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6 Posts
Posted - Jan 20 2012 :  09:34:46 AM  Show Profile  Reply with Quote
Hi,

I'm trying to submit a script to the cluster but it's been failing and bringing up an odd error message:

wc: .commands: No such file or directory
qsub: command required for a binary job

the script calls an FSL command, so I tried taking out the "export FSLSUBMIT=1" line to see, but the first line of the error is still coming up. Any advice?

Thanks!

petty
BIAC Staff

USA
453 Posts
Posted - Jan 20 2012 :  09:39:35 AM  Show Profile  Reply with Quote
i would try two things:

1) log out, then back in to make sure your profile gets reset ( incase anything has messed it up )

2) dos2unix on the script.

If qsub can't be found, it sounds like your profile, since that's where those paths are exported.
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n/a
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6 Posts
Posted - Jan 20 2012 :  09:49:32 AM  Show Profile  Reply with Quote
hmm, didn't help. Courtney also tried running it with a script she's used successfully in the past and got the same error (just the first line about wc: .commands).

This has come up in the FSL forums as something to do with fsl_sub; is this related?
https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0710&L=fsl&D=0&1=fsl&9=A&I=-3&J=on&d=No+Match%3BMatch%3BMatches&z=4&P=116735

Thanks!
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petty
BIAC Staff

USA
453 Posts
Posted - Jan 20 2012 :  09:56:17 AM  Show Profile  Reply with Quote
what are you using for EXPERIMENT ?
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n/a
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6 Posts
Posted - Jan 20 2012 :  10:05:36 AM  Show Profile  Reply with Quote
ok, we figured it out. We were running tbss_2_reg, and somehow there were a bunch of .msf files in the FA folder TBSS was using. Once I deleted those, it started working. Thanks!
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