Cant open file: _clustered.clstr

[albbaous]

I am running this in the same directory as my prokka gff files and I have 258 genomes:

roary -f roary_output -e -v --mafft -p 40 -i 70 -s -g 150000 -b "blastp num_threads 30 perc_identity = 70" *.gff

and getting this error:

2023/06/11 13:44:57 Extracting proteins from GFF files
Cant open file: _clustered.clstr
------------- EXCEPTION: Bio::Root::Exception -------------
MSG: Could not read file '_clustered': No such file or directory
STACK: Error::throw

I have updated all dependencies and I have the latest version (v 3.13.0)
I have the latest version of cd-hit but this is not recognised for some reason.

[albbaous]

I have made sure cd-hit is now recognised by changing the source code but this is still a problem.

[siobhanmccarthy10]

Hi @albbaous, could you please explain how you changed the source code? I'm having the same issues using roary on a HPC system through a miniconda install. I have tried a few other of the recommended solutions but have had no luck yet I'm afraid.

[taichu001]

Hi @albbaous, I'm facing a similar issue. My original version of cd-hit was 4.8.1, but after switching to version 4.6.8, it started running normally. My Roary version is 3.13.0.Good luck!