Troubleshooting and reproducibility

• A command fails before execution: check the CLI/error logs, activate the environment and use command -v nextflow coverm fastal to check dependencies.

• A task exceeds the memory budget: lower concurrency or adjust --memory/--max_memory to measured requirements; Slurm can enforce its allocation.

• Some MAG pathways are missing: inspect the entity’s last task status and logs. Expected MAG inference failure is distinct from missing annotation inputs.

• The portal says local explorer required: launch metapathways report -o OUTPUT --serve --no-rebuild and open the URL it prints.

• Results were changed after report generation: rebuild the report. It is an indexed snapshot, not a live view of files.

• A report rebuild fails: inspect the named source and expected schema. Fix/correct the source or report importer; do not invent missing identifiers or replace absent values with zero.

Record commands, Git commit, software versions, reference versions/checksums and input checksums for reproducible work. See reproducibility notes for the historical benchmark and the distinction between installation tests, synthetic software tests and full biological validation.