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update README.MD #34

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kalenkovich opened this issue Oct 4, 2021 · 2 comments
Open

update README.MD #34

kalenkovich opened this issue Oct 4, 2021 · 2 comments
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@kalenkovich
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  • update to running the full workflow (probably with --keep-going)
  • what to do with download errors (--until download_from_openneuro --restart-times 5)
  • what to do with segmentation fault or python dying (see the resources issue)
@kalenkovich kalenkovich self-assigned this Oct 4, 2021
@kalenkovich
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kalenkovich commented Oct 5, 2021

In case of errors in rule download_from_openneuro, use

snakemake --until download_from_openneuro --cores <n_cores> --restart-times 5

Then run the rest.

@kalenkovich
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In case of segmentation fault or Python dying while running jobs from rules apply_linear_filter and create_artifact_epochs, run

snakemake --cores <n_cores> --resources filtering_process=<n_cores> --default-resources filtering_process=1

The snakemake version that we use does not support --set-resources so we'll have to add them to Snakefile.

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