Entering edit mode
9.8 years ago
oscarjiao
•
0
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?
Hello oscarjiao!
It appears that your post has been cross-posted to another site: http://seqanswers.com/forums/showthread.php?t=45229
This is typically not recommended as it runs the risk of annoying people in both communities.
the -T option is correct
Only when pindel is loading the genome it will use at most 1 thread.
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?