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franciscozorrilla / metaGEM

:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
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-h hours to allocated to job runtime #99

Closed kunaljaani closed 2 years ago

kunaljaani commented 2 years ago

Hi Francisco,

I have query regarding the -h flag. I am running the bin reassembly and I had specified 24hrs but the job has not yet finished. Is there a way to resume the command from its last point?

bash metaGEM.sh -t binReassemble -c 28 -m 240 -h 24

Thank you Kunal

franciscozorrilla commented 2 years ago

Hi Kunal,

Looks like you probably figured it out. For that particular rule, I believe that metaWRAP does indeed have checkpointing, so re-submitting will simply resume where the last job left off. Did it work out for you?

Best wishes, Francisco

kunaljaani commented 2 years ago

Hi Francisco,

Thank you for your reply. Ya, I could fix it with the suggested "--rerun-incomplet" flag from one of your earlier comments.

Thanks, Kunal