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Old 08-16-2010, 11:24 AM   #1
Junior Member
Location: san diego

Join Date: Aug 2010
Posts: 3
Default SIFT on the command line

Hi, I am attempting to get 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.

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Old 08-17-2010, 09:12 AM   #2
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Location: Washington DC

Join Date: May 2010
Posts: 7

Did you check the permissions?
It should have execute permission on all the directories leading to the file.
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Old 08-17-2010, 09:32 AM   #3
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Location: san diego

Join Date: Aug 2010
Posts: 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.
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