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Bug #4728

closed

Makestack (mean filtering) fails

Added by Ashleigh Raczkowski almost 8 years ago. Updated almost 8 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Carl Negro
Category:
-
Target version:
Appion/Leginon 3.3
Start date:
01/28/2017
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.3
Show in known bugs:
No
Workaround:

Description

/opt/myamisnap/bin/appion stackFilter.py --old-stack-id=78 --description="2" --minx=35 --maxx=62 --miny=.7 --maxy=.85 --commit --rundir=/gpfs/appion/araczkowski/lkim/16dec23d/stacks/meanfilt78 --runname=meanfilt78 --projectid=256 --expid=3154 --jobtype=makestack

... Time stamp: 17jan28i52
 ... Function name: stackFilter
 ... Appion directory: /opt/myamisnap/lib
 ... Processing hostname: SEMC-head
!!! WARNING: There is more than one appion directory in your PYTHONPATH
['/home/anoble/myami/appion', '/home/cnegro/myami-trunk/appion/']
 ... Using split database
Connected to database: 'nyap_256'
 ... Committing data to database
 ... Run directory: /gpfs/appion/araczkowski/lkim/16dec23d/stacks/meanfilt78
!!! WARNING: directory '/gpfs/appion/araczkowski/lkim/16dec23d/stacks/meanfilt78' already exists.
 ... Writing function log to: stackFilter.log
 ... Uploading ScriptData....
 ... Found 24 processors on this machine
 ... Running Appion version 'trunk'
 ... querying stack particles from stackid=78 at Sat Jan 28 08:52:37 2017
 ... sorting particles
 ... received 172743 stack particles in 55.86 sec
 ... Getting stack data for stackid=78
Old stack info: 'first clean ... 172743 particle substack with 10,13,14,19 classes excluded'
 ... creating a new stack
    /gpfs/appion/araczkowski/lkim/16dec23d/stacks/meanfilt78/ali.hed
from the oldstack
    /gpfs/appion/araczkowski/lkim/16dec23d/stacks/alignsub19/ali.hed
... creating sub-stack from large stack
Traceback (most recent call last):
  File "/opt/myamisnap/bin/stackFilter.py", line 102, in <module>
    subStack.start()
  File "/opt/myamisnap/bin/stackFilter.py", line 88, in start
    apStack.makeNewStack(oldstack, newstack, self.params['keepfile'], bad=True)
  File "/opt/myamisnap/lib/appionlib/apStack.py", line 50, in makeNewStack
    stackTools.createSubStack(oldstack, newstack, listfile, msg=True)
  File "/opt/myamisnap/lib/appionlib/StackClass/stackTools.py", line 81, in createSubStack
    subStack.start(instack, partlist)
  File "/opt/myamisnap/lib/appionlib/StackClass/ProcessStack.py", line 115, in start
    partlist.sort()
AttributeError: 'str' object has no attribute 'sort'
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