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BFL-lab / Mfannot

MFannot is a program for the annotation of mitochondrial and plastid genomes
GNU General Public License v3.0
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ARRAY reference and Bio::SimpleAlign::column_from_residue_number problems #41

Open gettl008 opened 4 years ago

gettl008 commented 4 years ago

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

natacha-beck commented 4 years ago

@gettl008 It sometimes happen when searching for mini-exons. Using --partial option will skip the mini-exons but will normally allow you to get your result.