Saikat,
Your problem is very strange. I just ran one like yours except that I did as interactive qsub and I didn't have the problem.
One very strange thing is all those prints of parameters like
r ======= stackParams ========
stackParams {boxSize: 144, bin: 2, aceCutoff: None, correlationMin: None, correla
tionMax: None, checkMask: False, checkImage: None, norejects: True, minDefocus: N
one, maxDefocus: None, defocpair: False, tiltangle: all, rotate: None, phaseFlipp
ed: None, fliptype: None, fileType: imagic, inverted: True, normalized: True, xmi
pp-norm: 4.5, lowpass: None, highpass: None, startframe: 0, nframe: None, driftli
mit: None} {boxSize: 144, bin: 2, aceCutoff: None, correlationMin: None, correlat
ionMax: None, checkMask: False, checkImage: None, norejects: True, minDefocus: No
ne, maxDefocus: None, defocpair: False, tiltangle: all, rotate: None, phaseFlippe
d: None, fliptype: None, fileType: imagic, inverted: True, normalized: True, xmip
p-norm: 4.5, lowpass: None, highpass: None, startframe: 0, nframe: None, driftlim
it: None}
In your log. That is a sign of accessing someone's sandbox. It is not mine, for sure. Mine is not up to date but is consistent with a revision in svn which never has anything like these.
Check carefully your own .cshrc to see if you can spot something.