Bug #4653
openError when Centering a substack
0%
Description
Here is the log readout. It fails after just about 1 minute. It failed on both SEMC and Guppy clusters. Any ideas?
... Time stamp: 16dec07k48
... Function name: centerParticleStack
... Appion directory: /opt/myamisnap/lib
... Processing hostname: guppy-16
... Using split database
[0;32mConnected to database: 'nyap_251'
... Committing data to database
... Run directory: /gpfs/appion/kjordan/jrheinberger/16dec02d/stacks/centered10
!!! WARNING: directory '/gpfs/appion/kjordan/jrheinberger/16dec02d/stacks/centered10'
already exists.
... Writing function log to: centerParticleStack.log
... Uploading ScriptData....
... Found 1 processors on this machine
... Running Appion version 'trunk'
... Getting stack data for stackid=10
Old stack info: [0;36m'cleaned up stack from first class averages ... 27436 particle substack with ...
8,9 classes excluded'
... checking that original stack is numbered
!!! WARNING: Original stack is not numbered! numbering now...
!!! WARNING: old stack header exists in a READ-only directory and cannot be
numbered according to EMAN
... Centering stack: /gpfs/appion/kjordan/jrheinberger/16dec02d/stacks/clustersub3/start.hed
Traceback (most recent call last):
File "/opt/myamisnap/bin/centerParticleStack.py", line 85, in
cenStack.start()
File "/opt/myamisnap/bin/centerParticleStack.py", line 62, in start
apStack.centerParticles(oldstack, self.params['mask'], self.params['maxshift'])
File "/opt/myamisnap/lib/appionlib/apStack.py", line 424, in centerParticles
stacksize = apFile.stackSize(stack)
File "/opt/myamisnap/lib/appionlib/apFile.py", line 131, in stackSize
stats = os.stat(f)
OSError: [Errno 2] No such file or directory: '/gpfs/appion/kjordan/jrheinberger/16dec02d/stacks/clustersub3/start.hed'
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