Problem:
When importing tilt series for tomogram preprocessing and reconstruction, if the mdoc directory contains duplicate mdocs (for instance in my case Position_10_4.mdoc and Position_10_4_override.mdoc) the job runs, it correctly identifies the duplication (see output message below).
[10:33:43] Started import_tilt_series job. serialem.py:76
Creating output directory at Import/job001/tilt_series serialem.py:80
Found 268 mdoc files and 3491 image files. serialem.py:86
Wrote tilt-series data STAR file serialem.py:147
Import/job001/tilt_series.star
writing per tilt-series STAR files... serialem.py:150
Working... ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 0:00:54
[10:34:37] Wrote STAR files for 134 tilt-series. serialem.py:170
However, the names of the imported frames are incorrect. For instance:
data_Position_10_4
loop_
_rlnMicrographMovieName #1
_rlnTomoTiltMovieFrameCount #2
_rlnTomoNominalStageTiltAngle #3
_rlnTomoNominalTiltAxisAngle #4
_rlnMicrographPreExposure #5
_rlnTomoNominalDefocus #6
frames/Position_10_3_001_0.00_20241001_204903_Fractions.mrc 6 0.000000 95.500000 0.000000 -3.500000
frames/Position_10_3_002_3.00_20241001_204955_Fractions.mrc 6 3.000000 95.500000 2.950000 -3.500000
frames/Position_10_3_003_-3.00_20241001_205047_Fractions.mrc 6 -3.000000 95.500000 5.900000 -3.500000
etc....
The names are correct for tilt series which are named Position_x.mdoc, (Position_10.mdoc, Position_15.mdoc, etc) but becomes an issue if there is an underscore and number (Position_10_4.mdoc, Position_15_3.mdoc etc). All the mdocs, including the ones with override in its name contain the correct names of the frames.
The issue is fixed if you remove the duplicate override mdocs, so it is not a massive problem for my current processing, but I wanted to raise it in case you wanted to look into it or someone else had a similar problem of finding multiple identical tilt series/tomograms, as the issue only becomes apparent further into processing.
Environment:
- OS: Linux RHEL 9
- MPI runtime: Open MPI 5.0.3
- RELION version: RELION-5.0.1-commit-908525
- Memory: 527 GB
Job options:
Error message:
No error message is displayed during the import job. The bug only becomes apparent when looking at the star files in the Import/jobxxx/tilt_series directory
Problem:
When importing tilt series for tomogram preprocessing and reconstruction, if the mdoc directory contains duplicate mdocs (for instance in my case Position_10_4.mdoc and Position_10_4_override.mdoc) the job runs, it correctly identifies the duplication (see output message below).
However, the names of the imported frames are incorrect. For instance:
The names are correct for tilt series which are named Position_x.mdoc, (Position_10.mdoc, Position_15.mdoc, etc) but becomes an issue if there is an underscore and number (Position_10_4.mdoc, Position_15_3.mdoc etc). All the mdocs, including the ones with override in its name contain the correct names of the frames.
The issue is fixed if you remove the duplicate override mdocs, so it is not a massive problem for my current processing, but I wanted to raise it in case you wanted to look into it or someone else had a similar problem of finding multiple identical tilt series/tomograms, as the issue only becomes apparent further into processing.
Environment:
Job options:
Error message:
No error message is displayed during the import job. The bug only becomes apparent when looking at the star files in the Import/jobxxx/tilt_series directory