Database profiles¶
| Profile | Reference content | Additional content | Search indexes |
|---|---|---|---|
curated |
SILVA 138.2 NR99 and PR2 5.1.1 | None | Separate BLAST v5 indexes for 16S rRNA genes and 18S rRNA genes. |
img |
SILVA 138.2 NR99 and PR2 5.1.1 | IMG sequences from the eukcensus 16S rRNA gene and 18S rRNA gene collections | Separate BLAST v5 indexes for 16S rRNA genes and 18S rRNA genes. |
RF00177 routes to the 16S rRNA gene index. RF01960 routes to the 18S rRNA gene
index. The mapping is stored in config/model_markers.json.
Database packages use a version independent of the SSUextract application.
The version is stored in each profile's manifest.json and printed before a
pipeline run.
Installation and update checks¶
pixi run setup lists each profile with the version and compressed download
size from config/database_catalog.json. The selected path and profile are
stored as database_path and database_profile in config/local.config.
The installer accepts a Zenodo release only when all of these values agree:
- the configured concept record and the latest release record;
- the exact four-file release inventory and Zenodo MD5 values;
- the release manifest, archive sizes, and archive SHA-256 values;
- the two entries in
SHA256SUMS.
Archive extraction takes place in a staging directory. The profile becomes the installed profile after its manifest files and BLAST indexes validate. A failed replacement restores the installed profile.
Archive downloads use a 60-second network read timeout and stop after five consecutive transient failures. A partial archive is keyed by profile, database version, archive SHA-256 digest, and host. A later setup run resumes it only when the server returns a matching HTTP byte range. A rejected range or failed checksum permits one clean restart for that condition. The installer checks the final byte count and SHA-256 digest before extraction. It removes the verified download cache after using the archive.
Interactive terminals redraw a width-bounded progress line with written bytes, transfer rate, and estimated time remaining. Non-interactive logs include the start, completion, and intermediate progress every 10 seconds.
pixi run ssuextract and pixi run example check Zenodo before starting
Nextflow. The check has a five-second total timeout. Interactive runs offer to
install an available release. Non-interactive runs and runs with an explicit
--database_path report the update and continue with the installed profile. A
valid installed profile remains usable when the check times out, Zenodo is
unavailable, or the remote release contract fails validation.
Runtime files¶
| Path | Contents |
|---|---|
manifest.json |
Profile identity, artifact paths, sizes, and SHA-256 digests. |
provenance.json |
Source versions, build contracts, software versions, and source-tree fingerprints. |
blast/16S.* |
BLAST v5 nucleotide index for 16S rRNA genes. |
blast/18S.* |
BLAST v5 nucleotide index for 18S rRNA genes. |
tables/sequences.parquet |
Content-addressed sequence identifiers, lengths, hashes, and marker membership. |
tables/preferred_taxonomy.parquet |
Selected sequence taxonomy, centroid names and taxonomy, and explicit cross-domain conflict state. |
tables/source_records.parquet |
Normalized source record provenance. |
tables/taxonomy_assignments.parquet |
Native and derived taxonomy evidence. |
tables/img_location.parquet |
IMG taxon identifier and valid latitude/longitude values. |
Raw source FASTA files, source project descriptions, contacts, email addresses, comments, and cluster tables are not distributed in a runtime profile. The IMG profile retains only the centroid names required to interpret cluster-derived taxonomy.
Curated profile counts¶
The curated profile contains 609,298 unique exact sequences from 683,597
source records. The 16S rRNA gene index contains 416,021 sequences; the 18S
rRNA gene index contains 193,282. Exact sequences assigned across domains
remain marked as conflicts.