Hi,
"run.err" and "run.out" are written by the job system, not RELION
itself. You might want to test the job system by putting some "echo"s
in the script.
Best regards,
Takanori Nakane
> I've been using the Relion 3.0.7 but 2D classifications are sometimes
> running and sometimes not. When tyring to look for errors I noticed that
> even with a job that did run there are no run.err or run.out files (see
> below ls of all in the Class2D/job030 directory)
>
> This job ran ok after submitting to a queue, today a similar job (all
> parameters the same except the input contained fewer particles) submitted
> to the queue ok but then disappeared from the queue and the job directory
> only contained - default_pipeline.star job_pipeline.star note.txt
> run.job run_submit.script
>
> Any ideas?
> Thanks
> Sonya
>
>
> run_it001_sampling.star run_it008_optimiser.star
> .. run_it002_classes.mrcs
> run_it008_sampling.star
> default_pipeline.star run_it002_data.star
> run_it009_classes.mrcs
> job_pipeline.star run_it002_model.star
> run_it009_data.star
> note.txt run_it002_optimiser.star
> run_it009_model.star
> run.job run_it002_sampling.star
> run_it009_optimiser.star
> run_ct10_it010_classes.mrcs run_it003_classes.mrcs
> run_it009_sampling.star
> run_ct10_it010_data.star run_it003_data.star
> run_it010_classes.mrcs
> run_ct10_it010_model.star run_it003_model.star
> run_it010_data.star
> run_ct10_it010_optimiser.star run_it003_optimiser.star
> run_it010_model.star
> run_ct10_it011_classes.mrcs run_it003_sampling.star
> run_it010_optimiser.star
> run_ct10_it011_data.star run_it004_classes.mrcs
> run_it010_sampling.star
> run_ct10_it011_model.star run_it004_data.star
> run_it011_classes.mrcs
> run_ct10_it011_optimiser.star run_it004_model.star
> run_it011_data.star
> run_ct10_it011_sampling.star run_it004_optimiser.star
> run_it011_model.star
> run_ct10_it012_classes.mrcs run_it004_sampling.star
> run_it011_optimiser.star
> run_ct10_it012_data.star run_it005_classes.mrcs
> run_it011_sampling.star
> run_ct10_it012_model.star run_it005_data.star
> run_it012_classes.mrcs
> run_ct10_it012_optimiser.star run_it005_model.star
> run_it012_data.star
> run_ct10_it012_sampling.star run_it005_optimiser.star
> run_it012_model.star
> run_ct10_it013_classes.mrcs run_it005_sampling.star
> run_it012_optimiser.star
> run_ct10_it013_data.star run_it006_classes.mrcs
> run_it012_sampling.star
> run_ct10_it013_model.star run_it006_data.star
> run_it013_classes.mrcs
> run_ct10_it013_optimiser.star run_it006_model.star
> run_it013_data.star
> run_ct10_it013_sampling.star run_it006_optimiser.star
> run_it013_model.star
> run_ct10_unmasked_classes.mrcs run_it006_sampling.star
> run_it013_optimiser.star
> run_it000_classes.mrcs run_it007_classes.mrcs
> run_it013_sampling.star
> run_it000_data.star run_it007_data.star
> run_it014_classes.mrcs
> run_it000_model.star run_it007_model.star
> run_it014_data.star
> run_it000_optimiser.star run_it007_optimiser.star
> run_it014_model.star
> run_it001_classes.mrcs run_it007_sampling.star
> run_it014_optimiser.star
> run_it001_data.star run_it008_classes.mrcs
> run_it014_sampling.star
> run_it001_model.star run_it008_data.star
> run_submit.script
> run_it001_optimiser.star run_it008_model.star
> run_unmasked_classes.mrcs
>
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