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  • How can I monitor the progress of BWA?

    When aligning a fastq file with BWA, I would like to monitor the progres, to know how long it approx. will take until the alignment of the whole file is finished.

    Is there any way to do this?

    I was thinking about using pv (process viewer) but can't figure out how. Is it possible with pv, or maybe is there another way?
    Last edited by Azazel; 10-11-2013, 12:44 AM. Reason: typos

  • #2
    Hi,

    I'm guessing that you would like to see progress of the bwa aln command.
    I looked into this before for version 0.6.2 of bwa and found every so often the program will print this information.

    [bwa_aln_core] write to the disk... 0.03 sec
    [bwa_aln_core] 26188815 sequences have been processed.

    The ' X sequences have been processed' seems to be

    X = number of reads in the fastq file.

    So I took the the number of lines in the fastq file and divide it by 4 to get the number of reads. I could then write a script to capture the this information and the bwa progress information and calculate how far through the fastq file I was.

    Hope this helps,
    David

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