leginonbot
commented
8 months ago Original Redmine Comment Author Name: Anchi Cheng (@anchi2c) Original Date: 2014-08-21T14:03:44Z
ctffind can be downloaded from http://grigoriefflab.janelia.org/ctf
According to the log you posted, it needs to be in one of these directories
/usr/local/imod_4.5.8//bin:/home/fulab/Downloads/EMAN2/bin:/usr/local/Xmipp/bin:/usr/lib64/qt-3.3/bin:/usr/local/EMAN/bin:/usr/local/IMOD/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/bin/appion:/usr/lib64/opemmpi/bin:/home/fulab/bin
Author Name: ShinBo Chen (ShinBo Chen) Original Redmine Issue: 2910, https://emg.nysbc.org/redmine/issues/2910 Original Date: 2014-08-21 Original Assignee: ShinBo Chen
Is that ctffind install question or something ?
$ ctfestimate.py --runname=ctffindrun1 --rundir=/home/fulab/myamiImages/appion/14aug21w/ctf/ctffindrun1 --commit --preset=upload --projectid=10 --session=14aug21w --no-rejects --no-wait --continue --ampcarbon=0.15 --ampice=0.07 --fieldsize=512 --medium=carbon --bin=2 --resmin=100 --resmax=10 --defstep=1000 --numstep=25 --dast=100 --expid=6 --jobtype=ctfestimate
... Time stamp: 14aug21o02 ... Function name: ctfestimate ... Appion directory: /usr/lib/python2.6/site-packages ... Using split database Connected to database: 'ap10' ... Committing data to database ... Looking up session, 14aug21w ... Found project id=10 for session 14aug21w in 4.14 msec ... Run directory: /home/fulab/myamiImages/appion/14aug21w/ctf/ctffindrun1 ... Writing function log to: ctfestimate.log ... Running on host: 140.109.48.123 ... Uploading ScriptData.... ... Running on host: 140.109.48.123 ... Found 24 processors on this machine ... Running on host: 140.109.48.123 ... Looking up session, 14aug21w ... Running Appion version '3.0.0' ... Creating new done dictionary: ctfestimate.donedict ... Querying database for preset 'upload' images from session '14aug21w' ... ... Found 103 images in 107.57 msec ... Remove processed images .......... ... Process images old to new which: no ctffind64.exe in (/usr/local/imod_4.5.8//bin:/home/fulab/Downloads/EMAN2/bin:/usr/local/Xmipp/bin:/usr/lib64/qt-3.3/bin:/usr/local/EMAN/bin:/usr/local/IMOD/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/usr/bin/appion:/usr/lib64/opemmpi/bin:/home/fulab/bin) Traceback (most recent call last): File "/usr/bin/appion/ctfestimate.py", line 414, in
imgLoop.run()
File "/usr/lib/python2.6/site-packages/appionlib/appionLoop2.py", line 67, in run
self.preLoopFunctions()
File "/usr/bin/appion/ctfestimate.py", line 44, in preLoopFunctions
self.ctfprgmexe = self.getCtfProgPath()
File "/usr/bin/appion/ctfestimate.py", line 61, in getCtfProgPath
apDisplay.printError(exename+" was not found at: "+apParam.getAppionDirectory())
File "/usr/lib/python2.6/site-packages/appionlib/apDisplay.py", line 62, in printError
raise Exception, colorString("\n FATAL ERROR \n"+text+"\n\a","red")
Exception:
FATAL ERROR
ctffind64.exe was not found at: /usr/lib/python2.6/site-packages