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  • exonerate - how to use multiple cores?

    Hello,
    I used this command to run exonerate:

    exonerate -m p2g -q uniref90_modified.fasta -t all_LGs/PcapLG_18.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes --showquerygff no --percent 80 " > LG18_exonerate_pcap.gff

    This only use one core. I have 32 cores.
    It's getting too slow.

    Thanks

  • #2
    I would try running it in server-client mode:

    Comment


    • #3
      I tried exonerate-server too. This one is also slow.

      Comment


      • #4
        exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

        exonerate comes with a a tool, fastasplit, for this purpose

        Comment


        • #5
          Originally posted by Blahah404 View Post
          exonerate is simply a slow program. You can split the query file up into 32 files and run 32 exonerate commands simultaneously, then concatenate the results.

          exonerate comes with a a tool, fastasplit, for this purpose

          Thanks
          I tried that too. I made 100 parts. Running single file took more then 3 days and stopped, which means more then 300 days to go.

          Comment


          • #6
            GMAP might be suitable for your purposes (transcript mapping to GFF3), and is a lot quicker with good parallelization.

            Comment

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