Dear Andrew and Dave,
Thank you very much for offering help with the SGE scripts. Fortunately, the
system administrator, who manages the cluster, figured out what was wrong.
Originally I had asked him to help me modify the scripts based on the
configuration of the cluster at our university. While he was modifying it,
he had placed a line to test the queue assignment in the script. But that
line was directing its output to stdout, which prefixed the output that the
script was supposed to supply - the PID of the preprocess script to wait
for. This was then used as input to the next script which was expecting
only a number and instead got gibberish with the PID at the end, causing it
to choke. So, just commenting out the line fixed the problem.
kind regards,
Tugan Muftuler
Univ. California, Irvine
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