| T O P I C R E V I E W |
| n/a |
Posted - Jan 20 2012 : 09:34:46 AM
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! |
| 4 L A T E S T R E P L I E S (Newest First) |
| n/a |
Posted - Jan 20 2012 : 10:05:36 AM
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! |
| petty |
Posted - Jan 20 2012 : 09:56:17 AM
what are you using for EXPERIMENT ? |
| n/a |
Posted - Jan 20 2012 : 09:49:32 AM
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! |
| petty |
Posted - Jan 20 2012 : 09:39:35 AM
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. |
