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Bug #1244
closedSpider CorAn failing
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
Updated by Lauren Fisher over 13 years ago
Hi Becky,
I haven't figured out what causes this error, but I have seen it before. My solution was to try different binning factors. For example on one dataset, binx2 failed, binx4 failed, but binx8 worked. So that's my only suggestion to you at this point...try binning by 4 or 8 and see if that runs. We'll continue looking into this and see if we can find the cause.
Updated by Amber Herold over 10 years ago
- Status changed from New to Won't Fix or Won't Do
- Affected Version changed from Appion/Leginon 2.1.0 to Appion/Leginon 2.2.0
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