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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
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ctffind crash #35

Closed bforsbe closed 7 years ago

bforsbe commented 8 years ago

Originally reported by: bzuber (Bitbucket: bzuber, GitHub: Unknown)

Not sure if this is a relion issue and how often it would happen. I ran ctffind4 through relion on the betagal dataset. One ctffind run crashed.

relion command is: which relion_run_ctffind_mpi --i MotionCorr/movie_correction/corrected_micrographs.star --o CtfFind/job006/ --CS 2 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 3.54 --Box 512 --ResMin 30 --ResMax 7.1 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --ctffind_exe "/usr/bin/ctffind4 --omp-num-threads 1 --old-school-input" --ctfWin -1 --only_do_unfinished

run standard error is: WARNING: there was an error in executing: csh CtfFind/job006/Micrographs/Falcon_2012_06_12-15_53_09_0_ctffind3.com WARNING: cannot find line with Final values in CtfFind/job006/Micrographs/Falcon_2012_06_12-15_53_09_0_ctffind3.log WARNING: skipping, since cannot get CTF values for MotionCorr/job004/Micrographs/Falcon_2012_06_12-15_53_09_0.mrc

this faulty process logfile is: Welcome to CTFFind Version - 4.0.16

               Input Mode: Batch
              Date & Time: 2016-07-01 13:40:00

Copyright 2015 Howard Hughes Medical Institute. All rights reserved. Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html )

CS[mm], HT[kV], AmpCnst, XMAG, DStep[um] 2.0 300.0 0.10 10000.0 3.540

Total execution time : 0 seconds

2016-07-01 13:40:00: Fatal error (FileCopyRaw): Source file does not exist: .CTFFind_ikIiBXMT8XU7pCXT

this process com file is:

!/usr/bin/env csh

/usr/bin/ctffind4 --omp-num-threads 1 --old-school-input > CtfFind/job006/Micrographs/Falcon_2012_06_12-15_53_09_0_ctffind3.log << EOF CtfFind/job006/Micrographs/Falcon_2012_06_12-15_53_09_0.mrc CtfFind/job006/Micrographs/Falcon_2012_06_12-15_53_09_0.ctf 2, 300, 0.1, 10000, 3.54 512, 30, 7.1, 5000, 50000, 500, 100 EOF

I greped the weird file name from the logfile (.CTFFind_ikIiBXMT8XU7pCXT) on all file in the directory. three log files in addition to the one above contained that name but only had a warning and no fatal error. Here is one of them:

              **  Welcome to CTFFind  **
                   Version - 4.0.16

               Input Mode: Batch
              Date & Time: 2016-07-01 13:40:00

Copyright 2015 Howard Hughes Medical Institute. All rights reserved. Use is subject to Janelia Farm Research Campus Software Copyright 1.1 license terms ( http://license.janelia.org/license/jfrc_copyright_1_1.html )

CS[mm], HT[kV], AmpCnst, XMAG, DStep[um] 2.0 300.0 0.10 10000.0 3.540

**warning(FileDelete): attempt to delete file which does not exist: .CTFFind_ikIiBXMT8XU7pCXT

Summary information for file CtfFind/job006/Micrographs/Falcon_2012_06_12-15_56_10_0.mrc Number of columns, rows, sections: 1950 1950 1 MRC data mode: 2 Bit depth: 32 Pixel size: .000 .000 .000

Working on micrograph 1 of 1

SEARCHING CTF PARAMETERS...

100% [==============================] done! 

  DFMID1      DFMID2      ANGAST          CC
30000.00    30000.00      -15.00    -0.01708

REFINING CTF PARAMETERS... DFMID1 DFMID2 ANGAST CC 30212.82 30000.00 -21.18 -0.01676 Final Values

Estimated defocus values : 30212.82 , 30000.00 Angstroms Estimated azimuth of astigmatism: -21.18 degrees Score : -.01676 Thon rings with good fit up to : 19.9 Angstroms

Summary of results : CtfFind/job006/Micrographs/Falcon_2012_06_12-15_56_10_0.txt Diagnostic images : CtfFind/job006/Micrographs/Falcon_2012_06_12-15_56_10_0.ctf Detailled results, including 1D fit profiles: CtfFind/job006/Micrographs/Falcon_2012_06_12-15_56_10_0_avrot.txt Use this command to plot 1D fit profiles : ctffind_plot_results.sh CtfFind/job006/Micrographs/Falcon_2012_06_12-15_56_10_0_avrot.txt

Total execution time : 4 minutes and 7 seconds 2016-07-01 13:44:08 : CTFFind finished cleanly.

Cheers Ben

bforsbe commented 8 years ago

Original comment by bzuber (Bitbucket: bzuber, GitHub: Unknown):

Hi Alexis, Alright, thanks for your explanation! Cheers Ben

bforsbe commented 8 years ago

Original comment by Alexis Rohou (Bitbucket: arohou, GitHub: arohou):

Hi Ben,

This looks a bit like a ctffind bug to do with temporary files, which sometimes occurs when many ctffind processes are running in the same directory.

Ctffind 4.0.17 (already available) fixed this for most users and the problems should be completely gone with ctffind 4.1 (should be available in the next couple of weeks).

Cheers, Alexis

bforsbe commented 8 years ago

Original comment by bzuber (Bitbucket: bzuber, GitHub: Unknown):

I continued the job. As expected, only the failed one was restarted. This time it ran fine. At first glance, all CTF estimates look fine (the display of all CTFs at once is quite useful). So no idea what went wrong. I cannot exclude a problem with access to the disk. Let us see if this kind of error happen again... Ben

bforsbe commented 8 years ago

Original comment by Sjors Scheres (Bitbucket: scheres, GitHub: scheres):

Ben, could these be problems with access to the disk? What happens if you continue the same job? Do all micrographs get estimated OK in the end?