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Run the bundled example

Select the curated database profile for this tutorial.

Install the pinned environment

git clone https://github.com/NeLLi-team/ssuextract.git
cd ssuextract
pixi install --frozen

Check the installed version:

pixi run ssuextract --version

Install the reference database

pixi run setup

Setup lists both database profiles:

Available database profiles:
  1) curated v1.0.2 (345.4 MiB) - PR2 5.1.1 and SILVA 138.2
  2) img v1.0.2 (840.9 MiB) - Curated profile plus IMG 16S rRNA gene and 18S rRNA gene sequences
Database profile (1-2) [default: 1 (curated)]:

The current default appears in brackets. A previous selection becomes the default on later setup runs. Press Enter to keep it, or enter 1, 2, curated, or img. For this tutorial, select curated. Press Enter again to accept resources/database, or enter another writable directory. During the download, one terminal line shows written bytes, transfer rate, and estimated time remaining. It then reports extraction, file validation, and the installed database version. If the download stops, rerun pixi run setup. Setup continues the selected database download from the retained partial archive.

Run the bundled assemblies

pixi run example

The two assemblies contain 10 accepted loci: nine 16S rRNA gene annotations and one 18S rRNA gene annotation. The command checks every annotation against the selected database profile and stops if a marker, reference sequence, taxonomy, or assignment method differs from the expected result. The checked annotations are tied to the database version shown by setup. Update SSUextract when installing a later database release so the example contract and database remain in sync.

The run creates results/smoke/. Check the summary and ranked-hit files:

test -s results/smoke/cmsearch_summary.tsv
test -s results/smoke/cmsearch_summary.tab
test -s results/smoke/blast_top_hits.tsv

cmsearch_summary.tsv contains one row per extracted region; cmsearch_summary.tab contains per-sample counts by annotation category. View the sample, marker model, coordinates, reference source, final taxonomy, centroid evidence, and public reference identifier:

cut -f2,3,5,14,15,23-26 results/smoke/cmsearch_summary.tsv

View the ranked reference evidence:

cut -f1,4-5,7,9-10,17,19-20,28 results/smoke/blast_top_hits.tsv

Inspect an extracted sequence

find results/smoke/extracted -name '*.fna' -size +0 -print

Each FASTA record spans the complete 1-based inclusive interval reported by Infernal. Reverse-strand hits are reverse-complemented after interval extraction.

To use other FASTA files, continue with run assembled genomes or metagenomes. See the output reference for every result path.