Command-line interface¶
GVClass runs from the repository through pixi, or from the gvclass-a Apptainer wrapper. The entry point is src.bin.gvclass_cli:main, launched by the ./gvclass script.
Run this from the repository directory so the ./gvclass launcher can resolve src/. The gvclass-a Apptainer wrapper takes positional arguments in the order query_dir then results_dir (no -o) and exposes a subset of these flags: -t, --tree-method, --mode-fast, -j/--max-workers, --sensitive, --contigs.
CLI arguments override config keys, which override built-in defaults.
Input and output¶
Config keys are listed in configuration; database download and location are covered in configure the database.
| Option | Argument/Default | Description |
|---|---|---|
query_dir |
path (positional) | Directory with .fna/.faa inputs (also .fasta/.fas), or a single FASTA file when --contigs is set. |
-o, --output-dir |
path; default <query_dir>_results |
Output directory. |
-c, --config |
path; default config/gvclass_config.yaml |
Configuration file. |
-d, --database |
path | Database path. Overrides GVCLASS_DB and config. |
Parallelism¶
| Option | Argument/Default | Description |
|---|---|---|
-t, --threads |
int; default 4 (config) |
Total threads. Overrides config. |
-j, --max-workers |
int; auto if unset | Parallel workers. |
--threads-per-worker |
int; auto if unset | Threads per worker. |
Pipeline and markers¶
For choosing between these settings, see tune speed and accuracy.
| Option | Argument/Default | Description |
|---|---|---|
--tree-method |
{veryfasttree,iqtree,fasttree}; default veryfasttree |
Tree builder. fasttree is an alias for veryfasttree. |
--iqtree-mode |
{fast,ufboot}; default fast |
Species-tree IQ-TREE search mode. Per-marker trees always use --fast. |
--mode-fast |
flag; on by default | Enable fast mode. |
-e, --extended |
flag | Build trees for all markers. Turns fast mode off (slower). |
--sensitive |
flag; on by default | Force E=1e-5, domE=1e-5; skip GA cutoffs. |
--completeness-mode |
{legacy,novelty-aware}; default novelty-aware |
Completeness estimator surfaced as the primary estimate. |
Species tree¶
See build a species tree and the species tree.
| Option | Argument/Default | Description |
|---|---|---|
--species-tree |
flag | Build one supermatrix species tree per query. Writes species_tree/<query>/ and fills the four species_tree_* summary columns. |
--species-tree-combined |
flag | Implies --species-tree. Also builds one combined tree over all queries (species_tree/combined.*). |
--species-tree-trim |
{witchi,pytrimal,none}; default witchi |
Supermatrix column trimming. |
Inputs handling¶
| Option | Argument/Default | Description |
|---|---|---|
-C, --contigs |
flag | Split FNA into per-contig queries. Accepts a file or a directory. |
--allow-short |
flag | Accept FNA shorter than the 20 kb minimum. |
--resume |
flag | Skip completed queries (uses a .SUCCESS sentinel). |
--plain-output |
flag | Disable emojis and ANSI colors. Also env GVCLASS_PLAIN_OUTPUT=1. |
Cluster¶
See run on HPC.
| Option | Argument/Default | Description |
|---|---|---|
--cluster-type |
{local,slurm,pbs,sge}; default local |
Cluster scheduler. |
--cluster-queue |
string | Queue/partition for cluster jobs. |
--cluster-project |
string | Project/account for cluster billing. |
--cluster-walltime |
string; default 04:00:00 |
Walltime for cluster jobs. |
Other¶
| Option | Argument/Default | Description |
|---|---|---|
-v, --verbose |
flag | Verbose output. |
--version |
flag | Print version information and exit. |
Notes¶
Fast and sensitive modes default on
Fast mode (mode_fast: true) and sensitive mode (sensitive_mode: true) are both on by default. -e/--extended turns fast mode off and builds trees for all markers.
Database path precedence
The database path resolves in this order: --database, then the GVCLASS_DB environment variable, then database.path in the config, then the default <repo>/resources.