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Bug #1244

closed

Spider CorAn failing

Added by Rebecca Taurog over 13 years ago. Updated over 10 years ago.

Status:
Won't Fix or Won't Do
Priority:
Normal
Assignee:
Amber Herold
Category:
-
Target version:
-
Start date:
03/17/2011
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 2.2.0
Show in known bugs:
No
Workaround:

Description

I tried running Spider CorAn through Appion on both myamiweb and betamyamiweb, and it failed. I'm not sure why it's failing, but it worked for my other project a month ago. Below is the entire log from one attempt:

... Time stamp: 11mar17j49
... Function name: coranClassify
... Appion directory: /opt/myamisnap/lib
!!! WARNING: Using split database
Connected to database: 'ap252'
... Committing data to database
... Run directory: /ami/data00/appion/10aug18a/align/coran3
!!! WARNING: directory '/ami/data00/appion/10aug18a/align/coran3' already
exists.
... Writing function log to: coranClassify.log
... Found 4 processors on this machine
... Running Appion version 'trunk'
... Pixel mask radius=10.6447688564
... numpart=9919 in 4.04 sec
EMAN: proc2d /ami/data08/appion/10aug18a/align/maxlike2/alignstack.hed
/ami/data00/appion/1 ... ink=3 clip=72,72 edgenorm
EMAN 1.9 Cluster ($Date: 2009/02/18 05:12:22 $).
Run 'proc2d help' for detailed help.
10 complete
20 complete
30 complete
40 complete
50 complete
60 complete
70 complete
80 comple
... 9910 complete
9919 images
... completed in 3 min 1 sec
Running spider this can take awhile, estimated time: 8 min 12 sec
... Performing correspondence analysis (long wait)
executing command: ('CA S', 'alignstack_hed@******', '1-9919', '_9', '20',
'C', '10', 'coran/corandata')
  • ERROR: CORAN CAN NOT ACCEPT NEGATIVE PIXELS
    Traceback (most recent call last):
    File "/opt/myamisnap/bin/coranClassify.py", line 196, in ?
    coranClass.start()
    File "/opt/myamisnap/bin/coranClassify.py", line 171, in start
    numpart=numpart, numfactors=self.params['numfactors'])
    File "/opt/myamisnap/lib/appionlib/apSpider/classification.py", line 82, in correspondenceAnalysis
    contriblist = analyzeEigenFactors(alignedstack, rundir, numpart, numfactors, dataext)
    File "/opt/myamisnap/lib/appionlib/apSpider/classification.py", line 115, in analyzeEigenFactors
    apDisplay.printError("Failed to create Eigen images")
    File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 56, in printError
    raise Exception, colorString("\n * FATAL ERROR *\n"+text+"\n\a","red")
    Exception:
  • FATAL ERROR ***
    Failed to create Eigen images
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