aviary annotate¶
Annotate a given set of MAGs using EggNOG and GTDB-Tk.
This subcommand also accepts the common workflow, resource, output and execution options described under Shared options.
Examples¶
Full annotation (GTDB-tk + EggNOG)¶
The default annotate target runs GTDB-tk taxonomy and EggNOG functional annotation together
(CheckM2 is run separately, as part of the recover/complete binning pipeline rather than
here). Point at specific database locations with --gtdb-path/--eggnog-db-path if they
aren't already set via aviary configure:
Run a single annotator¶
Use -w/--workflow to target one annotation step instead of the full set — useful for
re-running just the step that failed, or when you only need one kind of annotation:
Taxonomy only (GTDB-tk):
Functional annotation only (EggNOG):
CheckM2 quality assessment is not run through aviary annotate — it runs as part of the
recover/complete binning pipeline, where it has access to the intermediate binning outputs
it depends on.
A different FASTA extension¶
--fasta-extension defaults to fna; set it to match your files if they use something else
(e.g. bins produced outside aviary):
Input options¶
-d, --genome-fasta-directory DIR
Directory containing MAGs to annotate.
-x, --fasta-extension EXT
File extension of FASTA files in --genome-fasta-directory. [default: fna]
-a, --assembly FILE [FILE ...]
FASTA file(s) containing scaffolded contigs to pass to QUAST for QC.
Annotation / bin processing options¶
--gtdb-path PATH
Path to local GTDB database files.
--eggnog-db-path PATH
Path to local EggNOG database files.
--singlem-metapackage-path PATH
Path to local SingleM metapackage.
--checkm2-db-path PATH
Path to CheckM2 database.
--metabuli-db-path PATH
Path to local Metabuli database.
Performance options¶
-t, --max-threads INT
Maximum threads per process. [default: 8]
-n, --n-cores INT
Maximum cores available. [default: 16]
-m, --max-memory INT
Maximum memory in gigabytes. [default: 250]
-p, --pplacer-threads INT
Threads for pplacer during GTDB-tk classification. Values above
--max-threads are capped to that limit. [default: 8]
Output options¶
-o, --output DIR
Output directory. [default: ./]
--tmpdir DIR
Temporary files directory.
Inherited QC options¶
The parser also accepts --gold-standard-assembly, --gsa-mappings,
--host-filter, --min-read-size, --min-mean-q, --keep-percent,
--min-short-read-length, --max-short-read-length,
--disable-adapter-trimming, --unqualified-percent-limit,
--quality-cutoff, --extra-fastp-params and --skip-qc because annotate
inherits Aviary's QC option group. They do not affect the default annotate
target. Use -a/--assembly to provide assemblies to a separately targeted
QC rule, and see aviary assemble → QC options for
the accepted values.