[maker-devel] Maker issues
Carson Holt
carsonhh at gmail.com
Sun Nov 25 21:10:11 MST 2012
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>
Date: Friday, 23 November, 2012 3:06 PM
To: Carson Holt <carsonhh at gmail.com>
Cc: Maker Mailing List <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> 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_7.1
> 869077-1869882.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_23/scaffold_2
> 3.716125-721460.0.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_23/comp58983_
> 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/comp5898
>> 3_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/comp5898
>> 3_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.186
>> 9077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno
>> tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/sc
>> affold_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.p
>> m:86 <http://splice_info.pm:86>
>> STACK: Widget::exonerate::est2genome::assemble
>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge
>> nome.pm:686 <http://est2genome.pm:686>
>> STACK: Widget::exonerate::est2genome::parse
>> /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/est2ge
>> nome.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:166>>
3
>> 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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