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Bug #5048

closed

Generating missing stack file error

Added by Ashleigh Raczkowski over 7 years ago. Updated almost 7 years ago.

Status:
Closed
Priority:
Urgent
Assignee:
Carl Negro
Category:
-
Target version:
Start date:
06/24/2017
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

Unable to generate missing stack file or create stack file when making a substack from 2D classes. Working as user mfalzone on SEMC cluster.

generateMissingStack.py --projectid=197 --expid=4260 --stackid=35
Connected to database: 'nyap_197'
 ... Getting stack data for stackid=35
Old stack info: 'sub ... 15881 particle substack with 4,7,9,11,13,15,16,19,21,43,40,59,58,36,57,81,99,50,29,25,24,66,47,48,69,93 classes included'
 ... Querying original particles from stackid=35
 ... original stackid: 33
connecting
Original stack: /gpfs/appion/mfalzone/17jun23b/stacks/centered31/ali.hed
 ... generating stack: '/gpfs/appion/mfalzone/17jun23b/stacks/alignsub18/ali.hed' with 15881 particles
 ... creating a new stack
        /gpfs/appion/mfalzone/17jun23b/stacks/alignsub18/ali.hed
from the oldstack
        /gpfs/appion/mfalzone/17jun23b/stacks/centered31/ali.hed

Traceback (most recent call last):
  File "/opt/myamisnap/bin/generateMissingStack.py", line 35, in <module>
    apVirtualStack.generateMissingStack(params['stackid'])
  File "/opt/myamisnap/lib/appionlib/apVirtualStack.py", line 25, in generateMissingStack
    apStack.makeNewStack(vstackdata['filename'], fname, plist)
  File "/opt/myamisnap/lib/appionlib/apStack.py", line 50, in makeNewStack
    partlist = emanLstFileToPartList(listfile)
  File "/opt/myamisnap/lib/appionlib/apStack.py", line 70, in emanLstFileToPartList
    f = open(listfile, "r")
TypeError: coercing to Unicode: need string or buffer, list found
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