Question: genome music bmr calc-covg [Run in parallel]
gravatar for Chirag Nepal
3.4 years ago by
Chirag Nepal2.2k
Chirag Nepal2.2k wrote:

I used genome music to calculate significant pathways, which works great.

In the first, where coverage is calculated,

genome music bmr calc-covg --gene-covg-dir geneCov_combined --bam-list $bamList --output-dir $outDir --reference-sequence $assembly --roi-file $roi

This step is very time consuming when you have 100s of samples.

Is there any way if this can be run in parallel ?

I think, dividing sample into subgroups also does not work here.

Any suggestions ?



coverage music • 1.1k views
ADD COMMENTlink modified 3.4 years ago by Chris Miller20k • written 3.4 years ago by Chirag Nepal2.2k
gravatar for Chris Miller
3.4 years ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k wrote:

I believe there is a --cmd-list-file argument to that tool which outputs a list of commands for each bam into a file. Those can then be run in parallel or submitted to a cluster.

ADD COMMENTlink written 3.4 years ago by Chris Miller20k

Also note the --cmd-prefix which allows you to specify the job submission command. Read The Fancy Manual for more information.

ADD REPLYlink written 3.3 years ago by Cyriac Kandoth5.2k
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