substr outside of string at .../Carp.pm 346

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substr outside of string at .../Carp.pm 346

Brandon Pickett
I completed the first round of Maker. I subsequently trained Snap, Genemark-es, and Augustus. I've since fed those results back into Maker for a second round. Some sequences were successful, others were not. On some, I encountered an error about calling translate without a seq argument. I read some other threads about similar issues, and I followed the advice to isolate a single sequence using -g and -base. My config files can be found at this link: https://byu.box.com/s/1tbp48djblo31ruuy8zm62k1vxoyozhq.

The following are the contents of stderr:

STATUS: Parsing control files...
STATUS: Processing and indexing input FASTA files...
STATUS: Setting up database for any GFF3 input...
A data structure will be created for you at:
/path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore

To access files for individual sequences use the datastore index:
/path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_master_datastore_index.log

STATUS: Now running MAKER...
examining contents of the fasta file and run log



--Next Contig--

#---------------------------------------------------------------------
Now starting the contig!!
SeqID: scaffold_66
Length: 2264627
#---------------------------------------------------------------------


setting up GFF3 output and fasta chunks
doing repeat masking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
doing repeat masking
collecting blastx repeatmasking
processing all repeats
in cluster::shadow_cluster...
...finished clustering.
preparing masked sequence
preparing ab-inits
running  snap.
#--------- command -------------#
Widget::snap:
/path/to/snap /path/to/data/snap/rnd1/genome.hmm /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0 > /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0.genome%2Ehmm.snap
#-------------------------------#
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
scoring....decoding.10.20.30.40.50.60.70.80.90.100 done
running  augustus.
#--------- command -------------#
Widget::augustus:
/path/to/apps/augustus/3.3.2/final/bin/augustus --AUGUSTUS_CONFIG_PATH=/path/to/data/augustus_config --species=pacbf --UTR=off /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0 > /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_masked.0.pacbf.augustus
#-------------------------------#
running  genemark.
#--------- command -------------#
Widget::genemark:
/path/to/apps/perl/5.28/perl/bin/perl /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/genemark/gmhmm_wrap -m /path/to/data/gmes/output/gmhmm.mod -g /path/to/apps/genemark-es/4.38/gmhmme3 -p /path/to/apps/genemark-es/4.38/probuild -o /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark /tmp/35082116/maker_0v5GGB/scaffold_66.abinit_nomask.0
#-------------------------------#
gathering ab-init output files
deleted:0 genes
deleted:0 genes
substr outside of string at /path/to/apps/perl/5.28/perl/lib/5.28.0/Carp.pm line 346.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Calling translate without a seq argument!
STACK: Error::throw
STACK: Bio::Root::Root::throw /path/to/apps/bioperl/1.7.2/perl5/lib/perl5/Bio/Root/Root.pm:447
STACK: Bio::Tools::CodonTable::translate /path/to/apps/bioperl/1.7.2/perl5/lib/perl5/Bio/Tools/CodonTable.pm:419
STACK: CGL::TranslationMachine::longest_translation_plus_stop /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/CGL/TranslationMachine.pm:280
STACK: maker::auto_annotator::get_translation_seq /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/maker/auto_annotator.pm:3575
STACK: Widget::snap::load_phat_hits /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/snap.pm:973
STACK: Widget::snap::parse /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Widget/snap.pm:689
STACK: GI::parse_abinit_file /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/GI.pm:1228
STACK: Process::MpiChunk::_go /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:1473
STACK: Process::MpiChunk::run /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:340
STACK: Process::MpiChunk::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiChunk.pm:356
STACK: Process::MpiTiers::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiTiers.pm:287
STACK: Process::MpiTiers::run_all /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/../lib/Process/MpiTiers.pm:287
STACK: /path/to/apps/maker/3.01.02-beta/gcc-8.3.0_mpich-3.3.1_perl-5.28.0/bin/maker:679
-----------------------------------------------------------
--> rank=NA, hostname=somenode.rc.byu.edu
ERROR: Failed while gathering ab-init output files
ERROR: Chunk failed at level:1, tier_type:2
FAILED CONTIG:scaffold_66

ERROR: Chunk failed at level:4, tier_type:0
FAILED CONTIG:scaffold_66

examining contents of the fasta file and run log



--Next Contig--

Processing run.log file...


Maker is now finished!!!

The command I ran was as follows:

maker -g /path/to/data/originalAssembly/split/scaffold_66.fasta \
    -base scaffolds -TMP /tmp/35082116 -cpus 1

I usually run maker with MPI (e.g., mpirun maker -TMP /tmp/abcdefg -cpus 1), but didn't see any need when I was running a single sequence as a test. Note that this output from this isolated run matches what I've been seeing in the mixed output from MPI, just slightly jumbled together with other things.

The following is the bottom of the run.log file for this sequence in the datastore:

LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0
LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0
LOGCHILD    /path/to/data/maker/rnd2/scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/run.log.child.0
STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.genome%2Ehmm.snap
FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.genome%2Ehmm.snap
STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.pacbf.augustus
FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_masked.0.pacbf.augustus
STARTED scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark
FINISHED    scaffolds.maker.output/scaffolds_datastore/92/0F/scaffold_66//theVoid.scaffold_66/scaffold_66.abinit_nomask.0.gmhmm%2Emod.genemark
DIED    RANK    0:4:0:0
DIED    COUNT   1
DIED    RANK    0
DIED    COUNT   1

The contents of theVoid directory can be viewed at this link: https://byu.box.com/s/hqwngdvehs8dfoymtrkjyismq3p8ayv1.

Do you have any suggestions on how I can resolve this error?

Thank you,
Brandon

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