can picard use multiple threads?
3
3
Entering edit mode
7.1 years ago
naruto1nrt ▴ 30

is there an argu can make picard multiple threads?

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

alignment • 18k views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
4
Entering edit mode
7.1 years ago

yes, but not all:

ADD COMMENT
1
Entering edit mode
5.5 years ago
l0o0 ▴ 210

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 COMMENT
1
Entering edit mode

It seems the Elapsed times have no difference.

ADD REPLY
0
Entering edit mode

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 REPLY
0
Entering edit mode
10 months ago

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 COMMENT
0
Entering edit mode

bash shows "parallel: command not found"

ADD REPLY

Login before adding your answer.

Traffic: 973 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6