Can't open file: proteome.faa

[alanxelena]

Dear Sanger team,

I'm having an issue running roary. I've run the following command: roary -p 20 -f ./Results *.gff. The Results directory together with the gff files gets created but I get the following error:

Cant open file: /home/service/Results/0G3_sO09fo/DNA1.gff.proteome.faa

I tried adding -z to the command to keep the temporary files but that doesn't help. Actually the file DNA1.gff.proteome.faa is not to be found in the 0G3_sO09fo directory but rather DNA1.gff.proteome.faa.tmp. This file is a protein multifasta.

I've also run roary -a and the only warning I get is

Looking for 'cd-hit' - found
Use of uninitialized value in concatenation (.) or string at /usr/perl5/Bio/Roary/External/CheckTools.pm line 131.
Determined cd-hit version is Use of uninitialized value in numeric lt (<) at /usr/perl5/Bio/Roary/External/CheckTools.pm line 132.
Roary needs cd-hit 4.6 or higher. Please upgrade and try again.

Still, I have cd-hit v4.8.1.

Any help on this issue would be really appreciated.

[ak-akku]

i had a problem where the folder in which the gff files were had a space in the naming. make sure the folder that is being accessed abd by that i mean all folder do not have space in the folder name

[alanxelena]

Hey @ak-akku !

Thanks for the reply, sadly the fix isn't that simple, none of my directories have spaces, only underscores if they're ever needed.