Question: Roary pan genome analysis error
0
gravatar for jeccy.J
3.1 years ago by
jeccy.J50
Argentina
jeccy.J50 wrote:

Does anyone one have idea what is the error in Roary pan genome analysis:

$ roary *.gff

Please cite Roary if you use any of the results it produces: Andrew J. Page, Carla A. Cummins, Martin Hunt, Vanessa K. Wong, Sandra Reuter, Matthew T. G. Holden, Maria Fookes, Daniel Falush, Jacqueline A. Keane, Julian Parkhill, "Roary: Rapid large-scale prokaryote pan genome analysis", Bioinformatics, 2015 Nov 15;31(22):3691-3693 doi: http://doi.org/10.1093/bioinformatics/btv421 Pubmed: 26198102

sh: line 1: 31387 Aborted (core dumped) /usr/bin/cdhit -i _combined_files -o _clustered -T 1 -M 1800 -g 1 -s 1 -d 256 -c 1 > /dev/null 2>&1

Cant open file: _clustered.clstr ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: Could not open _clustered: No such file or directory

STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:472 STACK: Bio::Root::IO::_initialize_io /usr/share/perl5/Bio/Root/IO.pm:351 STACK: Bio::SeqIO::_initialize /usr/share/perl5/Bio/SeqIO.pm:474 STACK: Bio::SeqIO::fasta::_initialize /usr/share/perl5/Bio/SeqIO/fasta.pm:93 STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:358 STACK: Bio::SeqIO::new /usr/share/perl5/Bio/SeqIO.pm:397 STACK: Bio::Roary::ChunkFastaFile::_input_seqio /home/Roary-d77b670/lib/Bio/Roary/ChunkFastaFile.pm:38 STACK: Bio::Roary::ChunkFastaFile::sequence_file_names /home/Roary-d77b670/lib/Bio/Roary/ChunkFastaFile.pm:59 STACK: Bio::Roary::ParallelAllAgainstAllBlast::_sequence_file_names /home/Roary-d77b670/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm:72 STACK: Bio::Roary::ParallelAllAgainstAllBlast::run /home/Roary-d77b670/lib/Bio/Roary/ParallelAllAgainstAllBlast.pm:117 STACK: Bio::Roary::run /home/Roary-d77b670/lib/Bio/Roary.pm:97 STACK: Bio::Roary::CommandLine::Roary::run /home/Roary-d77b670/lib/Bio/Roary/CommandLine/Roary.pm:302 STACK: /usr/local/bin/roary:14

roary pangenome • 1.7k views
ADD COMMENTlink written 3.1 years ago by jeccy.J50

I am not familiar with "roary" but the error is clear. It can't seem to be able to open files starting with an "_" in the name. Does that name ring a bell as an input/output option you had provided (or is that something the program did on its own)?

ADD REPLYlink written 3.1 years ago by genomax65k

the program did by own ....i have tested with several other dataset but unfortunately same problem. (FYI : the gff file was the direct output from prokka)

ADD REPLYlink written 3.1 years ago by jeccy.J50
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