How many .gbk files can big-scape process?

[chingciripit]

(i.e, what is the maximum number of .gbk files that big-scape can process?)

[jorgecnavarrom]

It depends only on the machine's resources, but it is unfortunately not possible to calculate it directly. For the publication, we did about 75k BGCs (which we ran in parts; first the domain annotation, then sets of biosynthetic classes)

There will be a more extensive benchmarking for BiG-SCAPE 2

[chingciripit]

Thanks, Jorge. I always have issues with IndexError: list index out of range so I was wondering if I input too many .gbk files.

The BiG-SCAPE always stops after this analysis. Do you know what the issue is and how to troubleshoot this?

Thank you.

Mix (5182 BGCs)
Calculating all pairwise distances
generate_network took 537.680 seconds
Writing output files
Calling Gene Cluster Families
Cutoff: 0.3

[jorgecnavarrom]

It's possible that the problem arises from a newer version of scikit-learn than the one we used. Could you double check if you have v0.19.2 (and install this version if not)?