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]] On Behalf Of Stamatios Sotiropoulos
Sent: Friday, August 26, 2016 11:24 AM
To: [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]> 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.