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linnabrown / run_dbcan

Run_dbcan V4, using genomes/metagenomes/proteomes of any assembled organisms (prokaryotes, fungi, plants, animals, viruses) to search for CAZymes.
http://bcb.unl.edu/dbCAN2
GNU General Public License v3.0
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--hmm_cpu doesn't work #85

Closed PandengWang closed 8 months ago

PandengWang commented 2 years ago

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 commented 2 years ago

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 commented 10 months ago

We used hmmsearch instead which utilized multiple CPUs.

HaidYi commented 8 months ago

Problem solved by replace hmmscan with hmmsearch