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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Cant open file: _clustered.clstr #600

Open albbaous opened 1 year ago

albbaous commented 1 year ago

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 commented 1 year ago

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

siobhanmccarthy10 commented 6 months ago

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.