After particle picking, the micrographs_selected.star file is not generated.

Jobs up to [Import][Motion correction][CTF estimation] are proceeding without problems. In [Manual picking] or [Auto picking], the particle picking is completed, the directory [AutoPick/jobXXX] is created, and [logfile.pdf] is successfully exported, but [micrographs_selected. star] is not generated. This prevents me from proceeding to the [Particle extraction] job. Please write a clear description of what the problem is.

Environment:

OS: [Ubuntu 22.04.2 LTS]
MPI runtime: [mpiexec (OpenRTE) 4.1.2]
RELION version: [4.0.1-commit-477a63]
Memory: [128 GB]
GPU: [GeForce RTX 2080 SUPER]

Dataset:

Box size: [e.g. 256 px]
Pixel size: [e.g. 0.88 Å/px]

Job options:

Type of job: [Auto picking]
Number of MPI processes: [8]
Number of threads: [8]

Full command (see note.txt in the job directory):


`which relion_autopick` --i Select/job005/micrographs_split1.star --odir AutoPick/job007/ --pickname autopick --LoG  --LoG_diam_min 200 --LoG_diam_max 250 --shrink 0 --lowpass 20 --LoG_adjust_threshold 0  --pipeline_control AutoPick/job007/

Error message:

＊The following message is displayed on the terminal, not on the RELION.

WARNING: output node AutoPick/job007/autopick.star does not exist, while job AutoPick/job007/ should have finished successfully. You can manually mark this job as failed to suppress this message.

＊The output of RELION is as follows

Run autopicking on the following micrographs:
- MotionCorr/job002/Movies/20230404_Tic_135_78-1_Apr04_12_07_03_X-1Y-1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-1_Apr04_12_07_15_X+0Y-1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-1_Apr04_12_07_22_X+0Y+0-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-1_Apr04_12_07_30_X-1Y+0-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-1_Apr04_12_07_38_X+0Y+1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-2_Apr04_12_09_18_X-1Y-1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-2_Apr04_12_09_29_X+0Y-1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-2_Apr04_12_09_37_X+1Y-1-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-2_Apr04_12_09_45_X+0Y+0-0.mrc
- MotionCorr/job002/Movies/20230404_Tic_135_78-2_Apr04_12_09_53_X-1Y+0-0.mrc
Will use following diameters for Laplacian-of-Gaussian filter:
- 40 (too low)
- 50 (too low)
- 67 (too low)
- 100 (too low)
- 200 (ok)
- 225 (ok)
- 250 (ok)
- 500 (too high)
- 750 (too high)
- 1000 (too high)
- 1250 (too high)
WARNING: Requested rescale of micrographs is 506 pixels. The largest prime factor in FFTs is 127
WARNING: Will change rescaling of micrographs to 504 pixels, because the prime factor then becomes 23
WARNING: add --skip_optimise_scale to your autopick command to prevent rescaling
WARNING: The calculations will be done at a lower resolution than requested. Autopicking ... 15/ 15 sec ............................................................~~(,,"> Generating logfile.pdf ... 0/ 0 sec ............................................................~~(,,"> Total number of particles from 10 micrographs is 1976 i.e. on average there were 198 particles per micrograph Done! Written: AutoPick/job007/logfile.pdf

3dem / relion

After particle picking, the micrographs_selected.star file is not generated. #965