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  • lamasmi
    Junior Member
    • Aug 2010
    • 3
    #1

    SIFT on the command line

    Hi, I am attempting to get sift.jcvi.org to work on our own local machine as a web page, but first let's just talk about getting it to work on the command line.

    I went through the README and attempted to run SIFT with their test files like so:

    $ bin/SIFT_for_submitting_fasta_seq.csh test/lacI.fasta /projects/cgl/data/swiss.uni test/lacI.subst 2.75

    and the result is this:
    tail is lacI.fasta
    query is /projects/cgl/projects/sift/sift4.0.3/tmp/lacI.fasta.query
    cp: cannot access /projects/cgl/projects/sift/sift4.0.3/tmp/lacI.fasta.query
    /projects/cgl/misc/biotools/blast-2.2.10/bin/blastpgp: Invalid argument
    exiting because stauts not equal to 0
    /projects/cgl/projects/sift/sift4.0.3/bin/info_on_seqs: Invalid argument
    Output in /projects/cgl/projects/sift/sift4.0.3/tmp/lacI.SIFTprediction

    I have searched for what the cp: line might mean, but I haven't gotten anywhere. Any suggestions would be appreciated.

    Emily
    Tags: None
  • anjana.vr
    Junior Member
    • May 2010
    • 7
    #2
    Did you check the permissions?
    It should have execute permission on all the directories leading to the file.

    Comment

    • lamasmi
      Junior Member
      • Aug 2010
      • 3
      #3
      Yes, all directories have rwxr-xr-x, rwxr-xr-t. I did some more searching and found that the problem is that when blastpgp runs, no matter what I do I get an "Invalid Argument" returned.

      Comment

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