LeandroRitter commented 8 months ago

Right now FasQC_Before/After_Trimming, the memory parameter is set to 1024 MB, which leads to this error message:

Memory value 10240 MB was outside the allowed range (100 - 10000) at /aMeta/.snakemake/conda/29408ff88243ec3671290557f41f37da_/bin/fastqc line 203.
logs/FASTQC_AFTER_TRIMMING/NW-17.log (END)

FreyaStein commented 4 months ago

What is the preliminary solution for that? Change it to a higher number? (it ran with 10240 MB) in the ../aMeta/.test/.snakemake/conda/e8531c7d541689213a8be8b131985ae0_/bin/fastqc?

ZoePochon commented 4 months ago

Hey Freya!

The preliminary solution is to specify in your slurm file how much memory to use within the range of 100 to 10000 like this for example:

Amount of threads per rule

set-threads:

FastQC_AfterTrimming=2
FastQC_BeforeTrimming=2
Amount of resources per rule

set-resources:
FastQC_AfterTrimming:mem_mb=6000
FastQC_BeforeTrimming:mem_mb=6000

If your running the snakemake pipeline and are stuck with this error, a good tip would be to run it with snakemake with the option --keep-going so that it doesn't stop the process at the first error but once there is nothing left to run.

Hope this helps!

LeandroRitter commented 4 months ago

Has been fixed centrally in the latest PR. Closing for now.

NBISweden / aMeta

mem_mb in FastQC rule should be changed #156

Amount of threads per rule

Amount of resources per rule