Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Core gene file missing error #241

Closed
duytintruong opened this issue Mar 22, 2016 · 3 comments
Closed

Core gene file missing error #241

duytintruong opened this issue Mar 22, 2016 · 3 comments
Labels

Comments

@duytintruong
Copy link
Contributor

Dear Andrew,

I ran roary on four reference genomes of Bacteroides ovatus, the fna and gff files obtained from prokka can be found here:

https://www.dropbox.com/sh/r7202w9dkmfjdcy/AADtcwR79F6wLKP2a2jzXKMVa?dl=0

The command I used was:

roary -p 60 -f output -e -g 1000000 -i 95 input/G000218325.gff input/G000154125.gff input/G000273195.gff input/G000273215.gff

And I got the following errors:

Use of uninitialized value in require at /home/e.pasolli/perl5/lib/perl5/File/Slurper.pm line 32.
Use of uninitialized value in require at /usr/lib/perl/5.18/Encode.pm line 60.
Use of uninitialized value in require at (eval 846) line 1.

Core gene file missing: pan_genome_sequences/group_9579.fa.aln
Core gene file missing: pan_genome_sequences/group_165.fa.aln
Core gene file missing: pan_genome_sequences/uidA_2.fa.aln
Core gene file missing: pan_genome_sequences/gno.fa.aln
Core gene file missing: pan_genome_sequences/group_119.fa.aln
Core gene file missing: pan_genome_sequences/group_457.fa.aln
Core gene file missing: pan_genome_sequences/topA.fa.aln
Use of uninitialized value in require at /home/e.pasolli/perl5/lib/perl5/File/Slurper.pm line 32.
Use of uninitialized value in require at /usr/lib/perl/5.18/Encode.pm line 60.
Use of uninitialized value in require at (eval 964) line 1.

------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file 'pan_genome_sequences/group_165.fa.aln': No such file or directory
STACK: Error::throw
STACK: Bio::Root::Root::throw /home/e.pasolli/perl5/lib/perl5/Bio/Root/Root.pm:449
STACK: Bio::Root::IO::_initialize_io /home/e.pasolli/perl5/lib/perl5/Bio/Root/IO.pm:270
STACK: Bio::SeqIO::_initialize /home/e.pasolli/perl5/lib/perl5/Bio/SeqIO.pm:499
STACK: Bio::SeqIO::fasta::_initialize /home/e.pasolli/perl5/lib/perl5/Bio/SeqIO/fasta.pm:87
STACK: Bio::SeqIO::new /home/e.pasolli/perl5/lib/perl5/Bio/SeqIO.pm:375
STACK: Bio::SeqIO::new /home/e.pasolli/perl5/lib/perl5/Bio/SeqIO.pm:421
STACK: Bio::Roary::SortFasta::_input_seqio /CIBIO/sharedCM/tools/roary/lib/Bio/Roary/SortFasta.pm:38
STACK: Bio::Roary::SortFasta::sort_fasta /CIBIO/sharedCM/tools/roary/lib/Bio/Roary/SortFasta.pm:79
STACK: Bio::Roary::CommandLine::GeneAlignmentFromNucleotides::run /CIBIO/sharedCM/tools/roary/lib/Bio/Roary/CommandLine/GeneAlignmentFromNucleotides.pm:112
STACK: /CIBIO/sharedCM/tools/roary/bin/protein_alignment_from_nucleotides:19


Use of uninitialized value in require at /home/e.pasolli/perl5/lib/perl5/File/Slurper.pm line 32.
Use of uninitialized value in require at /usr/lib/perl/5.18/Encode.pm line 60.
Use of uninitialized value in require at (eval 886) line 1.

Can you please check the issue?

Thanks,
Tin

@andrewjpage
Copy link
Member

resolved via email. The issue was all the genomes shared the same prefix, so giving them each a unique prefix made things work.

@Aliceall
Copy link

Hi Andrew,
I know the issue has been closed but I am having the same and I am not sure I understand how to fix this. I can send the prokka.giff files if needed. Thank you!

@igarrom
Copy link

igarrom commented Apr 7, 2020

Hello,
I know also the issue has been closed but I have the same problem: "Could not read file 'pan_genome_sequences/..." appears several times when running mafft and I do not know if now I can trust my results or they are incompleted.
Thank you!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
Projects
None yet
Development

No branches or pull requests

4 participants