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SSAHA keep on looping

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  • geeex20
    Hi there, Well, I manage to compile and run SSAHA after switching to Linux (Fedora core 5) and now another problem arise. I try to run the program will the
    Message 1 of 2 , Apr 27 2:38 AM
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      Hi there,

      Well, I manage to compile and run SSAHA after switching to Linux
      (Fedora core 5) and now another problem arise. I try to run the
      program will the following parameters:

      [root@hb1-c]# ssaha query.txt.fa data.txt.fa -wl 8

      But the program keep on display the same hit like this after the the
      headers:

      FF 8est 15 Sequence 593 600 8 100.00
      Alignment score: 8
      Q: 000000008 gagcgacg
      ||||||||
      S: 000000593 GAGCGACG

      It was alright when running without "-wl 8" but it doesn't return any hit.

      Any idea to solve this?


      Regards,
      Kelvin
    • Adam Spargo
      ... Hi, If you forward query.txt.fa and data.txt.fa I can take a look. Adam. -- Dr Adam Spargo High Performance Assembly Group email: aws@sanger.ac.uk
      Message 2 of 2 , Apr 27 2:51 AM
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        > [root@hb1-c]# ssaha query.txt.fa data.txt.fa -wl 8

        Hi,
        If you forward query.txt.fa and data.txt.fa I can take a look.

        Adam.

        --
        Dr Adam Spargo
        High Performance Assembly Group email: aws@...
        Wellcome Trust Sanger Institute Tel: +44 (0)1223 834244 x7728
        Hinxton, Cambridge CB10 1SA Fax: +44 (0)1223 494919
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