Commands
The supported command-line workflows and their important options. The installed --help output is the exact option reference for your version.
giftag build
giftag build [-d DIR] [--gifter-db PATH|URL] [--sources kofam,ncbifam,pfam,dbcan]Builds the local profile database from gifter’s marker list. With no --gifter-db, giftag reads the database at gifter’s current GitHub main; supply a local SQLite database or marker TSV to pin the marker catalogue. The default build includes all four supported sources.
| Option | Effect |
|---|---|
-d, --db |
Database directory; default is $GIFTAG_DB, then ~/.local/share/giftag. |
--gifter-db |
Gifter SQLite database or marker TSV, local path or URL. |
--sources |
Comma-separated sources to build. Omitted sources are marked source_skipped in markers.tsv. |
--kofam-release, --ncbifam-release, --dbcan-release |
Choose source releases. KOfam accepts current or an archive date. |
--kofam-dir, --ncbifam-dir, --pfam-dir, --dbcan-dir |
Use local copies of the source files. |
-t, --threads |
Parallel downloads; default 8. |
--force |
Replace an existing built database at the destination. |
The command downloads profiles from their publishers and redistributes none. Inspect source terms and coverage before choosing sources.
giftag annotate
giftag annotate -i FASTA... -o DIR [-d DIR] [-t THREADS]
giftag -i FASTA... -o DIR # shorthandSearches nucleotide or protein FASTA files, plain or gzipped, and writes gifter-ready marker rows. -i accepts multiple files or a directory. Input types are detected per file unless --input-type is given.
| Option | Effect |
|---|---|
-i, --input |
One or more FASTA paths, or directories containing FASTA files. |
-o, --outdir |
Directory for output tables, run manifest and predicted proteins. |
-d, --db |
Built giftag database; uses the same default as build. |
-t, --threads |
Search CPU threads; 0 uses all available threads. |
--input-type |
Set auto, nucleotide or protein instead of per-file detection. |
--mode |
Set auto, single or meta for nucleotide gene calling. In auto, single-genome training is used from 100 kb upward. |
--gate-subfamilies |
Search dbCAN-sub clusters only on proteins with a matching family domain. Faster, but stricter than the default run_dbcan-like search. |
For --gate-subfamilies, the validation comparison found 144 of 157 retained subfamily calls relative to the ungated search. Keep the default when reproducing run_dbcan-like evidence matters more than speed.
Inspect a build
giftag info
giftag info -d /path/to/giftag-db
giftag versioninfo reports source releases, marker coverage and terms of use. version reports the installed giftag package version.
Logs
Global logging options go before the command:
giftag --log-file run.log annotate -i genomes/ -o annotations/
giftag --quiet annotate -i genomes/ -o annotations/
giftag --verbose build--log-file writes UTC-stamped plain-text progress. --quiet keeps warnings and errors; --verbose shows debug messages. Progress bars become plain log lines when output is piped or sent to a job log.