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MaestSi / MetONTIIME

A Meta-barcoding pipeline for analysing ONT data in QIIME2 framework
GNU General Public License v3.0
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Can run MetONTIIME on a local computer? If yes: call sbatch on non-HPC hardware? #89

Closed richelbilderbeek closed 7 months ago

richelbilderbeek commented 7 months ago

Dear MetONTIIME developer,

When I try to run MetONTIIME on a local computer, I get an error Cannot run program "sbatch". I know sbatch is a common scheduler used on HPC hardware, so I wonder if I can run MetONTIIME on a local computer.

Can I run MetONTIIME on a local computer? If yes, when there are no HPC cluster profiles used, where could this sbatch come from?

No need to look too deeply, putting me onto the next step is enough, but below the details :-)

Thanks already, Richel

I have made a reprex that reproduces the error Cannot run program "sbatch". This GitHub Action log is here (let me know if you need access, I will give it!). I know sbatch at this GitHub repo where this script is run, with the most interesting line:

nextflow -c my.conf run metontiime2_9feb.nf -profile singularity

Note that the Nextflow .nf file is a modified MetONTIIME Nextflow file and my.conf is a modified user config file. There is an uppmax profile present, yet it is not used.

richelbilderbeek commented 7 months ago

I will close this question, as I predict it will take a maintainer unreasonably much time. The other Issues are easier to answer :-)