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ctf estimation complains about missing mrc files
Added by Abhiram Chintangal about 6 years ago
Hi,
A user in our lab is trying to run ctf estimation job from a recent Arctica session.
The images themselves have been uploaded into Appion using the imageuploader.
{}
Traceback (most recent call last):
File "/opt/qb3/myami-trunk/appion/bin/ctffind4.py", line 327, in <module>
imgLoop.run()
File "/opt/qb3/myami-trunk/appion/appionlib/appionLoop2.py", line 86, in run
results = self.loopProcessImage(imgdata)
File "/opt/qb3/myami-trunk/appion/appionlib/appionLoop2.py", line 136, in loopProcessImage
return self.processImage(imgdata)
File "
", line 267, in processImage
powspec = apImage.mrcToArray(inputparams['output'])
File "/opt/qb3/myami-trunk/appion/appionlib/apImage/imagefile.py", line 133, in mrcToArray
numer = mrc.read(filename)
File "/opt/qb3/myami-trunk/pyami/mrc.py", line 748, in read
f = open(filename, 'rb')
IOError: [Errno 2] No such file or directory: '18oct02w_18Oct01_map7-l-mts-p_0022-pow.mrc'
The weird thing is that the we can process the images directly via cttfind4 executable. It only fails with
the python script, and only on some images.
After digging around the python script, I noticed these temporary files created by ctffin4 are stored in the folder
opimages folder /k2data/appion/lisa/18oct02w/ctf/ctffind4run2.
Here is the command:
ctffind4.py --ampcontrast=0.07 --fieldsize=512 --resmin=50 --resmax=10 --defstep=0.1 --numstep=25 --dast=0.05 --bestdb --runname=ctffind4run2 --rundir=/k2data/appion/lisa/18oct02w/ctf/ctffind4run2 --commit --preset=upload --projectid=81 --session=18oct02w --no-rejects --no-wait --continue --expid=3123 --jobtype=ctfestimate
Any ideas?
Replies (1)
RE: ctf estimation complains about missing mrc files - Added by Anchi Cheng about 6 years ago
_your_filename-pow.mrc is the diagnosis output file ctffind4 generated. The error indeed indicates that ctffind4 failed.
What appion does different from direct ctffind4 run is that it tried to give the program a more precise defocus range for the program to do the initial search. You may want to see if there is any correlation between the defocus deviation from your nominal value (what you set during upload) and the failure.
If you can find the log from ctffind4 during the appion run that contains what is right before the crash. It should have all the parameters used as the input. This is normally also saved as _your_filename-pow.txt in the appion rundir. Since it crashed, it might not be written in time. But that will give you a way to repeat it.
Let us know if you find more clues.