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SionBayliss / PIRATE

A toolbox for pangenome analysis and threshold evaluation.
GNU General Public License v3.0
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stuck at threshold 60 during MCL clustering #86

Closed jiyanxu closed 9 months ago

jiyanxu commented 9 months ago

Hi,

I have installed PIRATE and its dependencies, PIRATE -c shows it's no problem. But when I apply to my own test data (gff, annotated by prokka), at the beginning everything is fine, when it comes to MCL clustering:

-- running mcl on pan_sequences at 50 -- 3824 clusters at 50% - completed in 37 secs -- running mcl on pan_sequences at 60

Then I never get further results. I checked the statue in htop, it is always D

How do you think? I really need your help.

All the best

SionBayliss commented 9 months ago

Hi,

This seems more likely to be a system issue than one caused by the software. My limited understanding is that state D in htop has to do with memory I/O issue. Could your disk be slow or otherwise overloaded. Have you tried running the dataset on a different device? Please let me know if that resolves the issue.

All the best, Sion

jiyanxu commented 9 months ago

Hi Sion,

thank you very much for the reply! I would try on another device and let you know.

All the best, Jiyan

jiyanxu commented 9 months ago

Dear Sion,

I successfully got the result when the HPC was not highly demanded. Thank you very much for the timely reply!

All the best, Jiyan