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CAF help

2008-10-28
2013-04-18
  • Brian Forde
    Brian Forde
    2008-10-28

    Hi,
    I just started using CAFTOOLS and I am currently trying to run phrap2gap on a test group of 10 EXP files.

    The process fails continously (no matter which options i choose) with the error

    Bad file descriptor

    I guess what I am looking for is an example (other than those on the CAF website or in the paper "sequnce Assemply with CAFTOOLS" to steer me down the right path. Can anyone help me with this.

    regards

    Brian

     
    • Brian Forde
      Brian Forde
      2008-10-28

      alternatively if i simply run caf_phrap on my caf db after some processing i get the following error

      Aligning reads to contigs ...sh: line 1: 11008 Segmentation fault      phrap ./Phrap/CAF -old_ace -forcelevel 0 >./Phrap/CAF.stdout
      Failed: phrap ./Phrap/CAF -old_ace -forcelevel 0   > ./Phrap/CAF.stdout: No such file or directory