Output files

Path	Contents
cmsearch_summary.tsv	One row per extracted SSU region with coordinates and selected taxonomy.
cmsearch_summary.tab	Per-sample unique-contig counts by annotation category.
blast_top_hits.tsv	Ranked BLAST evidence with source identifiers, taxonomy metadata, and extracted query sequences.
tree_nearest_neighbors.tsv	References ordered by patristic distance from each query. Header only when tree mode is off.
phylogeny/<sample>/<detected-model>/<query-key>/	Per-query reference FASTA, covariance-model alignment, trimmed alignment, IQ-TREE files, assignment, neighbor table, and QC. Written in tree mode.
extracted/*.fna	Extracted SSU sequences for each sample/model pair.
stats/*.hits.tsv	Parsed covariance-model hit metadata.
out/*.out	Raw Infernal cmsearch --tblout output.
m8/*.m8	BLAST tabular output for each sample/model pair.
m8/*.top_hits.tsv	Per-model input rows for blast_top_hits.tsv.
m8/merged.m8	Deterministically merged BLAST output.
pipeline_info/	Nextflow timeline, report, trace, and DAG.

Detailed taxonomy fields

Column	Contents
blast_sseqid	Stable identifier of the selected database sequence.
reference_identifiers	Public source identifier for the selected sequence, prefixed by IMG:, PR2:, or SILVA:. Multiple exact-sequence records are separated by |.
reference_versions	Deduplicated reference releases for the selected sequence, prefixed by source.
centroid_names	Cluster centroid names associated with that sequence, separated by | when exact-sequence deduplication links more than one centroid. Empty for native SILVA and PR2 records.
centroid_taxonomy	Lowest common calibrated SILVA or PR2 taxonomy supported for those centroids before the cluster-member propagation limit is applied.
centroid_taxonomy_source	SILVA, PR2, or a joined source value for the centroid taxonomy.
reference_source	Source of the selected database sequence: SILVA, PR2, IMG, or an explicit joined value.
taxonomy	Taxonomy assigned to the selected sequence. IMG cluster-member assignments stop at domain.
taxonomy_assignment_method	Native, lowest-common-ancestor, ambiguity, or IMG cluster-assignment method.
query_sequence	Extracted 16S rRNA gene or 18S rRNA gene sequence.
taxonomy_mode	blast or tree, identifying which method supplied taxonomy.
blast_taxonomy, blast_taxonomy_source, blast_taxonomy_domain, blast_compartment, blast_taxonomy_assignment_method, blast_taxonomy_alternatives	Complete BLAST assignment retained independently of tree mode.
tree_model, tree_marker	Covariance model and marker selected after searching both marker indexes.
tree_route_decision, tree_route_16s_votes, tree_route_18s_votes, tree_route_16s_best_bitscore, tree_route_18s_best_bitscore	Hit counts and best scores used to select the alignment route.
tree_taxonomy, tree_taxonomy_source, tree_taxonomy_domain, tree_compartment	Taxonomy resolved from the nearest named tree references.
tree_assignment_method, tree_basis_neighbors	Neighbor rule and number of named references used for the taxonomy LCA.
tree_nearest_sseqid, tree_nearest_reference_identifiers, tree_nearest_distance	Closest reference sequence and its patristic distance from the query.
tree_query_edge_support	SH-aLRT support on the query's adjacent internal branch when that branch is represented in the rooted output.
tree_inference_model	Nucleotide substitution model used by IQ-TREE.

Exact-sequence deduplication can associate one database sequence with more than one source cluster. centroid_names retains every centroid among the selected taxonomy assignments; centroid_taxonomy is their lowest common taxonomy. SILVA centroid names omit the semicolon-delimited lineage from the source header. PR2 centroid names retain the original public PR2 header label.

Ranked BLAST evidence

blast_top_hits.tsv reports the first --top_hits subjects for each extracted query. It also reports the highest-ranked IMG, PR2, and SILVA subject among the fetched BLAST candidates when that source occurs below the requested cutoff. hit_rank is the rank among those candidates. selection_reason distinguishes overall_top_n, equal_best_assignment, best_IMG, best_PR2, and best_SILVA rows.

Each row joins the stable blast_sseqid to its public source identifier, reference version, preferred taxonomy, centroid evidence, BLAST statistics, and the extracted query sequence. The table can contain more than --top_hits rows per query because all equal-best assignment subjects and the best subject from another reference source are retained. The source-specific supplemental rows do not change the selected taxonomy in cmsearch_summary.tsv.

An IMG subject without native or calibrated centroid taxonomy remains Unclassified. SSUextract reports the best PR2 and SILVA evidence as separate rows instead of assigning a lower-scoring lineage to that IMG subject.

Tree-neighbor evidence

tree_nearest_neighbors.tsv contains every reference used in a tree. Rows are ordered by tree_distance within each query. tree_lineage_basis identifies whether classification used preferred taxonomy, calibrated IMG centroid taxonomy, or a domain-only value. used_for_assignment marks the nearest named references included in the LCA. Every named reference tied by distance at the configured neighbor boundary is included, so tree_basis_neighbors can exceed --tree_assignment_neighbors.

Each per-query directory retains references.tsv, references.fna, cmalign_input.fna, the raw and trimmed covariance-model alignments, alignment_qc.json, the IQ-TREE report and tree, the assignment and neighbor tables, and tool_versions.txt. references.tsv links the compact tree leaf labels to stable database IDs and public source identifiers. The query directory uses a deterministic q_<hex> key; task.json records the original query name and the detected and tree-selected models.

If the selected marker has fewer than three reference subjects, no tree is inferred for that query. Its BLAST assignment remains selected with taxonomy_mode=blast, and tree_assignment_method records tree_skipped_insufficient_references. Other queries in the same run continue.

Counting behavior

cmsearch_summary.tsv retains hits after overlapping RF00177 and RF01960 matches on the same strand have competed by Infernal E-value and bit score. In cmsearch_summary.tab, one contig contributes at most once to each sample-level annotation category.

Samples without accepted hits remain in cmsearch_summary.tab. Their detailed summary contains a header and no data rows; per-model hit tables also contain headers only.

Coordinates and strand

Hit coordinates are the 1-based inclusive values reported by Infernal. The extracted sequence includes both endpoints. Reverse-strand records contain the reverse complement of that interval.