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  • Can SAMtools be parallelized

    I am trying to use multiple threads to run SAMtools jobs, for example

    "qsub -pe threads 8 pileup.sh"

    But it looks like SAMtools is not parallel..Anyone knows anything about it?

    Also, is there any memory limit for SAMtools?

    All your information will be appreciated!

  • #2
    Originally posted by JCYAO View Post
    I am trying to use multiple threads to run SAMtools jobs, for example

    "qsub -pe threads 8 pileup.sh"

    But it looks like SAMtools is not parallel..Anyone knows anything about it?

    Also, is there any memory limit for SAMtools?

    All your information will be appreciated!
    Samtools is not parallel. Besides SNP calling functions, most of the operation deal with I/O, SAM and BAM do not support parallel I/O,
    Besides, what are you trying to achieve?

    Comment


    • #3
      I specified 4G virtual memory for running samtools command in our cluster. But then I noticed it just used ~500-900M memory.

      what I am trying to do is to use all of our memory to speed up the samtools jobs.

      Does SAMtools just use some limited amount of memory no matter how much I specify?


      Thanks

      Comment


      • #4
        Originally posted by JCYAO View Post
        I specified 4G virtual memory for running samtools command in our cluster. But then I noticed it just used ~500-900M memory.

        what I am trying to do is to use all of our memory to speed up the samtools jobs.

        Does SAMtools just use some limited amount of memory no matter how much I specify?


        Thanks
        AFAIK samtools doesn't need so much memory... Luckily... I also believe that even if you find the way to increase the reading buffer in samtools, you won't gain so much speed, as the disk I/O would be the bottleneck.
        If you want to speed things up you may try to convert sam files into paralle HDF5 and use some MPI software to access the h5 in a parallel way...

        Comment

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