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a-h-b / dadasnake

Amplicon sequencing workflow heavily using DADA2 and implemented in snakemake
GNU General Public License v3.0
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Runtime of 120 hours in some rules #28

Closed velma-te-a closed 2 years ago

velma-te-a commented 2 years ago

Hi, just thought I'd drop a note about something that seemed like a bit odd to me: I was trying to run dadasnake in batch mode on our HPC cluster with a single-end setup, and kept getting an error message "sbatch: error: Batch job submission failed: Requested time limit is invalid (missing or exceeds some limit)". Looking into this, I found that the file "workflow/rules/dada.single.smk" included "runtime="120:00:00"" for several rules. After changing the requested time to 12:00:00 instead, everything worked fine. At a quick check, a few other files/rules also have this 120 hour runtime request. Is this on purpose?

a-h-b commented 2 years ago

Hi there- yes, you're right, this can be too long for some systems. There are some historic reasons for why it was necessary to have really long running times in a project. I'll change it in the development (devel11) branch, so it'll be fixed with the next release. Thanks! A