How to run pindel with multithreading?

[nasreddin]

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?

[lindenb]

cross posted: https://www.biostars.org/p/107405/

[KaiYe]

Pindel is multi-threaded when processing reads but single thread while loading reference genome and read bam files.

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?

[nasreddin]

Pindel is multi-threaded when processing reads but single thread while loading reference genome and read bam files.

What do you mean by "processing reads"? There is a different opinion here saying it is using multithread only when loading the genome. I am confused.

https://www.biostars.org/p/107405/

By the way what exactly does "-w" option do? It is said to save memory. How is so? And for a cluster with each node boarded 32 GB memory, what value should I specify for -w? The default is 10.