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  • pblat empty output

    Hi,

    I have a single computer with multiple cores, I use pblat at http://icebert.github.io/pblat/

    I got only empty temp files as well as empty outpout

    I really do not understand what is the nature of the problem, I think a memory problem

    I run it like following : nohup `sudo ./Jobs_pblat.sh` &

    the Jobs_pblat.sh contains : $PRGEXEC/pblat -threads=12 -prot -trimT -out=blast9 -minIdentity=25 $DB/db.faa $INFILE/"Orfs.faa" -out=blast9 $RESULTDIR/"Orfs_blat_outblast9_results.out"

    Anybody has the same issue with pblat

    Thanks for reading my thread
    __Bach__

  • #2
    Has this worked before or this is the first time you are using this program?

    Comment


    • #3
      Is the first time I used It
      I tried parallel blat (pblat ) and blat, I got the same behaviour
      __Bach__

      Comment


      • #4
        Can you take a few sequences from each file and run them against each other using blat/pblat to ensure that you have a working program before trying to tackle the full dataset?

        BTW: Why are you adding sudo to your job?

        Comment


        • #5
          With a small number of sequences it works fine
          I think my database is huge (38 G) may I have to divide my database into several parts and do several blat

          thanks again for advices
          __Bach__

          Comment


          • #6
            Or you could reverse the roles and make the database into query.

            Comment


            • #7
              It works too ! thanks
              __Bach__

              Comment

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