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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 2.1K • | written by naruto1nrt 5

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 4.5K • | written by Martombo 320

3 answers

yes, but not all:

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updated by Ram 4.5K • | written by Pierre Lindenbaum 17K

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 4.5K • | written by l0o0 22

It seems the Elapsed times have no difference.

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written by Zhilong Jia 222

I don't think this option turns on multithreading for picard. In fact, -XX:ParallelGCThreads is just about how JVM implements the garbage collection. It may have some impact on the overall performance, but the argument itself by no means has anything to do with picard multithreading.

Here's an in-depth introduction to parallel GC in JVM: https://docs.oracle.com/javase/8/docs/technotes/guides/vm/gctuning/parallel.html

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written by haizi.zh 2

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 5

bash shows "parallel: command not found"

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written by szp770 1

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