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AlexanderLabWHOI / EUKulele

Automatic eukaryotic taxonomic classification
MIT License
28 stars 7 forks source link

diamond --threads #50

Closed alephreish closed 4 weeks ago

alephreish commented 1 year ago

EUKulele (testing on 2.0.0) doesn't appear to be setting the --threads argument for diamond, irrespective of whether --CPUs argument was set or not. By default, diamond uses all available CPU power, so the user of EUKulele has no control over how many cores are actually used.

akrinos commented 1 year ago

An update on this: adding the feature of --CPUs being leveraged for all DIAMOND calls, which was not true previously. Will push an update this week of this + dependency version fix

akrinos commented 1 year ago

@alephreish Were you ever able to install a newer version of EUKulele to test this out? thanks!

hrzolix commented 1 year ago

I was testing EUKulele 2.0.6 with tutorial on official page. I put CPUs: 6 in the curr_config.yaml, even tried with command line --CPUs 6, still diamond uses all of the cpus available.

akrinos commented 4 weeks ago

@hrzolix let me know how this turned out and feel free to reopen - at present I am getting the right CPU behavior locally