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... Time stamp: 11may04z17
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... Function name: sortJunkStack
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... Appion directory: /leginon/appion/lib
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[1;33m!!! WARNING: There is more than one appion directory in your PYTHONPATH[0m
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[1;33m!!! WARNING: There is more than one leginon directory in your PYTHONPATH[0m
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[1;33m!!! WARNING: Using split database[0m
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[32mConnected to database: 'ap16'[0m
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... Committing data to database
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... Run directory: /leginon/rawimage/Titan/appion/feisun/11apr19f/stacks/sortjunk1
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[1;33m!!! WARNING: directory '/leginon/rawimage/Titan/appion/feisun/11apr19f/stacks/sortjunk1' already exists.[0m
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... Writing function log to: sortJunkStack.log
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... Found 24 processors on this machine
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... Running Appion version '2.1.3'
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... Getting stack data for stackid=3
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Old stack info: [36m'start image'[0m
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[36mBreaking up spider stack into single files, this can take a while[0m
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... processStack: Free memory: 34.9 GB
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... processStack: Box size: 128
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... processStack: Memory used per part: 64.0 kB
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... processStack: Max particles in memory: 571138
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... processStack: Particles allowed in memory: 28556
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... processStack: Number of particles in stack: 10034
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... processStack: Particle loop num chunks: 1
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... processStack: Particle loop step size: 10034
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... processStack: Splitting 10034 particles into 4 folders with 3344 particles per folder
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... processStack: partnum 1 to 3344 of 10034
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... processStack: partnum 3345 to 6688 of 10034, 15.5 sec remain
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... processStack: partnum 6689 to 10032 of 10034, 7.44 sec remain
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... processStack: partnum 10033 to 10034 of 10034, 4.28 msec remain
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... processStack: finished processing stack in 21.86 sec
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[36mxmipp_sort_by_statistics -i partlist.doc[0m
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WARNING: ** You are using an old file format (SELFILE) which is going to be deprecated in next Xmipp release **
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Processing training set ...
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[36mMerging files into a stack, this can take a while[0m
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... Using 4096 particle per iteration
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.........................................
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... writing single particles to file /public/appion/feisun/11apr19f/stacks/sortjunk1/sorted-4096.hed
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['/leginon/appion/lib', '/leginon/appion/3rPackage/EMAN1.9/bin', '/leginon/appion/3rPackage/EMAN1.9/lib']
|
|
['/leginon/appion/lib', '/leginon/appion/3rPackage/EMAN1.9/bin', '/leginon/appion/3rPackage/EMAN1.9/lib']
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Traceback (most recent call last):
|
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File "/leginon/appion/bin/sortJunkStack.py", line 153, in ?
|
|
sortJunk.start()
|
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File "/leginon/appion/bin/sortJunkStack.py", line 59, in start
|
|
apXmipp.gatherSingleFilesIntoStack("sort_junk.sel","sorted.hed")
|
|
File "/leginon/appion/lib/appionlib/apXmipp.py", line 193, in gatherSingleFilesIntoStack
|
|
apImagicFile.writeImagic(stackarray, stackname, msg=False)
|
|
File "/leginon/appion/lib/appionlib/apImagicFile.py", line 250, in writeImagic
|
|
shape = part.shape
|
|
AttributeError: 'NoneType' object has no attribute 'shape'
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