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  • Exonerate uniref90.fasta alignment to 65MB genome

    Hello,

    I was trying to align uniref90.fasta (10 gb) to genome for annotation.
    I have 64 GB ram with 32 core.
    It is already running since a month.
    I was wondering if it is normal or there is other way to run quicker?

    Thanks in advance
    Sandesh

  • #2
    A month already .. wow you are patient.

    Are you sure something is happening as far as output being produced/CPU cycles being used productively?

    Comment


    • #3
      I used command below. uniref90 has got more then 22 M proteins.
      I am not sure if the CPU are used properly.
      I have been trying different ways like just running single scaffolds but run forever.
      I am running this for EVM.
      I also tried with targetchunk1-10 but no luck.


      exonerate -m p2g -q uniref90_modified.fasta -t Pcap_genome.fasta --softmasktarget yes --showvulgar no --showalignment no --showtargetgff yes --showquerygff no --geneseed 200 --percent 80 --ryo "AveragePercentIdentity: %pi\n" > exonerate_pcap.gff

      Please any suggestion.

      Comment

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