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MSG: The sequence does not appear to be FASTA format (lacks a descriptor line '>') #346
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The pyA GFF3 file is a bit unusual. it has the I loaded your pyA file into http://genometools.org/cgi-bin/gff3validator.cgi and got this error
The convertor you used has a problem... The You could try |
Thank you very much for your soon reply!! I fixed the py_* files in order to solve all the issues I found via the GFF3 validator and I put the ##sequence region lines at the top. However, Roary dies with the same message even though the GFF3 online validator says that the validation was successful for each of the files A_sp_B1.gff3.txt Could you please help us to find what else is wrong with the converted files?
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If the filename ends in '.gff' it is assumed to be a GFF file, otherwise it
is assumed to be a FASTA file of genes. So the solution is to rename your
file extensions from '.gff3.txt' to '.gff'. I've run your data and it
works fine after renaming.
…On 5 September 2017 at 02:22, Semiramis C ***@***.***> wrote:
Thank you very much for your soon reply!!
I fixed the py_* files in order to solve all the issues I found via the
GFF3 validator and I put the ##sequence region lines at top. However, Roary
dies with the same message even though the GFF3 online validator says
"Validation successful!"
A_sp_B1.gff3.txt
<https://github.com/sanger-pathogens/Roary/files/1275756/A_sp_B1.gff3.txt>
A_denitrificans_K601.gff3.txt
<https://github.com/sanger-pathogens/Roary/files/1275757/A_denitrificans_K601.gff3.txt>
A_denitrificans_BC.gff3.txt
<https://github.com/sanger-pathogens/Roary/files/1275758/A_denitrificans_BC.gff3.txt>
Could you please help us to find what else is wrong with the converted
files?
Thank you very much in advance and best regards.
2017/09/04 20:14:31 Fixing input GFF files
2017/09/04 20:14:42 Extracting proteins from GFF files
MSG: The sequence does not appear to be FASTA format (lacks a descriptor
line '>')
STACK: Error::throw
STACK: Bio::Root::Root::throw /usr/local/share/perl5/Bio/Root/Root.pm:472
STACK: Bio::SeqIO::fasta::next_seq /usr/local/share/perl5/Bio/SeqIO/
fasta.pm:126
STACK: Bio::Roary::FilterUnknownsFromFasta::_filter_fasta_sequences_and_return_new_file
/usr/local/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm:58
STACK: Bio::Roary::FilterUnknownsFromFasta::filtered_fasta_files
/usr/local/share/perl5/Bio/Roary/FilterUnknownsFromFasta.pm:28
STACK: Bio::Roary::PrepareInputFiles::_input_fasta_files_filtered
/usr/local/share/perl5/Bio/Roary/PrepareInputFiles.pm:58
STACK: Bio::Roary::PrepareInputFiles::fasta_files
/usr/local/share/perl5/Bio/Roary/PrepareInputFiles.pm:82
STACK: Bio::Roary::CommandLine::Roary::run /usr/local/share/perl5/Bio/
Roary/CommandLine/Roary.pm:277
STACK: /usr/local/bin/roary:14
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Additionally I have updated Roary to capture this case and fix it on the fly. |
@semiramisCJ do use the auto-detect you will need to upgrade via CPAN. |
We don't have problems running Roary with GFF3 files from Prokka, but Roary dies when we try to use different GFF3 files (described at the end), even though all the GFF3 files have the nucleotide sequence at the end of the file, they have the optional '##FASTA' line and they have the fasta headers.
Roary gives the following message:
I converted the GBK files to GFF3 with:
a) seqret module + python to send the all fasta records at the end of the file [seqret_* files]
b) GFF in BCBio and SeqIO in python 2.7 + SeqIO (again) to add the nucleotide sequence at the end [py_* files]
py_A_sp_B1.gff3.txt
py_A_denitrificans_K601.gff3.txt
py_A_denitrificans_BC.gff3.txt
seqret_A_sp_B1.gbk.gff3.txt
seqret_A_denitrificans_K601.gbk.gff3.txt
seqret_A_denitrificans_BC.gbk.gff3.txt
Could somebody help us to find out how to solve this issue?
Thanks in advance & best regards.
P.S.-
roary -a
gives the following detailsThe text was updated successfully, but these errors were encountered: