Calling uri_escape at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m line 433.
>>> Calling File::Path::mkpath at
>>>/N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.p
>>>m 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> 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
>
>Jason Stajich
>jason.stajich at gmail.com
>jason at bioperl.org
>
>
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