Feature/16s standalone

[KWchip]

Description

This PR introduces a 16s standalone mode and significantly improves the execution time of the IMNGS ecological analysis through multithreading.

As a researcher utilizing Protologger for environmental ecosystem profiling, I found the IMNGS module incredibly powerful, but frequently needed to contextualize 16S isolates without running the full WGS pipeline.

Key Changes

• Added 16s execution mode: Bypasses WGS requirements (CheckM, GTDB-Tk, PROKKA, etc.) to strictly execute taxonomic placement, tree building, and IMNGS prevalence analysis.
• Multithreaded IMNGS BLAST: Implemented concurrent.futures.ThreadPoolExecutor for the IMNGS amplicon BLAST loop. Controlled via a new -t / --threads argument (default: 1). In local testing on 70 threads, this reduced the ecological analysis step time by ~91%.
• Tool Compatibility Updates: * Updated muscle command flags to be compatible with Muscle v5 (-align and -output).
  • Added a safety catch for fastANI to prevent crashes when GTDB-Tk does not return reference genomes (e.g., when using modern GTDB releases like r226 that lack the fastani database folder).
  • Bypassed the UCHIME chimera check, as usearch is proprietary and frequently unavailable in standard bioinformatics environments.

Testing

• Tested 16s mode: Successfully completes taxonomic and ecological analysis, exiting cleanly before genome steps.
• Tested full mode: Successfully runs end-to-end, inheriting the new multithreaded IMNGS logic. Ecological prevalence outputs have been verified 1:1 against the original sequential pipeline.