Maker train SNAP: substr outside of string at Carp.pm

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Maker train SNAP: substr outside of string at Carp.pm

Yuna
Hi,

I ran MAKER successfully to generate data for training SNAP. However,
now I want to run the training round with MAKER (run MAKER with the hmm
file), but MAKER fails for every contig it processed till now. The
"evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except
the gff header line) and the error massage is attached below. I can not
figure out what the problem is.

I  appreciate any help. Thank you!

Log:
gathering ab-init output files

deleted:0 genes
substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw
/vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447
STACK: Bio::Tools::CodonTable::translate
/vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419
STACK: CGL::TranslationMachine::longest_translation_plus_stop
/vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280
STACK: maker::auto_annotator::get_translation_seq
/vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236
STACK: Widget::snap::load_phat_hits
/vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974
STACK: Widget::snap::parse
/vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690
STACK: GI::parse_abinit_file
/vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194
STACK: Process::MpiChunk::_go
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469
STACK: Process::MpiChunk::run
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341
STACK: Process::MpiChunk::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357
STACK: Process::MpiTiers::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all
/vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686
-----------------------------------------------------------
--> rank=NA, hostname=snorf
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:chr1

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:chr1

examining contents of the fasta file and run log


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Re: Maker train SNAP: substr outside of string at Carp.pm

Carson Holt-2
It dies trying to read SNAP’s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using.

—Carson


> On Jun 25, 2019, at 7:54 AM, Yuna <[hidden email]> wrote:
>
> Hi,
>
> I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is.
>
> I  appreciate any help. Thank you!
>
> Log:
> gathering ab-init output files
>
> deleted:0 genes
> substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Calling translate without a seq argument!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447
> STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419
> STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280
> STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236
> STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974
> STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690
> STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194
> STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469
> STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341
> STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357
> STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
> STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
> STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686
> -----------------------------------------------------------
> --> rank=NA, hostname=snorf
> ERROR: Failed while gathering ab-init output files
> ERROR: Chunk failed at level:1, tier_type:2
> FAILED CONTIG:chr1
>
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:chr1
>
> examining contents of the fasta file and run log
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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Re: Maker train SNAP: substr outside of string at Carp.pm

Xabier Vázquez-Campos
Hi Yuna,
adding to Carson's answer, check the output of maker2zff. If you don't have RNAseq data or any other high-quality evidences for annotation, chances are that the default parameters of maker2zff are too strict and are producing empty output files.
Check the maker2zff --help and adjust the options as needed. In "worst case scenario" you may need to run it with "-n", which has no filtering at all in regards about which genes from the gff file to select.
Cheers,
Xabi

On Wed, 26 Jun 2019 at 07:17, Carson Holt <[hidden email]> wrote:
It dies trying to read SNAP’s result file. Check earlier in the log to see if there are any other errors. If not, run maker without MPI on a single CPU. You should be able to copy the command MAKER is using to call SNAP right before the failure. You can try running it outside of MAKER. My guess is there is a problem with SNAP failing and leaving a truncated report, or something in wrong with the training file SNAP is using.

—Carson


> On Jun 25, 2019, at 7:54 AM, Yuna <[hidden email]> wrote:
>
> Hi,
>
> I ran MAKER successfully to generate data for training SNAP. However, now I want to run the training round with MAKER (run MAKER with the hmm file), but MAKER fails for every contig it processed till now. The "evidence_3.gff.ann" and "evidence_3.gff.def" files are empty (except the gff header line) and the error massage is attached below. I can not figure out what the problem is.
>
> I  appreciate any help. Thank you!
>
> Log:
> gathering ab-init output files
>
> deleted:0 genes
> substr outside of string at /usr/share/perl5/vendor_perl/Carp.pm line 346.
>
> ------------- EXCEPTION: Bio::Root::Exception -------------
> MSG: Calling translate without a seq argument!
> STACK: Error::throw
> STACK: Bio::Root::Root::throw /vol/perl/v5.28.1/lib/perl5/Bio/Root/Root.pm:447
> STACK: Bio::Tools::CodonTable::translate /vol/perl/v5.28.1/lib/perl5/Bio/Tools/CodonTable.pm:419
> STACK: CGL::TranslationMachine::longest_translation_plus_stop /vol/biotools/lib/maker-2.31.10/bin/../lib/CGL/TranslationMachine.pm:280
> STACK: maker::auto_annotator::get_translation_seq /vol/biotools/lib/maker-2.31.10/bin/../lib/maker/auto_annotator.pm:3236
> STACK: Widget::snap::load_phat_hits /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:974
> STACK: Widget::snap::parse /vol/biotools/lib/maker-2.31.10/bin/../lib/Widget/snap.pm:690
> STACK: GI::parse_abinit_file /vol/biotools/lib/maker-2.31.10/bin/../lib/GI.pm:1194
> STACK: Process::MpiChunk::_go /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:1469
> STACK: Process::MpiChunk::run /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:341
> STACK: Process::MpiChunk::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiChunk.pm:357
> STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
> STACK: Process::MpiTiers::run_all /vol/biotools/lib/maker-2.31.10/bin/../lib/Process/MpiTiers.pm:287
> STACK: /vol/biotools/lib/maker-2.31.10/bin/maker:686
> -----------------------------------------------------------
> --> rank=NA, hostname=snorf
> ERROR: Failed while gathering ab-init output files
> ERROR: Chunk failed at level:1, tier_type:2
> FAILED CONTIG:chr1
>
> ERROR: Chunk failed at level:4, tier_type:0
> FAILED CONTIG:chr1
>
> examining contents of the fasta file and run log
>
>
> _______________________________________________
> maker-devel mailing list
> [hidden email]
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org


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--
Xabier Vázquez-Campos, PhD
Research Associate
NSW Systems Biology Initiative
School of Biotechnology and Biomolecular Sciences
The University of New South Wales
Sydney NSW 2052 AUSTRALIA

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