Added

• --max_parallel_downloads parameter to control how many downloads can occur in parallel. This can be used in HPC/cloud contexts to raise the default maximum that is process-specific and generally below 10 to avoid exceeding API limits when running locally. The cloud profile was added to provide environment-specific defaults for this parameter and any other relevant ones in the future.
• --cpu_scale parameter to scale the number of CPUs used by multithreaded processes. This allows users to adjust CPU usage across all multithreaded processes proportionally (e.g., setting to 0.5 will halve CPU usage, setting to 2 will double it).
• skip_core_phylogeny parameter to skip the core phylogeny step if not required.

Changed

• INITIAL_CLASSIFICATION now includes taxa with representatives within 1% of the highest ANI match for each rank if there are no matches that pass the quality thresholds.
• New and much better tree plotting widget for the main report.
• 4 samples/references are now required to make variant trees to allow for bootstrapping.

Fixed

• Removed redundant reference_id column in output of PICK_ASSEMBLIES
• Made FIND_ASSEMBLIES not error when exit code is 0 (e.g. when “New version of client…” output in standard error).
• Fixed bakta database download error.
• Updated NCBI tools use to download data, fixing error with downloads.

Dependencies

• Various modules updates.