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Bug #4124
openerror msg from CTFFIND4
Start date:
04/20/2016
Due date:
% Done:
0%
Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:
Description
There is a error msg after I submit a job in CTF estimate
Expected (tolerated) astigmatism [100.0] : 500.0
Find additional phase shift? [no] : no
warning(FileDelete): attempt to delete file which does not exist:
Summary information for file 16apr19f_03sq_01hl_05en.mrc
Number of columns, rows, sections: 2048 2048 1
MRC data mode: 2
Bit depth: 32
Pixel size: 4.000 4.000 4.000
Working on micrograph 1 of 1
0% [ ] ???h:??m:??s 6% [= ] 0h:0 ... ==================] done!
*warning(Image::ComputeRotationalAverageOfPowerSpectrum): unable to rescale 1D average of experimental
power
forrtl: error (65): floating invalid
Image PC Routine Line Source
ctffind4 00000000016B81B9 Unknown Unknown Unknown
ctffind4 00000000016B6B30 Unknown Unknown Unknown
ctffind4 00000000015D85D2 Unknown Unknown Unknown
ctffind4 0000000001578928 Unknown Unknown Unknown
ctffind4 000000000157F631 Unknown Unknown Unknown
ctffind4 0000000001563EB0 Unknown Unknown Unknown
ctffind4 00000000017B7BDB Unknown Unknown Unknown
ctffind4 000000000174B496 MAIN__ 788 ctffind.f90
ctffind4 0000000000400566 Unknown Unknown Unknown
ctffind4 00000000016C1DFB Unknown Unknown Unknown
ctffind4 0000000000400429 Unknown Unknown Unknown
... ctf estimation completed in 46.78 sec
... reading 16apr19f_03sq_01hl_05en-pow.txt
Found ctf values
Traceback (most recent call last):
File "/opt/myamisnap/bin/ctffind4.py", line 338, in
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 87, in run
results = self.loopProcessImage(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 137, in loopProcessImage
return self.processImage(imgdata)
File "/opt/myamisnap/bin/ctffind4.py", line 272, in processImage
apDisplay.printError("CTFFIND4 program did not produce valid results in the log file")
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR **\n"+text+"\n\a","red")
Exception:
Expected (tolerated) astigmatism [100.0] : 500.0
Find additional phase shift? [no] : no
warning(FileDelete): attempt to delete file which does not exist:
Summary information for file 16apr19f_03sq_01hl_05en.mrc
Number of columns, rows, sections: 2048 2048 1
MRC data mode: 2
Bit depth: 32
Pixel size: 4.000 4.000 4.000
Working on micrograph 1 of 1
0% [ ] ???h:??m:??s 6% [= ] 0h:0 ... ==================] done!
*warning(Image::ComputeRotationalAverageOfPowerSpectrum): unable to rescale 1D average of experimental
power
forrtl: error (65): floating invalid
Image PC Routine Line Source
ctffind4 00000000016B81B9 Unknown Unknown Unknown
ctffind4 00000000016B6B30 Unknown Unknown Unknown
ctffind4 00000000015D85D2 Unknown Unknown Unknown
ctffind4 0000000001578928 Unknown Unknown Unknown
ctffind4 000000000157F631 Unknown Unknown Unknown
ctffind4 0000000001563EB0 Unknown Unknown Unknown
ctffind4 00000000017B7BDB Unknown Unknown Unknown
ctffind4 000000000174B496 MAIN__ 788 ctffind.f90
ctffind4 0000000000400566 Unknown Unknown Unknown
ctffind4 00000000016C1DFB Unknown Unknown Unknown
ctffind4 0000000000400429 Unknown Unknown Unknown
... ctf estimation completed in 46.78 sec
... reading 16apr19f_03sq_01hl_05en-pow.txt
Found ctf values
Traceback (most recent call last):
File "/opt/myamisnap/bin/ctffind4.py", line 338, in
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 87, in run
results = self.loopProcessImage(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 137, in loopProcessImage
return self.processImage(imgdata)
File "/opt/myamisnap/bin/ctffind4.py", line 272, in processImage
apDisplay.printError("CTFFIND4 program did not produce valid results in the log file")
File "/opt/myamisnap/lib/appionlib/apDisplay.py", line 65, in printError
raise Exception, colorString("\n * FATAL ERROR **\n"+text+"\n\a","red")
Exception:
- FATAL ERROR ***
CTFFIND4 program did not produce valid results in the log file
Updated by Anchi Cheng over 8 years ago
- Related to Bug #4148: continue AppionLoop if a image gives invalid result added
Updated by Anchi Cheng over 8 years ago
- Status changed from New to In Test
- Assignee changed from Anchi Cheng to Zhening Zhang
- Priority changed from Urgent to Normal
This is again a problem of bad ctf estimation from a bad image. I add a feature to skip the image and continue rather than crash as in Issue #4148
After myami-beta is updated tomorrow, these images will be skipped, but it will fail if you try to use them for ctf correction. You should have these images hidden. I can not do that automatically because it might fail because of incorrect input parameters.
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