You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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!
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!
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
The text was updated successfully, but these errors were encountered: