Hi All,
Been having some trouble running the 2D classification job in Relion 3.0.
I have been submitting to a queue and everything has been running fine - 2D classification to produce templates for autopick worked fine, as did the autopicking but the 2D classification of the extracted autopicked particles doesnt run. it just gets aborted for exceeding the walltime (which I have set to 60hrs) - if I go back to the GUI to continue when I browse there's only run_it000_optimiser.star so it doesnt look like it ever gets started. And there are no error messages.......
Input parameters;
I/O - Extract/job13/particles.star (21395 particles)
CTF - No (negative staining)
Optimsation
- Classes 50 (I tried 100 first)
- T=2
- Iteration = 20 (I tried 25 first)
- Mask =250
Sampling - default settings
Helix - default settings
Compute - default settings
Running
- MPI=16
- Threads=1
- Queue=yes
- Name=batch
- Command=qsub
- Max hrs= 60 (I've tried 20, 30, 40)
- Submission = /local/software/relion/3.0/bin/qsub.bash (I was asked by my IT dept to remove the 'double' in order to get it to submit - could this be the problem?)
- Cores per node=1
Any suggestions?
Thanks
Sonya
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