leginonbot
commented
6 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-08-05T18:13:55Z
Probably just need a better way out of the situation.
Closed leginonbot closed 5 months ago
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-08-05T18:13:55Z
Probably just need a better way out of the situation.
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2013-08-07T10:59:14Z
Hi Anchi, it appears that the "First peak of CTF is greater than FFT resolution", which is not surprising with a defocus of 0.14 microns. I still need to fix the corresponding ctfdisplay file.
I have so many changes to my apCtf files I am hesitant to commit all of them, until I get some more testing in.
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2013-08-07T11:17:35Z
Should work now.
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2013-08-07T14:37:03Z
The error shifted.
If you can't fix this in this round, I will put the Status to Won't Do. This is unusual anyway.
Traceback (most recent call last):
File "/home/acheng/myami/appion/bin/ctfestimate.py", line 414, in
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Amber Herold (Amber Herold) Original Date: 2014-01-13T16:00:15Z
Can this one be updated to won't fix at this point?
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2014-01-13T16:37:00Z
I just reran it, and got
PART 7: MAKE 1D PLOT SUMMARY FIGURE
Traceback (most recent call last):
File "/home/acheng/myami/appion/bin/ctfestimate.py", line 414, in <module>
imgLoop.run()
File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 97, in run
self.loopCommitToDatabase(imgdata)
File "/home/acheng/myami/appion/appionlib/appionLoop2.py", line 146, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/home/acheng/myami/appion/bin/ctfestimate.py", line 322, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['rundir'])
File "/home/acheng/myami/appion/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTFData
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir, fftpath, fftfreq)
File "/home/acheng/myami/appion/appionlib/apCtf/ctfinsert.py", line 80, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues, fftpath, fftfreq)
File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1120, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata, fftpath, fftfreq, twod=twod)
File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 1002, in CTFpowerspec
normpowerspec = self.normalizeCtf(powerspec, twod=twod)
File "/home/acheng/myami/appion/appionlib/apCtf/ctfdisplay.py", line 307, in normalizeCtf
confraddatasq = confraddata**2
TypeError: unsupported operand type(s) for ** or pow(): 'NoneType' and 'int'
As this very unlikely to happen with real data, we will put it as won't fix.
leginonbot
commented
6 months ago Original Redmine Comment Author Name: Neil Voss (@vosslab) Original Date: 2014-01-13T18:06:55Z
I am okay with that, let me know if you need any other fixes.
Author Name: Anchi Cheng (@anchi2c) Original Redmine Issue: 2461, https://emg.nysbc.org/redmine/issues/2461 Original Date: 2013-08-05 Original Assignee: Neil Voss
Traceback (most recent call last): File "/opt/myamisnap/bin/ctfestimate.py", line 414, in
imgLoop.run()
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 97, in run
self.loopCommitToDatabase(imgdata)
File "/opt/myamisnap/lib/appionlib/appionLoop2.py", line 146, in loopCommitToDatabase
return self.commitToDatabase(imgdata)
File "/opt/myamisnap/bin/ctfestimate.py", line 322, in commitToDatabase
ctfinsert.validateAndInsertCTFData(imgdata, self.ctfvalues, self.ctfrun, self.params['
rundir'])
File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 45, in validateAndInsertCTF
Data
ctfvalues = runCTFdisplayTools(imgdata, ctfvalues, opimagedir)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfinsert.py", line 80, in runCTFdisplayTools
ctfdisplaydict = ctfdisplay.makeCtfImages(imgdata, ctfvalues)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 1108, in makeCtfImages
ctfdisplaydict = a.CTFpowerspec(imgdata, ctfdata)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 991, in CTFpowerspec
normpowerspec = self.normalizeCtf(powerspec)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfdisplay.py", line 271, in normalizeCtf
normpeakdata, ctffitdata, peak, self.trimfreq)
File "/opt/myamisnap/lib/appionlib/apCtf/ctfres.py", line 51, in getCorrelationProfile
xsqEndPre = raddatasq[startindex]
IndexError: index out of bounds
Test image from ctf challenge simulated image set_001_test_mic_000.mrc which I uploaded into Appion.
Failed script ctfestimate.py \ --projectid=351 --preset=upload --session=13jun05v --runname=ctffindrun2 \ --rundir=/ami/data15/appion/13jun05v/ctf/ctffindrun2 --no-rejects \ --no-wait --commit --continue --ampcarbon=0.15 --ampice=0.07 \ --fieldsize=512 --medium=ice --bin=2 --resmin=100 --resmax=10 \ --defstep=1000 --numstep=25 --dast=10000 --expid=11804
ctffind actually completed its job with an estimation. Appion crashed during the commit part.
Other info: I was able to run the following parameters successfully:
ctfestimate.py \ --projectid=351 --preset=upload --session=13jun05v --runname=ctffindrun3 \ --rundir=/ami/data15/appion/13jun05v/ctf/ctffindrun3 --no-rejects \ --no-wait --commit --continue --ampcarbon=0.10 --ampice=0.07 \ --fieldsize=512 --medium=carbon --bin=2 --resmin=100 --resmax=4 \ --defstep=1000 --numstep=25 --dast=2000 --expid=11804 --jobtype=ctfestimate
Attached are the two appionsub log