--hmm_cpu doesn't work

[PandengWang]

Thanks for providing this useful tool!

Although I have set '--hmm_cpu 30', the hmmscan only used 1 core. This problem may come from the hmmer software.

I suggest to use any way to speed up hmmscan.

1. split input protein file into several small datasets
2. use parallel to run hmmscan

[linnabrown]

Thank you for letting us know. We are considering replacing hmmer with pyhmmer which really run hmmer in parallel. We will update it in the future version.

[linnabrown]

We used hmmsearch instead which utilized multiple CPUs.

[HaidYi]

Problem solved by replace hmmscan with hmmsearch