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bhattlab / phanta

Workflow to rapidly quantify taxa from all domains of life, directly from short-read human gut metagenomes
MIT License
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How to run it using SLURM #23

Closed Sanrrone closed 1 year ago

Sanrrone commented 1 year ago

Dears, I am trying to run multiple samples but I cannot find the correct documentation about run the jobs using slurm. I noticed that using the pipeline following the documentation led to serialize the samples instead of run multiple instances. Is it possible to submit slurm jobs for each instance? how could I configure the files to make it?.

thanks in advance!.

meenachakra commented 1 year ago

Hi Sandro,

Thanks for the question! We have been using slurm to run Phanta for multiple samples and they run in parallel. Do you have multiple samples listed in your sample file?

Sanrrone commented 1 year ago

yes, but I am not sure how to configure it to make it work with slurm. could you share the config file?

yipinto commented 1 year ago

Phanta's config will be the same. You can get the slurm snakemake profile (also see in Phanta's manual) or follow the suggestions here. Let us know if that helps

yipinto commented 1 year ago

@Sanrrone, I'm closing this issue. You may open it to share how you solved you issue or if you have any further questions!