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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?

  • #2
    cross posted: https://www.biostars.org/p/107405/

    Comment


    • #3
      Pindel is multi-threaded when processing reads but single thread while loading reference genome and read bam files.


      Originally posted by nasreddin View Post
      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?

      Comment


      • #4
        Originally posted by KaiYe View Post
        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.


        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.

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