CTFFIND4 compatibility

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Originally reported by: craigyk (Bitbucket: craigyk, GitHub: craigyk)

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Hi,

I don't know if this is a CTFFIND4 version compatibility thing, but I've run into some problems with the run_ctffind on our version of CTFFIND4 4.0.16.

I've fixed these problems and could submit a pull request. It essentially boiled down to using bash instead of csh in the wrapper, and tweaking the delimiter and word counts used for parsing the output file.

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• Bitbucket: https://bitbucket.org/tcblab/relion2-beta/issue/6

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

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Hi Craigyk,
Sorry, cannot see your code right now. But did you use the CTFFIND3 or CTFFIND4.1 wrapper from the GUI? CTFFIND4.0 still needs to be run through the CTFFIND3-wrapper (using the --old_school_input argument as in relion-1.4). The CTFFIND4 wrapper is made for CTFFIND4.1 (which I understand from Alexis will come soon). There, the order/number of some words in the output file will change.
What was the problem with csh?

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Original comment by craigyk (Bitbucket: craigyk, GitHub: craigyk):

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OK, I thought it might be a version issue, unfortunately we only have 4.0 so I had to make the changes for now on our install.

Not sure what exactly the problem is with the generated .com files, but when run through csh they seem to occasionally return a non-zero result which writes warning to stderr. The executable seems to still complete successfully though. The returned exit codes look like they might be pids... but I did not verify. I fixed this (on my setup at least) by adding an exit 0 to the generated .com script and running it through bash. Sorry, I don't have more detailed info for you.

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

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Alexis Rohou mentioned a bug in ctffind 4.0 (and early versions of 4.1) to do with temporary files. This may be fixed in the latest 4.1 (to be released soon). Hopefully, his fix will solve this issue.

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

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Hi all - I would be interested in recruiting testers for ctffind 4.1. Please contact me directly if you'd like a preview version of this. I believe the relion2 wrapper for the new version will be available shortly.

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Original comment by Özkan Yildiz (Bitbucket: oeyildiz, GitHub: Unknown):

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We tested Ctffind4.1.5 within the relion GUI, but it behaves quite slow with roughly 1500 micrographs and it keeps on giving following error messages for every file several times:

1.02/63.22 hrs ~~(,_,">13:02:19: Error: File 'CtfFind/job325/Micrographs/160804_0001.txt' couldn't be removed (error 2: No such file or directory)

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Original comment by Bjoern Forsberg (Bitbucket: bforsbe, GitHub: bforsbe):

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@craigyk Can we resolve or does the problem persist?

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Original comment by craigyk (Bitbucket: craigyk, GitHub: craigyk):

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The last time I tried it with ctffind 4.1 and the latest Relion 2 source it worked. I'm not sure if ctffind 4.1 is officially released.

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

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ctffind 4.1 is released. I believe it's distributed as part of sbgrid for example. The binaries & source code are available from grigoriefflab.janelia.org. The current version (4.1.5) has a broken tar ball, which means you can look at the source but it won't build. This will be fixed with minor release 4.1.6, soon.