minillinim/Mannotator — Issue #1: Error in combineGffOrfs
Author: ctSkennerton
Created: 2012-02-13 12:03:11+00:00
State: open

There's just something special about Mads' data that makes all our software crash
```
Step 1: Splitting GFF and FASTA files into temporary directories
Parsing GFF file prodigal_orfs.gff
Step 2: Combining Gffs

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not open mannotator_64791329134147_Prodigal_Seq_4/sequence.fa: No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/Root/Root.pm:472
STACK: Bio::Root::IO::_initialize_io /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/Root/IO.pm:351
STACK: Bio::SeqIO::_initialize /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/SeqIO.pm:474
STACK: Bio::SeqIO::fasta::_initialize /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/SeqIO/fasta.pm:93
STACK: Bio::SeqIO::new /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/SeqIO.pm:358
STACK: Bio::SeqIO::new /srv/whitlam/bio/apps/sw/cpan-modules/lib/perl5//Bio/SeqIO.pm:397
STACK: /srv/whitlam/bio/apps/sw/mannotator/github_version/Mannotator//combineGffOrfs.pl:92
-----------------------------------------------------------
Error: Command 'combineGffOrfs.pl -c mannotator_64791329134147_Prodigal_Seq_4/sequence.fa -g mannotator_64791329134147_Prodigal_Seq_4/prodigal_orfs.gff -o mannotator_64791329134147_Prodigal_Seq_4/combined.gff3 -a mannotator_64791329134147_Prodigal_Seq_4/unknowns.fa -m 100' failed with return status 512
```