Cannot get roary to run

[mradz19]

I have annotated several assmbled plasmids from several isolates using Prokka, and I am attempting to analyse them with roary. I installed roary using conda, added the gff files from the prokka output into a single directory and tried running:

roary -e -n -f roary_out *.gff

But it will not run at all. This is the output

2020/03/25 09:34:10 Output directory created: out 2020/03/25 09:34:10 Fixing input GFF files 2020/03/25 09:34:11 Extracting proteins from GFF files Extracting proteins from New assemblies/gff_2/PROKKA_5101_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_5102_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_5103_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_5104_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_5105_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_7501_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_7502_03242020.gff Extracting proteins fromNew assemblies/gff_2/PROKKA_7503_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_7504_03242020.gff Extracting proteins fromNew assemblies/gff_2/PROKKA_7505_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_86901_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_86902_03242020.gff Extracting proteins from New assemblies/gff_2/PROKKA_86903_03242020.gff Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Error: Cant access file assemblies/gff_2/out/Nyhyvcm5Ds Usage: extract_proteome_from_gff [options] *.gff Take in GFF files and create FASTA files of the protein sequences

Options: -o STR output suffix [proteome.faa] -t INT translation table [11] -f filter sequences with missing data -v verbose output to STDOUT -d STR output directory -w print version and exit -h this help message

For further info see: http://sanger-pathogens.github.io/Roary/ Combine proteins into a single file Cant open file: New_assemblies/gff_2/out/Nyhyvcm5Ds/PROKKA_5101_03242020.gff.proteome.faa

I tried manually running extract_proteome_from_gff manually which worked, a proteome.faa file was generated for each gff file. However running roary again I get the exact same error.

Can anyone help with this?

[RodriguesJA]

I've been looking for solutions for a similar issue. Have you tired this https://github.com/sanger-pathogens/Roary/issues/403 Might be a directory problem.