Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • 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.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Non-Coding RNA Research and Technologies
          by seqadmin




          Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.

          Nobel Prize for MicroRNA Discovery
          This week,...
          10-07-2024, 08:07 AM
        • seqadmin
          Recent Developments in Metagenomics
          by seqadmin





          Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...
          09-23-2024, 06:35 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, Today, 06:35 AM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, Yesterday, 02:44 PM
        0 responses
        7 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-11-2024, 06:55 AM
        0 responses
        15 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 10-02-2024, 04:51 AM
        0 responses
        112 views
        0 likes
        Last Post seqadmin  
        Working...
        X