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Bug #2303
openrunXmippCL2D.py cannot generate average.mrc
Status:
New
Priority:
Normal
Assignee:
-
Category:
-
Target version:
-
Start date:
03/22/2013
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:
Description
This bug crashes my CL2D runs. It seems to be specific to a particular stack, so that may be a clue.
...
merged 1866 particles in 13.33 sec
... Getting stack data for stackid=1171
Old stack info: 'initial stack ... combined stack ids 1170,1169'
... Stack 1171 pixel size: 2.05
... averaging stack for summary web page
!!! WARNING: could not create stack average, average.mrc
... Inserting CL2D Run into DB
Traceback (most recent call last):
File "/opt/applications/myami/2.2/bin/runXmippCL2D.py", line 624, in <module>
cl2d.start()
File "/opt/applications/myami/2.2/bin/runXmippCL2D.py", line 605, in start
self.insertAlignStackRunIntoDatabase("alignedStack.hed")
File "/opt/applications/myami/2.2/bin/runXmippCL2D.py", line 386, in insertAlignStackRunIntoDatabase
apDisplay.printError("could not find average mrc file: "+avgmrcfile)
File "/opt/applications/myami/2.2/lib/python2.6/site-packages/appionlib/apDisplay.py", line 57, in printError
raise Exception, colorString("\n *** FATAL ERROR ***\n"+text+"\n\a","red")
Exception:
*** FATAL ERROR ***
could not find average mrc file: /ami/data15/appion/13feb17a/align/cl2d3/average.mrc
I ran the following command to generate this error:
runXmippCL2D.py --description="further refining raw particles for proj. matching" --stack=1171\
--lowpass=20 --highpass=0 --num-part=1866 --num-ref=64 --bin=2 --max-iter=15 --nproc=$nproc --fast --classical_multiref --correlation --commit\
--rundir=/ami/data15/appion/13feb17a/align/cl2d3 --runname=cl2d3 --projectid=391 --expid=11189 --jobtype=partalign
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