Bio::Root::Exception thrown during core genome alignment, missing some sequence in core_gene_alignment.aln #224
Comments
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Wondering if there has been any progress on this? Another person in my lab is now using roary with a different dataset on a different computer / linux install and encountering the same error. Surely we're not the only ones? |
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I have this issue also essentially the same error: Use of uninitialized value in require at (eval 77612) line 1. ------------- EXCEPTION: Bio::Root::Exception ------------- |
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I have the same issue running Roary on Biolinux 8. I have checked all the dependencies and have ran the install_dependencies.sh. Is there some package I should update or install that I am unaware of? ------------- EXCEPTION: Bio::Root::Exception ------------- |
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BioLinux 8 was last updated 4 years ago, so there could be many dependancy issues. I would start with upgrading the underlying OS. |
I had mentioned this when trying to figure out my roary_plots issue, but it appears to be separate so I wanted to post it here as I think I have noticed a real consequence to this error.
The error below appears during the MAFFT core genome alignment step. I have noticed when scanning through core_gene_alignment.aln that there are stretches where one strain in the alignment is missing a gene and only has "-" listed across the length of the gene as opposed to bases. As this is a core genome alignment, it seems to me that no strain should be lacking an entire gene, especially when core is defined at present in 99% and we're looking at 5 genomes. This is visible in the Cdiff data which I have posted at my github.
Error is:
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open pan_genome_sequences/group_16429.fa.aln: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:486
STACK: Bio::Root::IO::_initialize_io /usr/share/perl5/Bio/Root/IO.pm:351
STACK: Bio::SeqIO::_initialize /usr/share/perl5/Bio/SeqIO.pm:491
STACK: Bio::SeqIO::fasta::_initialize /usr/share/perl5/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:372
STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:413
STACK: Bio::Roary::SortFasta::_input_seqio /usr/local/share/perl/5.18.2/Bio/Roary/SortFasta.pm:27
STACK: Bio::Roary::SortFasta::sort_fasta /usr/local/share/perl/5.18.2/Bio/Roary/SortFasta.pm:68
STACK: Bio::Roary::CommandLine::GeneAlignmentFromNucleotides::run /usr/local/share/perl/5.18.2/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm:107
STACK: /usr/local/bin/protein_alignment_from_nucleotides:14
And the error seems to occur multiple times during the MAFFT step. I'm running Biolinux 8, other dependency info available upon request. Also, the MAFFT step seems to usually take a particularly long time especially if more than a few strains are used (say 50 instead of 5). Not sure if this is the expected behavior or not.
Best,
S. Wesley Long
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