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moiexpositoalonsolab / grenepipe

A flexible, scalable, and reproducible pipeline to automate variant calling from raw sequence reads, with lots of bells and whistles.
http://grene-net.org
GNU General Public License v3.0
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threads for bwa-mem2 via slurm #29

Closed RvV1979 closed 1 year ago

RvV1979 commented 1 year ago

Hi Lucas, I am running the pipeline via slurm and using bwa-mem2 for mapping. In the config.yaml file, have kept the default 

bwamem2:
    threads: 12

Accordingly, the snakemake log shows threads: 12 for mapping jobs and slurm jobs are submitted requesting 12 cores. However, progress is slower than expected and when logging into a compute node and running htop there seem to be only 4 bwa-mem2 processes running. These are shown as bwa-mem2 mem -t {snakemake.threads}...... Are the number of threads perhaps not correctly transmitted to the bwa-mem2 call?

Note that when specifying bwa-mem as mapping tool, things work as expected (i.e. 12 processes running on the compute node).

Thanks

lczech commented 1 year ago

Hi @RvV1979,

haha damn, that was the same type of error as #28, just in a different spot... Sorry for having missed that before, should be fixed now (in the latest commit on the master branch).

Cheers Lucas

RvV1979 commented 1 year ago

It is indeed fixed now. Thanks for solving this so fast!