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3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
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Ctffind4.1 is not working on relion2.1beta #276

Closed psryubh closed 4 years ago

psryubh commented 7 years ago

As the title is, Ctffind4.1 is not working on relion2.1beta(b0 or b1 whatever..)

Running ctf estimation job with Ctffind4.1 produced empty micrographs_ctf.star file, although Run.err file said just "warning".

Briefly, two types of warning come; 1) error in executing csh 2) skipping, cannot get CTF value

However, Gctf works fine, and therefore I guess this is not simple input error but some problem in relion(specifically, the ctf estimation function or related script?) when it communicates with ctffind4.1. Since I am a kind of novice, I cannot solve out this issue.

How can I solve out?

Remark : this issue is slightly different with #186 in the following 2 aspects. *1) The difference to #186 that produced the same errors with my case, is that I could get ctf estimation with Gctf(v1.6) successfully. 2) Plus, nothing have done with ctffind4.1, resulting in empty _ctf.star file. And even repetition of the job did not work at all, which is unlike the solution suggested in #186; repeat this until all micrographs is done.**

The following are the details of the Note.txt, Run.out and Run.err files.

Note.txt

++++ Executing new job on Fri Aug 18 11:31:23 2017 ++++ with the following command(s): which relion_run_ctffind --i ./MotionCorr/job002/corrected_micrographs.star --o CtfFind/job003/ --CS 0.002 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 1.4 --Box 512 --ResMin 30 --ResMax 5 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --ctffind_exe "/home/sbl/relion_acc/ctffind-4.1.8/ctffind --omp-num-threads 1 --old-school-input" --ctfWin -1 --is_ctffind4
++++

Run.out

Using CTFFIND executable in: /home/sbl/relion_acc/ctffind-4.1.8/ctffind --omp-num-threads 1 --old-school-input to estimate CTF parameters for the following micrographs:

Run.err

sh: 1: csh: not found WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0005_ctffind4.com sh: 1: csh: not found WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0006_ctffind4.com sh: 1: csh: not found WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0007_ctffind4.com WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0005.mrc WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0006.mrc WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0007.mrc

ashkumatov commented 7 years ago

had a same error. You simply have no c-shell on your machine. please install the tcsh package and it will work. csh (and its improved version tcsh) are shell script programms similar to bash which is (almost) exclusively used by current linux distributions. HTH, Alex

psryubh commented 7 years ago

Dear Alex,

Thank you for your kind advice.

However, ctffind4.1 did not work even after I have installed tcsh.

It seems like the problem is not that simple.

Somehow, I appreciate your concern.

Sincerely, Han

Bum Han Ryu

Ph.D student (Combined) Structural Biology LAB., Dept. of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea

      1. 오후 6:56, ashkumatov notifications@github.com 작성:

had a same error. You simply have no c-shell on your machine. please install the tcsh package and it will work. csh (and its improved version tcsh) are shell script programms similar to bash which is (almost) exclusively used by current linux distributions. HTH, Alex

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ashkumatov commented 7 years ago

Hey Han what is the error message you are getting now? what do you get when typing in command line "csh"? Alex

psryubh commented 7 years ago

Exactly the same message I left above.

When I typed csh in command line, I found just sbl:~% (sbl is the hostname, though) and That's all. It seems like csh works normally. Should I run relion and CTFFIND on that csh shell mode?

Han

baibing7713661 commented 6 years ago

I got the similar error and did not get how to solve it when running CTFFIND4

run.err ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory ../../../../../home/admin/relion/build/bin/ctffind: error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28648625_Data_28649089_28649090_20170828_1554-2548_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28648625_Data_28649125_28649126_20170828_1555-2549_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28648626_Data_28649528_28649529_20170828_1608-2552_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28648626_Data_28649552_28649553_20170828_1606-2550_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28648626_Data_28649558_28649559_20170828_1606-2551_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28652968_Data_28649552_28649553_20170828_1652-2555_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654029_Data_28654529_28654530_20170828_1748-2559_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654029_Data_28654643_28654644_20170828_1746-2557_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654029_Data_28654652_28654653_20170828_1747-2558_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654029_Data_28654662_28654663_20170828_1749-2560_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654029_Data_28654670_28654671_20170828_1745-2556_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654030_Data_28654670_28654671_20170828_1750-2561_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654031_Data_28654529_28654530_20170828_1825-2565_MC_DW.mrc WARNING: skipping, since cannot get CTF values for stacks/Motioncor/FoilHole_28654031_Data_28654643_28654644_20170828_1823-2563_MC_DW.mrc

runout === RELION MPI setup ===

ashkumatov commented 6 years ago

You are missing libtiff lib (it can be sometimes named differently and creating soft link may fix the problem): error while loading shared libraries: libtiff.so.3: cannot open shared object file: No such file or directory

Alternatively, get the precompiled version of CTFFIND.

HTH, Alex

yijianSU22 commented 3 months ago

As the title is, Ctffind4.1 is not working on relion2.1beta(b0 or b1 whatever..)

Running ctf estimation job with Ctffind4.1 produced empty micrographs_ctf.star file, although Run.err file said just "warning".

Briefly, two types of warning come; 1) error in executing csh 2) skipping, cannot get CTF value

However, Gctf works fine, and therefore I guess this is not simple input error but some problem in relion(specifically, the ctf estimation function or related script?) when it communicates with ctffind4.1. Since I am a kind of novice, I cannot solve out this issue.

How can I solve out?

Remark : this issue is slightly different with #186 in the following 2 aspects. *_1) The difference to #186 that produced the same errors with my case, is that I could get ctf estimation with Gctf(v1.6) successfully. 2) Plus, nothing have done with ctffind4.1, resulting in empty ctf.star file. And even repetition of the job did not work at all, which is unlike the solution suggested in #186; repeat this until all micrographs is done.

The following are the details of the Note.txt, Run.out and Run.err files.

Note.txt

++++ Executing new job on Fri Aug 18 11:31:23 2017

++++ with the following command(s): which relion_run_ctffind --i ./MotionCorr/job002/corrected_micrographs.star --o CtfFind/job003/ --CS 0.002 --HT 300 --AmpCnst 0.1 --XMAG 10000 --DStep 1.4 --Box 512 --ResMin 30 --ResMax 5 --dFMin 5000 --dFMax 50000 --FStep 500 --dAst 100 --ctffind_exe "/home/sbl/relion_acc/ctffind-4.1.8/ctffind --omp-num-threads 1 --old-school-input" --ctfWin -1 --is_ctffind4 ++++

Run.out

Using CTFFIND executable in: /home/sbl/relion_acc/ctffind-4.1.8/ctffind --omp-num-threads 1 --old-school-input to estimate CTF parameters for the following micrographs:

  • MotionCorr/job002/rawframes/P97-fullcomplex_0005.mrc
  • MotionCorr/job002/rawframes/P97-fullcomplex_0006.mrc
  • MotionCorr/job002/rawframes/P97-fullcomplex0007.mrc Estimating CTF parameters using Alexis Rohou's and Niko Grigorieff's CTFFIND4.1 ... 0/ 0 sec ............................................................~~(,,"> Done! Written out: CtfFind/job003/micrographs_ctf.star

Run.err

sh: 1: csh: not found

WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0005_ctffind4.com sh: 1: csh: not found WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0006_ctffind4.com sh: 1: csh: not found WARNING: there was an error in executing: csh CtfFind/job003/rawframes/P97-fullcomplex_0007_ctffind4.com WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0005.mrc WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0006.mrc WARNING: skipping, since cannot get CTF values for MotionCorr/job002/rawframes/P97-fullcomplex_0007.mrc

Hey Han Have you resolved this error when you run relion_run_ctffind in relion2? I met the same error in relion2? Can you give me some suggestions?

Succi

biochem-fan commented 3 months ago

Please stop using such an old version of RELION! Use at least RELION 4, ideally 5.

In RELION 4 and later, you can set the RELION_SHELL environmental variable to bash if you don't have csh.