Monitoring and logs¶

Start the terminal monitor with:

omnomnomics monitor -i EXPERIMENT

The step table uses the assay step numbers accepted by -j and distinguishes running, pending/waiting, completed, and failed work. A later step can run for one sample while an earlier step is still completing other samples because Snakemake schedules dependencies per output, not as global barriers.

Provenance locations¶

Location	Content
run_logs/omnomnomics.run.*.log	run settings, stage events, cleanup decisions, and final status
run_logs/steps/	step summaries, commands, and notes
run_logs/*.tools.log	tool versions and tool-provenance records
run_configs/	resolved run configuration and controller script
slurm_logs/controller/	Snakemake controller output
slurm_logs/<rule>/	rule-specific worker output and exceptions
.snakemake/log/	native Snakemake execution log

When the monitor shows a failed step, inspect the corresponding worker log first. Controller output identifies the failed rule and external Slurm job ID.