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Bug #4476

open

RELION 1.4 (not from Appion)

Added by Giovanna Scapin about 8 years ago. Updated about 8 years ago.

Status:
New
Priority:
Normal
Assignee:
Sargis Dallakyan
Category:
Image Processing
Target version:
-
Start date:
09/29/2016
Due date:
% Done:

0%

Estimated time:
Affected Version:
Appion/Leginon 3.2
Show in known bugs:
No
Workaround:

Description

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

Actions #1

Updated by Sargis Dallakyan about 8 years ago

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

Actions #2

Updated by Giovanna Scapin about 8 years ago

Thanks Sargis I will look into it

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