Troubleshooting

Symptom	Check
Missing minimap2, samtools, depth-summary tool, or dedupe.sh	Activate the complete Mamba environment or use the container. Pip alone does not install these executables.
Python import/ABI error	Use the supported environment specification; do not mix incompatible NumPy, pandas, SciPy, HDBSCAN, or Python builds.
Reads not found	Inspect each manifest row from the launch directory or container; paired paths require a literal tab.
Different samples overwrite mapping files	Use distinct read basenames; duplicates are rejected before analysis.
Trusted references are not discovered	Check accepted filename extensions and that the files are nonempty.
No anchored bins	Inspect reference matches and retained sequence lengths; no supported anchors need not mean a successful genome recovery.
Changed settings seem ignored	Check logged effective parameters. Use a new output or --force for changed settings; incomplete runs cannot silently reuse partial files.
Memory exhaustion	Reduce workload/tile count or request more memory; -t does not cap RAM.

Report a reproducible problem at GitHub. Include scarab info, installation route, software revision or image tag, the exact command, relevant log lines, and a minimal non-sensitive input example. Do not post credentials or private study data.