Cant open file: 14L9VpZJtx/DNA16.gff.proteome.faa Please, help with this issue

[alanxelena]

Dear all,

I came across an issue that seems to be common but I can't solve using previously suggested answers. My problem is as described in the title, I initially ran roary as follows: roary -e --mafft *.gff3 and got the error message. After some reading, a user suggested to run:

roary -e --mafft -z *.gff3 to keep temporary files but that doesn't change the result. In fact, the temporary file that is looked for in the temporary folder is DNA16.gff.proteome.faa but I have DNA16.gff.proteome.faa.tmp.filtered instead.
The file is a protein multifasta.
I've also tried running the command with sudo but nothing changed.
While checking the dependencies I get an error with the cd-hit version which should be higher than 4.6 even if I have 4.8.1, this makes me think this might be the cause of everything but I can't seem to be able to fix this: i) A fresh apt-get install didn't solve the issue, ii) conda install roary gets stuck at

Collecting package metadata

and eventually returns

Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.

In the past I came across a similar issue with Snippy in which a minor change to the source code made the dependencies version detection run smoothly, however I'm not sure if and how I should do it in this case.

Thanks a lot for any orientation and help.