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How to run pindel with multithreading?

I was trying to run pindel with multithreading turned on by the following command:

pindel -f Homo_sapiens_assembly19.fasta -i ConfigHF.txt -T 4 -c 1 -o HF_chr_1 > HFchr1.log.

However when I do top while the job is running, it only shows single thread. And I am using the current version 0.2.4.

Is there something needs to be done differently to enable threading during installation?

threading pindel
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updated by Ram Ram • written by oscarjiao • oscarjiao

the -T option is correct

Only when pindel is loading the genome it will use at most 1 thread.

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written by Wai Yi Leung • Wai Yi Leung

But I thought more threads should at least speed it up a little bit and it turned out not the case.

So I picked chromosome 21 this time (since it is the shortest) and ran pindel with 4 cores and 16 cores. It actually took 16 cores longer to finish the same job than 4 cores (29 mins vs 23 mins) How is that possible?

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written by oscarjiao • oscarjiao

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