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EmptyDataError / ' Updating to current Sample Annotation' always triggers #677
Description
(Potentially related to #676)
While trying to run using the --slurm parameter, I've encountered the following error in one of jobs:
This seems to be an error, possibly caused by an incomplete file. However, the other jobs despatched in the same run do not choke at this point, as in this example:
I think this is being caused by the jobs always determining that the sample annotation has changed (even though it hasn't - indeed cannot have - changed between these jobs starting to run). If two jobs hit that point at the same time, concurrency means that one finds an empty or missing file as the other is writing it. I would have thought that this check and update should only happen at most once, when the main snakemake thread begins; either by explicitly skipping that part when the sub-jobs run or because the initial input files have not changed.
What might be causing the scripts to attempt to update those .csv files on every run, and what can I do to fix it?
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