Output files

SCARAB writes logs, feature matrices, clustering assignments, and FASTA products under -o. It does not provide the report/explorer interface of MetaPathways or ASPIRE.

OUTPUT/
├── SCARAB_log.txt
├── scarab_run.json
├── scarab_status.json
├── *.subcontigs.fasta
├── *.mbacov.tsv
├── *.coverage.scaled.tsv
├── feature/signature/parameter intermediates
└── <autoopt-method>/<selected-setting>/
    ├── *.tsv
    ├── denovo/
    ├── hdbscan/
    ├── ocsvm/
    ├── intersect/
    └── xpgs/

The method and setting names are resolved by AutoOpt and printed in the log. Some intermediate names and optional products depend on which paths ran; this is a guide to the layout, not a promise that every directory will contain sequences.

Product	Interpretation
*.mbacov.tsv	Raw MetaBAT depth-summary table used for abundance features.
*.coverage.scaled.tsv	Scaled abundance matrix used by clustering.
*.denovo_clusters.tsv and *.denovo_noise.tsv	De novo assignments and unassigned/noise records.
*.hdbscan_clusters.tsv	Trusted-anchor HDBSCAN assignments.
*.ocsvm_clusters.tsv	One-class SVM recruitment assignments.
*.inter_clusters.tsv	Pairwise-agreement recruitment plus qualifying anchors; see the workflow set formula.
*.denovo.fasta	Original contigs assigned to de novo bins.
*.hdbscan.fasta, *.ocsvm.fasta, *.intersect.fasta	Recruited contig sets from the anchored approaches.
*.xPG.fasta	Trusted reference plus recruits after BBTools deduplication.

Recruited FASTAs and xPG FASTAs answer different questions: the first contains recruited metagenomic sequence; the latter also contains the trusted reference. The deduplication command uses a 97% minimum identity setting. Independently validate genome quality and interpret overlap between recruitment approaches.

The abundance stage removes SAM/BAM and selected tool-output intermediates after coverage generation. Retain final FASTAs, assignment tables, logs, input manifests, and the software revision for downstream review. Avoid manually pruning a partially completed output if you intend to reuse it.

For guided assemblies derived from these products, see reassembly.