Not sure if rsem is using --num-threads option...

deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

http://deweylab.biostat.wisc.edu/rsem/

GNU General Public License v3.0

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Not sure if rsem is using --num-threads option... #217

Open siyer-broad opened 1 week ago

siyer-broad commented 1 week ago

Hello,

I am running rsem-calculate-expression on a 20-vCPU, 200G RAM google VM instance for processing a STAR output Aligned.toTranscriptome.out.bam file with approximately 100 million reads. It takes approximately an 1-1.25 hours.

Is this expected? Is there a way to check the trace if the EM algorithm is using all cores?