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ARRAY reference and Bio::SimpleAlign::column_from_residue_number problems #41
Description
I'm trying to run mfannot on a number of yeast mitochondrial assemblies. Nearly all of them worked perfectly but I am getting two separate errors in two separate assemblies. The command to run all of the assemblies is the same:
mfannot \
--genetic 3 \
--outputfile $prefix.mitochondrial_genome.mfannot.out \
--logfile $prefix.mitochondrial_genome.mfannot.log \
--T $(pwd)/tmp \
$prefix.assembly.mitochondrial_genome.fa
Any ideas what might be going wrong here?
Error 1:
Can't use an undefined value as an ARRAY reference at /home/travisan/public/local/bin/mfannot line 5490.
Input fasta: error1_assembly.fa.txt
Debug output: error1_debug.txt
Error 2:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not find a sequence segment in myProt containing residue number 492
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/travisan/public/local/lib/perl5/site_perl/5.30.2/Bio/Root/Root.pm:449
STACK: Bio::SimpleAlign::column_from_residue_number /home/travisan/public/local/lib/perl5/site_perl/5.30.2/Bio/SimpleAlign.pm:2683
STACK: main::DefineSeqOfHypprotAndPosOfIntronInAlignment /home/travisan/public/local/bin/mfannot:3491
STACK: /home/travisan/public/local/bin/mfannot:3130
-----------------------------------------------------------
Input fasta: error2_assembly.fa.txt
Debug output: error2_debug.txt
Activity
natacha-beck commentedon May 13, 2020
@gettl008 It sometimes happen when searching for mini-exons. Using
--partialoption will skip the mini-exons but will normally allow you to get your result.