Open DrJesseHansen opened 3 months ago
Hi, It's a little hard to diagnose the problem, but one thing really stands out: the input file you've used is called micrographs_ctf.star which is what I would expect the star file to be called if you used the SPA pipeline. When you're using the tomo pipeline I'd expect that file to be called: tilt_series_ctf.star. Are you absolutely sure you loaded relion with: relion --tomo? For all steps? Can you please post the note.txt from the import job, and the CTF job?
Running on a Linux Deb 12 compute cluster, have tried on various GPU nodes.
Running relion/5 beta-3-commit-6331fe.
For example when I run the command below:
relion_python_tomo_align_tilt_series AreTomo --sample-thickness-nanometers 120 --gpu 0 --gpu 1 --gpu 2 --gpu 3 --tilt-series-star-file CtfFind/job002/micrographs_ctf.star --output-directory AlignTiltSeries/job003/ --pipeline_control AlignTiltSeries/job003/
The error can be reduced to these lines of code:
import starfile filename='/nfs/scistore14/itgrp/schloegl/tests_relion5_jesse/CtfFind/job002/micrographs_ctf.star' star = starfile.read(filename, always_dict=True)
global_df = star['global'].set_index('rlnTomoName', drop=False)
which then fails with:
Traceback (most recent call last): File "", line 1, in
KeyError: 'global'
If the code is correct, the data set must be wrong, because star['global'] does not get defined by starfile.read(...). Or the code is wrong.
thank you in advance
best
Jesse
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