The speed of hmmscan

[yl2420841262]

My input file is a gbk file with 394 antismash results, py -i /mnt/f/ NDC-blastp /bigscape -o /mnt/f/ NDC-blastp /results has now been running python bigscape.py -i/MNT /f/ NDC-blastp /results for more than two days, and the code says to start with 394 files
Files that had its sequence extracted: 394

Creating output directories

Trying threading on 32 cores

Predicting domains using hmmscan
Predicting domains for 394 fasta files, I wonder how long it will take

[jorgecnavarrom]

That definitely sounds too slow.

My input file is a gbk file with 394 antismash results

Predicting domains for 394 fasta files

Could it be that BiG-SCAPE is processing 394 gbks corresponding to whole-genomes? By default, it will only include files that contain the word 'cluster' or 'region' but that can be changed if you used the --include-gbk-string/--exclude_gbk_str parameters

[yl2420841262]

The 393 gbk files are derived from antismash's analysis and have names similar to NPDC020737.ctg-0001.region001.gbk, 394gbk with a total file size of just 48.6 MB. It now shows that it is still running, but it uses memory instead of cpu

[yl2420841262]