Question: can picard use multiple threads?
3
gravatar for naruto1nrt
6.4 years ago by
naruto1nrt30
Australia
naruto1nrt30 wrote:

is there an argu can make picard multiple threads?

in the picard home page,i didn't find it.

alignment • 16k views
ADD COMMENTlink modified 12 weeks ago by Benedek Dankó10 • written 6.4 years ago by naruto1nrt30
1

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

ADD REPLYlink written 6.4 years ago by Martombo2.7k
4
gravatar for Pierre Lindenbaum
6.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum131k wrote:

yes, but not all:

ADD COMMENTlink modified 11 months ago by _r_am31k • written 6.4 years ago by Pierre Lindenbaum131k
1
gravatar for l0o0
4.8 years ago by
l0o0210
China
l0o0210 wrote:

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.

ADD COMMENTlink modified 11 months ago by _r_am31k • written 4.8 years ago by l0o0210
1

It seems the Elapsed times have no difference.

ADD REPLYlink written 3.4 years ago by Zhilong Jia1.6k

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

ADD REPLYlink written 7 months ago by haizi.zh0
0
gravatar for Benedek Dankó
12 weeks ago by
Budapest, Hungary
Benedek Dankó10 wrote:

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"
ADD COMMENTlink written 12 weeks ago by Benedek Dankó10
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