[maker-devel] Problem before running ab-initio predictors

[Carson Holt]

Could you make sure trna=0 is set in the maker_opt.ctl file, and leave that
off for the time being.  It is a new feature that was added since 2.28, and
may be a little buggy.  I’ll try and replicate the error here.  Could you
send me a copy of your maker_opts.ctl file.  For the mean time just turn off
the trna option and you should be able to run, you can always run with
trna=1 later (even by itself as a separate run) without loosing anything.

Thanks,
Carson

From:  carlos vargas <charlos9 at gmail.com>
Date:  Wednesday, January 22, 2014 at 5:34 PM
To:  "maker-devel at yandell-lab.org" <maker-devel at yandell-lab.org>
Subject:  [maker-devel] Problem before running ab-initio predictors

Hello,

I finally was able to install maker with mpi support, however now I see a
new error which I wasn't seeing before. Both for mpiexec and single maker
runs I observe the following error just after it finishes running exonerate.


Thank you for your time!

Carlos

deleted:0 hits
collecting blastx reports
flattening protein clusters
prepare section files
processing the chunk divide
preparing evidence clusters for annotations
Preparing evidence for hint based annotation
cleaning clusters....
total clusters:1 now processing 0
cleaning clusters....
total clusters:1 now processing 0
annotating transcripts
Making transcripts
 ...processing 0 of 1
ERROR: Not a valid predictor in auto_annoator::get_pred_shot
 at /home/cvargas/maker/bin/../lib/maker/auto_annotator.pm
<http://auto_annotator.pm>  line 2155.
maker::auto_annotator::get_pred_shot(FastaSeq=HASH(0x3eb6920), ">2973",
"/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"..., undef,
HASH(0x3eeb9f8), 0, "trnascan", HASH(0x3fb1f80), runlog=HASH(0x3ec6e38),
...) called at /home/cvargas/maker/bin/../lib/maker/auto_annotator.pm
<http://auto_annotator.pm>  line 1923
maker::auto_annotator::run_it(ARRAY(0x3fab4d0),
"/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"...,
FastaSeq=HASH(0x3eb6920), FastaSeq=HASH(0x3ed42d0), ">2973", "trnascan",
HASH(0x3fb1f80)) called at
/home/cvargas/maker/bin/../lib/maker/auto_annotator.pm
<http://auto_annotator.pm>  line 920
maker::auto_annotator::annotate_trans(FastaSeq=HASH(0x3ed42d0),
FastaSeq=HASH(0x3eb6920), ">2973", 2973, ARRAY(0x3e818f8),
"/gnmP05/Carlos/mpiannotatetest/longest.maker.output/longest_d"...,
HASH(0x3fb1f80), runlog=HASH(0x3ec6e38)) called at
/home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 3775
Process::MpiChunk::__ANON__() called at
/home/cvargas/maker/bin/../lib/Error.pm line 415
eval {...} called at /home/cvargas/maker/bin/../lib/Error.pm line 407
Error::subs::try(CODE(0x3eb6d58), HASH(0x3eb74b8)) called at
/home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 4215
Process::MpiChunk::_go(Process::MpiChunk=HASH(0x3e90218), "run",
HASH(0x3e81748), 1, 4) called at
/home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 341
Process::MpiChunk::run(Process::MpiChunk=HASH(0x3e90218), 0) called at
/home/cvargas/maker/bin/../lib/Process/MpiChunk.pm line 357
Process::MpiChunk::run_all(Process::MpiChunk=HASH(0x3e90218), 0) called at
/home/cvargas/maker/bin/../lib/Process/MpiTiers.pm line 287
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3ea34b8), 0) called at
/home/cvargas/maker/bin/../lib/Process/MpiTiers.pm line 287
Process::MpiTiers::run_all(Process::MpiTiers=HASH(0x3e733e8), 0) called at
/home/cvargas/maker/bin/maker line 670
--> rank=NA, hostname=Ritchie
ERROR: Failed while annotating transcripts
ERROR: Chunk failed at level:1, tier_type:4
FAILED CONTIG:2973

ERROR: Chunk failed at level:6, tier_type:0
FAILED CONTIG:2973

examining contents of the fasta file and run log

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