synolog_run.py [-h] -p path --orgs org_1,org_2,[...] -o path [--tree path] [--bin path] [-t num] [--metric [evalue|bitscore]] [--dry-run]

• -p path, --path path — Specify the base path to the Synolog data cache.
• --orgs org_1,org_2,[...] — A comma-separated list of organisms, must match integragtions available in data cache (as listed by synolog_cctrl.py integrations...).
• -o path, --out-path path — Specify the output path to write Synolog results (must exist prior to execution).
• --tree path — Specify the path to a tree in Newick format describing the species.
• --bin path — Specify a custom path to find the synolog binaries.
• -t num, --threads num — Specify the number of threads for synolog to use (default 1).
• --metric [evalue|bitscore] — Specify BLAST hit metric (default 'evalue').
• --dry-run — Do not execute synolog, just print the command that would be exectued.