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Bug #2356

open

stack creation

Added by David Veesler over 11 years ago. Updated over 11 years ago.

Status:
Assigned
Priority:
Normal
Assignee:
Category:
-
Target version:
-
Start date:
05/06/2013
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.1.0
Show in known bugs:
No
Workaround:

Description

I am currently trying to create a stack and the job crashes with an error message I have never seen before.

... Time stamp: 13may06l59
... Function name: makestack2
... Appion directory: /opt/myamisnap/lib
... Using split database
Connected to database: 'ap373'
... Committing data to database
... Boxsize 1024 contains the primes: [2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
... Found project id=373 for session 12nov30d in 9.11 msec
... Run directory: /ami/data15/appion/12nov30d/stacks/stack38
!!! WARNING: directory '/ami/data15/appion/12nov30d/stacks/stack38' already exists.
... Writing function log to: makestack2.log
... Running on host: guppy-26
... Uploading ScriptData....
... Running on host: guppy-26
... Found 4 processors on this machine
... Running Appion version 'trunk'
... Creating new done dictionary: makestack2.donedict
... Querying database for preset 'es-a' images from session '12nov30d' ...
... Found 1046 images in 2.35 sec
... Remove processed images
skipping images
........................................................................................
..............................................................................................
...............................................................................................
.........................................................................................................................

!!! WARNING: skipped 295 of 1046 images
... [[ 0 no reprocess | 294 rejected | 0 wrong tilt | 0 in donedict ]]
... Process images old to new
!!! WARNING: Checking for dd
... Stack pixelsize = 1.210 A
... Looking up session, 12nov30d
... Found project id=373 for session 12nov30d in 11.01 msec
... missing acecutoff

Traceback (most recent call last):
File "/opt/myamisnap/bin/makestack2.py", line 1182, in <module>
makeStack.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 90, in run
self.preLoopFunctions()
File "/opt/myamisnap/bin/makestack2.py", line 1049, in preLoopFunctions
super(Makestack2Loop,self).preLoopFunctions()
File "/opt/myamisnap/lib/appionlib/apParticleExtractor.py", line 529, in preLoopFunctions
super(ParticleBoxLoop,self).preLoopFunctions()
File "/opt/myamisnap/lib/appionlib/apParticleExtractor.py", line 402, in preLoopFunctions
self.setStartingParticleNumber()
File "/opt/myamisnap/bin/makestack2.py", line 1036, in setStartingParticleNumber
self.resetStack()
File "/opt/myamisnap/bin/makestack2.py", line 1029, in resetStack
self.insertStackRun()
File "/opt/myamisnap/bin/makestack2.py", line 875, in insertStackRun
apDisplay.printError("Weird, run data without stack already in the database")
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 61, in printError
raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
Exception: * FATAL ERROR *
Weird, run data without stack already in the database

Actions #1

Updated by Anchi Cheng over 11 years ago

  • Status changed from New to Assigned

This is caused by having another stack with the same name but not with the same path since the old one has been moved to long-term storage disk. This problem of hard to find previousStack by name alone will need to be solved.

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