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jhu99 / miteFinder

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miteFinder running very slow #12

Open amnghn opened 1 month ago

amnghn commented 1 month ago

Hello, I'm running miteFinder on a Slurm cluster but it's running super slow. The input file size is only 40M (one chromosome of a plant species). Based on the paper I expected it to finish quickly (within an hour on one CPU core) but even after 6 hours it did not generate any output. It seems the run.bat script can only be run on a Windows machine. Is there any way to multithread this pipeline on a slurm cluster?

Thanks in advance for your help.

jhu99 commented 2 weeks ago

Hi there, Could you please add more details, e.g. release version? It sounds a bit weird because it runs smoothly in the past years. Best, Jialu

jhu99 commented 2 weeks ago

please try to use https://github.com/jhu99/miteFinder/releases/tag/v2.0 because it's more stable than the latest version.

amnghn commented 2 weeks ago

Hi @jhu99 Thanks for your reply. I managed to solve the issue. It was caused by a technical problem on our HPC cluster. miteFinder is indeed very fast and running smoothly at the moment.

Best, Amin