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can picard use multiple threads?

Is there an argument can make Picard multiple threads?

In the picard home page, I didn't find it.

picard
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updated by cpad0112 cpad0112 • written by naruto1nrt • naruto1nrt

I think it's implemented only for very few functions (like IlluminaBasecallsToFastq). which tool do you want to use?

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updated by Ram Ram • written by Martombo Martombo

3 answers

yes, but not all:

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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

I have the same problem. And finally found solutions in picard faq.

You can not set number of threads for some picard packages, but you can set threads number for java

Try to the code below:

java -XX:ParallelGCThreads=<num of  threads> -jar <picard-package-name>.jar

I hope this will help.

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updated by Ram Ram • written by l0o0 l0o0

It seems the Elapsed times have no difference.

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written by Zhilong Jia Zhilong Jia

You can use for example GNU parallel. Something like this:

ls *.bam | sed 's/.bam.*//' | parallel --eta -j <num of threads> "java -jar picard <package> I={}.bam O={}_out.bam"
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written by Benedek Dankó • Benedek Dankó

bash shows "parallel: command not found"

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written by szp770 • szp770

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