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That wasn’t the issue, but I think I figured it out anyway. Hopefully this is useful for someone else down the line. I had to type both of the following commands: unset SGE_ROOT unset FSLPARALLEL So far there are no warnings and no errors. It’s been a (long) while since I used bedpost, but so far here’s my output. Is it normal to be stuck on the ‘Bedpostx Monitor’ for a long time with no terminal output? $ bedpostx bedpostx -b 1000 -n 2 -j 1250 -s 25 -w 1.00 subjectdir is /remote_home/grayson/bedpostx Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage ----- Bedpostx Monitor ----- From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Moises Hernandez Sent: Tuesday, August 30, 2016 3:50 AM To: [log in to unmask] Subject: Re: [FSL] bedpostx error on SGE enabled machine Hi David, these errors suggest me that something is going wrong with your shell. I would check that the file /bin/sh is linked to the correct shell (bash normally). Typing ls -l /bin/sh you should get something like lrwxrwxrwx 1 root root r rrr rr xx:cc /bin/sh -> bash If it is not linked to bash, you can create the link typing: ln -s /bin/bash /bin/sh Moises. On 26 August 2016 at 19:37, David Grayson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi Stam, This produces error messages too. See below: $ unset SGE_ROOT; bedpostx bedpostx -b 1000 -n 2 -j 1250 -s 25 -w 1.00 subjectdir is /remote_home/grayson/bedpostx Making bedpostx directory structure Queuing preprocessing stages Unable to initialize environment because of error: Please set the environment variable SGE_ROOT. Exiting. Queuing parallel processing stage Unable to initialize environment because of error: Please set the environment variable SGE_ROOT. Exiting. Queuing post processing stage exit: 412: Illegal number: -1 Type /remote_home/grayson/bedpostx.bedpostX/monitor to show progress. Type /remote_home/grayson/bedpostx.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage. From: FSL - FMRIB's Software Library [mailto:[log in to unmask]<mailto:[log in to unmask]>] On Behalf Of Stamatios Sotiropoulos Sent: Friday, August 26, 2016 11:24 AM To: [log in to unmask]<mailto:[log in to unmask]> Subject: Re: [FSL] bedpostx error on SGE enabled machine Hi try unset SGE_ROOT and then run bedpostx. That way you bypass the grid engine. Cheers Stam On 26 Aug 2016, at 19:20, David Grayson <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hi folks, I am getting a strange error when I try to run bedpostx. There appear to be some issues related to detection of the gridengine. I am on a machine that can submit jobs, but would prefer to simply run without bedpostx doing so. Can anyone help with this? The full command output is shown below. $ bedpostx bedpostx -b 1000 -n 2 -j 1250 -s 25 -w 1.00 [: 205: -a: unexpected operator subjectdir is /remote_home/grayson/bedpostx Making bedpostx directory structure Queuing preprocessing stages Queuing parallel processing stage qsub: command required for a binary job Queuing post processing stage exit: 412: Illegal number: -1 Type /remote_home/grayson/bedpostx.bedpostX/monitor to show progress. Type /remote_home/grayson/bedpostx.bedpostX/cancel to terminate all the queued tasks. You will get an email at the end of the post-processing stage.