rki-mf1 / clean

A nextflow pipeline for decontamination of short reads, long reads and contigs

BSD 3-Clause "New" or "Revised" License

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Increase memory when bbduk runs out #82

Open MarieLataretu opened 10 months ago

MarieLataretu commented 10 months ago

bbduk can use a lot of memory and that can cause it to fail, especially in a shared computing environment like an HPC. Detect this, and auto increase the amount of memory reserved for the task then rerun the process. Additionally, increase the default memory reservation.

MarieLataretu commented 9 months ago

The command exit status of the bbduk process is 1, if it runs out of memory

hoelzer commented 2 months ago

101 fixes this issue with BBDUK