ctffind4 error within Relion-1.4

Submitted by donghua on Fri, 2015-12-11 13:06

Forums

ctffind & ctftilt

Hi, I am using ctffind4 version 4.0.16 in Relion-1.4:

"/home/donghuac/ctffind --omp-num-threads 1 --old-school-input"

But still got the following error:

Estimating CTF parameters using Niko Grigorieff's CTFFIND ...
6.68/6.68 min ............................................................~~(,_,">
ERROR: cannot find line with Final values in Micrographs/12102015stack0004_ctffind3.log
File: src/ctffind_runner.cpp line: 299
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.

I had run ctffind3 with no problem. Any clue?

Thanks,
Dong-Hua

Alexis Fri, 2015-12-11 13:09

Hi Dong-Hua,

Can you look in the *_ctffind3.log files to see if any errors are reported there? The error you report isn't generated by ctffind, so it's hard to tell what happened.

Are only some of the ctffind runs failing, or all of them?

Alexis

Alexis Fri, 2015-12-11 15:41

Hi Dong-Hua,

I have just uploaded a new version, 4.0.17. Please try to use this new version and let me know whether you still get this problem. If so, please try to find the actual error message by showing me the contents of the log files where the error occurred, rather than the generic MPI error message.

Alexis

donghua Mon, 2015-12-14 17:53

Hi Alexis,

Thanks for your version update. I just tested and this new version worked very well for me. I guess the previous version (4.0.16) might have some temporary-files-overwritten issue.

Thanks again,
Dong-Hua