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marcelauliano / MitoHiFi

Find, circularise and annotate mitogenome from PacBio assemblies
MIT License
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Singularity run does not seem to limit threads #95

Open crcardenas opened 5 months ago

crcardenas commented 5 months ago

Hello,

On a server without any job submission structure, I am running mitohifi with singularity. I have it limited to 4 threads:

singularity run  -B /data/raw/Calosoma/NANOPORE/blobtools/CBX1139/mitohifi:/data/raw/Calosoma/NANOPORE/blobtools/CBX1139/mitohifi mitohifi_master.sif \
mitohifi.py -c /data/raw/Calosoma/NANOPORE/blobtools/CBX1139/mitohifi/assembly.fasta \
-f /data/raw/Calosoma/NANOPORE/blobtools/CBX1139/mitohifi/NC_016469.1.fasta \
-g /data/raw/Calosoma/NANOPORE/blobtools/CBX1139/mitohifi/NC_016469.1.gb \
-t 4 -o 5

Currently there are at most 16 of 24 cores being used. When I running, during annotation step CPU usage goes up to 30-32 CPUs.

Do you have any advice on how to prevent this?