leginonbot
commented
8 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-10-28T19:05:52Z
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.
Author Name: Saikat Chowdhury (Saikat Chowdhury) Original Redmine Issue: 2570, https://emg.nysbc.org/redmine/issues/2570 Original Date: 2013-10-28 Original Assignee: Saikat Chowdhury
Dear Anchi, I am getting error while running stack creation job after particle picking on Garibaldi. It complains about pixel size being different from before. The session id is 12569 and the session name is 13oct25c. The path to the directory where I was running this job on Garibaldi is "/gpfs/home/saikat/TNP". The job file is "stack.job" and the error/output log file is "stk_TNP.o2646062". Thanks Saikat