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Bug #2570

open

Pixel error while creating particle stack using Appion

Added by Saikat Chowdhury about 11 years ago. Updated about 11 years ago.

Status:
New
Priority:
Normal
Assignee:
Saikat Chowdhury
Category:
-
Target version:
Appion/Leginon 3.0.0
Start date:
10/28/2013
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.0.0
Show in known bugs:
No
Workaround:

Description

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

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 #1

Updated by Anchi Cheng about 11 years ago

  • Project changed from Leginon to Appion
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 #2

Updated by Anchi Cheng about 11 years ago

  • Assignee changed from Anchi Cheng to Saikat Chowdhury

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.

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