Solved - user error/typo -trouble with ctffind4 in Relion

Submitted by Michael on Mon, 2015-02-02 11:56

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ctffind & ctftilt

Hello, I recently installed ctffind4.0.7 and used it successfully from Relion1.3. Now, without any changes to the system, I get the following error (with 4.0.7 and 4.0.8). The images were converted from dm3 to mrc in em2em. Some help will be appreciated. Michael

Executing: `which relion_run_ctffind` --i "all_micrographs.star" --o "all_micrographs_ctf.star" --ctfWin -1 --CS 2.2 --HT 120 --AmpCnst 0.1 --XMAG 61868 --DStep 11.26 --Box 512 --ResMin 100 --ResMax 7 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --ctffind3_exe "/usr/local/progs/ctffind4.0.8/ctffind --omp-num-threads 1 –old-school-input" &
Using CTFFINDs executable in: /usr/local/progs/ctffind4.0.8/ctffind --omp-num-threads 1 –old-school-input
to estimate CTF parameters for the following micrographs:
* Micrographs/140822-D5-df1000-01.mrc
* Micrographs/140822-D5-df1000-02.mrc
etc ...
* Micrographs/140822-D5-df2000-25.mrc

Estimating CTF parameters using Niko Grigorieff's CTFFIND3 ...
000/??? sec ~~(,_,"> [oo]forrtl: severe (24): end-of-file during read, unit 5, file /proc/1472/fd/0
Image PC Routine Line Source
ctffind 000000000159F026 Unknown Unknown Unknown
ctffind 0000000001788F61 Unknown Unknown Unknown
ctffind 0000000001781D98 Unknown Unknown Unknown
ctffind 0000000001743DFB ctffind_IP_main_ 276 ctffind.f90
ctffind 0000000001740F46 MAIN__ 60 ctffind.f90
ctffind 0000000000400566 Unknown Unknown Unknown
ctffind 00000000016C111B Unknown Unknown Unknown
ctffind 0000000000400429 Unknown Unknown Unknown
0/ 0 sec ..~~(,_,">forrtl: severe (24): end-of-file during read, unit 5, file /proc/1477/fd/0
Image PC Routine Line Source
ctffind 000000000159F026 Unknown Unknown Unknown
ctffind 0000000001788F61 Unknown Unknown Unknown
ctffind 0000000001781D98 Unknown Unknown Unknown
ctffind 0000000001743DFB ctffind_IP_main_ 276 ctffind.f90
ctffind 0000000001740F46 MAIN__ 60 ctffind.f90
ctffind 0000000000400566 Unknown Unknown Unknown
ctffind 00000000016C111B Unknown Unknown Unknown
ctffind 0000000000400429 Unknown Unknown Unknown
0/ 0 sec ....~~(,_,">forrtl: severe (24): end-of-file during read, unit 5, file /proc/1482/fd/0

etc ...

ERROR: cannot find line with Cs[mm], HT[kV], etc values in Micrographs/140822-D5-df1000-01_ctffind3.log
File: src/ctffind_runner.cpp line: 297

Alexis Mon, 2015-02-02 11:59

Hello Michael,

Can you confirm that you are giving it --old-school-input (note the two minus signs)?

In your text here, it looks like you are using some other dash symbol in front of old-school-input

Alexis