leginonbot
commented
6 months ago Original Redmine Comment Author Name: Sargis Dallakyan (@dallakyan) Original Date: 2016-09-29T16:35:57Z
I suggest looking at the CTFFIND forum for a possible solution. I searched for "ERROR: cannot find line with Final values in" and found this - http://grigoriefflab.janelia.org/node/4766
Author Name: Giovanna Scapin (Giovanna Scapin) Original Redmine Issue: 4476, https://emg.nysbc.org/redmine/issues/4476 Original Date: 2016-09-29 Original Assignee: Sargis Dallakyan
Sorry this is not a true Appion issue but it is the best way I could think to reach out. I am running Relion 1.4 (not up to 2.0 yet) following Ed instructions to move from Appion to Relion. For the third time, with different data sets, my CTFFIND4 run fails (at the very end, so after many many hours) with the following message (this is the end of the log file):
Estimating CTF parameters using Niko Grigorieff's CTFFIND ... 27.76/27.76 hrs ............................................................~~(,,"> ERROR: cannot find line with Final values in Micrographs/16sep17b_IrIn7_00003gr_00002sq_v02_00003hln_v01_00002epn-a_ctffind3.log File: src/ctffind_runner.cpp line: 299
Primary job terminated normally, but 1 process returned a non-zero exit code.. Per user-direction, the job has been aborted.
mpiexec detected that one or more processes exited with non-zero status, thus causing the job to be terminated. The first process to do so was:
Process name: [[11301,1],19] Exit code: 1_
The line it's looking for exist (Anchi and I went through this once already). As a result it does not generate the star file necessary to move on. Downloading the .star file from Appion does not solve the problem, since it still looks for the original files (.txt, .log etc in the Micrographs directory). Please advise.
Thanks - Giovanna