8000 Snakemake reports non-zero error code when checkpoints execute successfully · Issue #7 · bhattlab/lathe · GitHub
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Snakemake reports non-zero error code when checkpoints execute successfully #7

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bsiranosian opened this issue Oct 7, 2019 · 0 comments
Open

Snakemake reports non-zero error code when checkpoints execute successfully #7

bsiranosian opened this issue Oct 7, 2019 · 0 comments

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@bsiranosian
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This affects checkpoint medaka_ranges, checkpoint pilon_ranges, checkpoint extract_bigtigs

Snakemake will exit even though the command executed successfully. For now, the only way I see around this is to execute the command in the shell manually.

This is a known issue, see: https://bitbucket.org/snakemake/snakemake/issues/1303/snakemake-checkpoint-throws-exited-with
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