search

3dem / relion

Image-processing software for cryo-electron microscopy
https://relion.readthedocs.io/en/latest/
GNU General Public License v2.0
453 stars 202 forks source link

Preprocessing::initialise ERROR: Input micrograph STAR file has no rlnMicrographName column! #773

Closed yongshuo-Z closed 3 years ago

yongshuo-Z commented 3 years ago

Describe your problem After importing raw micrographs and its corresponding coordinates, I tried to extract particles. But error occurs as the issue title. But I tried to read the .star file using python myself, I found the exact rlnMicrographName as below. I wonder what should I do to extract particles?

image

Environment:

Dataset:

Job options:

relion_import --do_movies --optics_group_name "opticsGroup1" --angpix 1.4 --kV 300 --Cs 2.7 --Q0 0.1 --beamtilt_x 0 --beamtilt_y 0 --i "data/empiar10017/*.mrc" --odir Import/job001/ --ofile movies.star --continue --pipeline_control Import/job001/

relion_import --do_coordinates --i "data/empiar10017/*_checked.star" --odir Import/job002/ --ofile coords_suffix_checked.star --continue --pipeline_control Import/job002/

relion_preprocess` --i Import/job001/movies.star --coord_dir Import/job002/ --coord_suffix _checked.star --part_star Extract/job003/particles.star --part_dir Extract/job003/ --extract --extract_size 128 --norm --bg_radius 48 --white_dust -1 --black_dust -1 --invert_contrast --only_do_unfinished --pipeline_control Extract/job003/


**Error message:**

in: /root/cryo/code/relion/relion/src/preprocessing.cpp, line 138 ERROR: Preprocessing::initialise ERROR: Input micrograph STAR file has no rlnMicrographName column! === Backtrace === ./relion_preprocess(_ZN11RelionErrorC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_l+0x77) [0x7f8dc2d4d7a7] ./relion_preprocess(_ZN13Preprocessing10initialiseEv+0xcfe) [0x7f8dc2d70b8e] ./relion_preprocess(main+0x49) [0x7f8dc2d422f9] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xe7) [0x7f8db83afbf7] ./relion_preprocess(_start+0x2a) [0x7f8dc2d453da]

ERROR: Preprocessing::initialise ERROR: Input micrograph STAR file has no rlnMicrographName column!

biochem-fan commented 3 years ago

You cannot extract from movies. Run motion correction first.

njxisang commented 2 years ago

How do you solve it? I have met the same error after I use the motion correction.

biochem-fan commented 2 years ago

Did you run motion correction inside RELION?

njxisang commented 2 years ago

Did you run motion correction inside RELION?

Yes, I have done it, I get the corrected_micrographs.star and then I use the ctf estimation based on corrected_micrographs.star to get the micrographs_ctf.star. The micrographs_ctf.star is as follows and I use Relion-3.1.3

version 30001

data_optics

loop_ _rlnOpticsGroupName #1 _rlnOpticsGroup #2 _rlnMicrographPixelSize #3 _rlnMicrographOriginalPixelSize #4 _rlnVoltage #5 _rlnSphericalAberration #6 _rlnAmplitudeContrast #7 opticsGroup1 1 1.400000 1.400000 300.000000 2.700000 0.100000

biochem-fan commented 2 years ago

The micrographs_ctf.star is as follows and I use Relion-3.1.3

Is this all? Don't you have the data_micrographs table after what yo have cited?

njxisang commented 2 years ago

I am not very familiar with this. I use this MRC file （stack_0220_2x_SumCorr.mrc） as the single particle extraction. By import, correction and ctf, I get the file micrographs_ctf.star: version 30001 data_optics

loop_ _rlnOpticsGroupName #1 _rlnOpticsGroup #2 _rlnMicrographPixelSize #3 _rlnMicrographOriginalPixelSize #4 _rlnVoltage #5 _rlnSphericalAberration #6 _rlnAmplitudeContrast #7 opticsGroup1 1 1.400000 1.400000 300.000000 2.700000 0.100000

Yes, it is all I get.

biochem-fan commented 2 years ago

Is stack_0220_2x_SumCorr.mrc the original file you started with? The file name suggests that your inputs are not movies but motion corrected micrographs.

So "Did you run motion correction inside RELION?" "Yes, I have done it" is not correct. You cannot perform motion correction on non-movies!

Import these files as micrographs, not movies, and then perform CTF estimation and extraction.

njxisang commented 2 years ago

Is stack_0220_2x_SumCorr.mrc the original file you started with? The file name suggests that your inputs are not movies but motion corrected micrographs.

So "Did you run motion correction inside RELION?" "Yes, I have done it" is not correct. You cannot perform motion correction on non-movies!

Import these files as micrographs, not movies, and then perform CTF estimation and extraction.

Yes, I have imported it as micrographs and the perform CTF estimation. Then, I get micrographs_ctf.star as follows:

version 30001

data_optics

loop_ _rlnOpticsGroupName #1 _rlnOpticsGroup #2 _rlnMtfFileName #3 _rlnMicrographPixelSize #4 _rlnMicrographOriginalPixelSize #5 _rlnVoltage #6 _rlnSphericalAberration #7 _rlnAmplitudeContrast #8 opticsGroup1 1 stack_0220_2x_SumCorr.mrc 1.400000 1.400000 300.000000 2.700000 0.100000

However, when I use it to extraction, it also report the bug: Preprocessing::initialise ERROR: Input micrograph STAR file has no rlnMicrographName column!

The imported file I get is micrographs.star as follows:

version 30001

data_optics

loop_ _rlnOpticsGroupName #1 _rlnOpticsGroup #2 _rlnMtfFileName #3 _rlnMicrographPixelSize #4 _rlnMicrographOriginalPixelSize #5 _rlnVoltage #6 _rlnSphericalAberration #7 _rlnAmplitudeContrast #8 opticsGroup1 1 stack_0220_2x_SumCorr.mrc 1.400000 1.400000 300.000000 2.700000 0.100000

biochem-fan commented 2 years ago

You are importing in a wrong way. Why did you specify the image as an MTF file?

If this is your first time using RELION, please practice on our tutorial first.

njxisang commented 2 years ago

You are importing in a wrong way. Why did you specify the image as an MTF file?

If this is your first time using RELION, please practice on our tutorial first.

Oh, I am sorry. However, it is my first time to use Relion. However, the first I import the file is not MTF file and I get the file is:

version 30001

data_optics

loop_ _rlnOpticsGroupName #1 _rlnOpticsGroup #2 _rlnMicrographPixelSize #3 _rlnMicrographOriginalPixelSize #4 _rlnVoltage #5 _rlnSphericalAberration #6 _rlnAmplitudeContrast #7 opticsGroup1 1 1.400000 1.400000 300.000000 2.700000 0.100000

version 30001

data_micrographs

loop_ _rlnMicrographName #1 _rlnOpticsGroup #2 stack_0220_2x_SumCorr.mrc 1

But it also reports the same bug. Thank you very much for your kind reply.

biochem-fan commented 2 years ago

It is getting better. Now you have the data_micrographs table. But why do you have only one file? Did you use the wild card?

However, it is my first time to use Relion.

PLEASE go through the tutorial first! Since this is not a RELION bug but your wrong usage, I stop answering this issue here.

If the problem persists even after you learn the tutorial, please ask in the CCPEM mailing list.

njxisang commented 2 years ago

I am so sorry to bother you. I will learn it carefully, thank you for kind reply again.