Frealign submission fails on SGE cluster due to improper shell interpreter

Hi all,

We had a symptom that was debugged, which might be informative for the forum.

The "new" Frealign scripts were failing for me, and I was not able to get any output from a reconstruction. Examples of some of the symptoms/errors in 'stderr' were:

line 3: limit: command not found
line 24: syntax error near unexpected token `set'
...
line 128: syntax error: unexpected end of file

We are using an SGE cluster. No additional terms were being added to the 'qsub_string_rec' and 'qsub_string_ref' parameters to this submission, and the standard terms in the frealign scripts were used, e.g. '-cwd -r y -V -e ..., etc.'

After some debugging, the issue came down to the fact that, apparently, the csh interpreter was not properly being specified during job submission with qsub.

Thus, the solution was to add the parameters ' -S /bin/csh ' to 'qsub_string_ref' and 'qsub_string_rec' inside mparameters. This will explicitly specify the shell when the job is submitted.

Hope this helps,

Dmitry