---
title: Galah process
---
# galah process
Runs both analyse and cluster in sequence.
Determines the MIMAG quality score based on completeness, contamination, rRNA, and tRNA presence.
Completeness and contamination are estimated using CheckM2 by default, unless CheckM1/2 quality reports are provided.
Cluster genomes into ANI-based groups for downstream analysis.
```bash
# Example: process genomes to produce cluster definition and MIMAG summary
CHECKM2DB=CheckM2_database/uniref100.KO.1.dmnd galah process \
--genome-fasta-files genome1.fna genome2.fna \
--output-cluster-definition clusters.tsv \
--output-mimag-summary mimag.tsv
```
# GENOME INPUT
**-f**, **\--genome-fasta-files** *PATH ..*
Path(s) to FASTA files of each genome e.g.
`pathA/genome1.fna pathB/genome2.fa`.
**-d**, **\--genome-fasta-directory** *PATH*
Directory containing FASTA files of each genome.
**-x**, **\--genome-fasta-extension** *EXT*
File extension of genomes in the directory specified with
`-d/--genome-fasta-directory`. [default: `fna`]
**\--genome-fasta-list** *PATH*
File containing FASTA file paths, one per line.
# QUALITY PARAMETERS
**\--quality-method** *NAME*
method for finding genome quality. \'`checkm2`\' for CheckM2.
[default: `checkm2`]
**\--checkm2-db-path** *PATH*
Path to CheckM2 database (required for CheckM2 quality method). If
not given, will use CHECKM2DB environment variable if set.
**\--checkm2-quality-report** *PATH*
Path to pre-generated CheckM2 quality_report.tsv file. If given,
will use this file instead of running quality method.
**\--checkm-tab-table** *PATH*
Path to pre-generated CheckM tab table file. If given, will use this
file instead of running quality method.
# RNA PARAMETERS
**\--rrna-method** *NAME*
method for finding rRNA genes. \'`barrnap`\' for Barrnap. [default:
`barrnap`]
**\--trna-method** *NAME*
method for finding tRNA genes. \'`trnascan`\' for tRNAscan-SE.
[default: `trnascan`]
**\--barrnap-gff-list** *PATH*
Path to two-column TSV file mapping genome paths (as given in input)
to Barrnap GFF paths (no headers). If given, will use these files
instead of running rRNA method.
**\--trnascan-out-list** *PATH*
Path to two-column TSV file mapping genome paths (as given in input)
to tRNAscan-SE output paths (no headers). If given, will use these
files instead of running tRNA method.
# FILTERING PARAMETERS
**\--checkm2-quality-report** *PATH*
CheckM version 2 quality_report.tsv (i.e. the `quality_report.tsv`
in the output directory output of `checkm2 predict ..`) for defining
genome quality, which is used both for filtering and to rank genomes
during clustering.
**\--checkm-tab-table** *PATH*
CheckM tab table (i.e. the output of
`checkm .. --tab_table -f PATH ..`). The information contained is
used like `--checkm2-quality-report`.
**\--genome-info** *PATH*
dRep style genome info table for defining quality. The information
contained is used like `--checkm2-quality-report`.
**\--min-completeness** *FLOAT*
Ignore genomes with less completeness than this percentage.
[default: not set]
**\--max-contamination** *FLOAT*
Ignore genomes with more contamination than this percentage.
[default: not set]
**\--run-checkm2**
Run CheckM2 to generate quality scoring used for clustering.
Requires \--checkm2-db-path or CHECKM2DB env variable to be set.
**\--checkm2-db-path** *DB_PATH*
Path to CheckM2 database (required for running CheckM2) [default:
from CHECKM2DB environment variable]
# CLUSTERING PARAMETERS
**\--ani** *FLOAT*
Overall ANI level to dereplicate at with the primary clusterer.
[default: `95`]
**\--min-aligned-fraction** *FLOAT*
Min aligned fraction of two genomes for clustering. [default:
`15`]
**\--small-genomes**
Use small-genomes settings in skani calculation. Recommended for
sequences \< 20kb.
**\--fragment-length** *FLOAT*
Length of fragment used in FastANI calculation (i.e. `--fragLen`).
[default: `3000`]
**\--quality-formula** *FORMULA*
Scoring function for genome quality [default:
`Parks2020_reduced`]. One of:
| `Parks2020_reduced` | (default) A quality formula described in Parks et. al. 2020 https://doi.org/10.1038/s41587-020-0501-8 (Supplementary Table 19) but only including those scoring criteria that can be calculated from the sequence without homology searching: `completeness-5*contamination-5*num_contigs/100-5*num_ambiguous_bases/100000` |
| `completeness-4contamination` | `completeness-4*contamination` |
| `completeness-5contamination` | `completeness-5*contamination` |
| `dRep` | `completeness-5*contamination+contamination*(strain_heterogeneity/100)+0.5*log10(N50)` |
**\--precluster-ani** *FLOAT*
Require at least this precluster-derived ANI for preclustering and
to avoid primary clustering on distant lineages within preclusters.
[default: `90`]
**\--precluster-method** *NAME*
method of calculating rough ANI for dereplication. \'`finch`\' for
finch MinHash, \'`skani`\' for Skani. [default: `skani`]
**\--cluster-method** *NAME*
method of calculating ANI. \'`fastani`\' for FastANI, \'`skani`\'
for Skani. [default: `skani`]
**\--cluster-contigs**
Cluster contigs within a fasta file instead of genomes. When used,
either \--small-contigs or \--large-contigs must be specified.
**\--small-contigs**
Use small-genomes settings in skani when clustering contigs.
Recommended for contigs \< 20kb. Mutually exclusive with
\--large-contigs.
**\--large-contigs**
Do not use small-genomes settings in skani when clustering contigs.
Recommended for contigs \>= 20kb. Mutually exclusive with
\--small-contigs.
**\--low-memory**
Reduce memory use by sketching to file and searching it instead.
**\--reference-genomes** *PATH \...*
Reference genomes to cluster against. These should be pre-clustered
at the chosen %ANI. If quality is provided for representative
selection, values for these genomes must also be provided. Genomes
within the precluster ANI cutoff of each reference will be placed in
the same precluster. Mutually exclusive with
\--reference-genomes-list.
**\--reference-genomes-list** *PATH*
File containing paths to reference genomes (one per line). These
should be pre-clustered at the chosen %ANI. If quality is provided
for representative selection, values for these genomes must also be
provided. Genomes within the precluster ANI cutoff of each reference
will be placed in the same precluster. Mutually exclusive with
\--reference-genomes.
# OUTPUT
**\--output-mimag-summary** *PATH*
Output a tsv file summarising the MIMAG status for each genome.
**\--output-quality-report** *PATH*
Output a CheckM2-format quality report TSV file.
**\--output-cluster-definition** *PATH*
Output a file of representative\<TAB\>member lines.
**\--output-representative-fasta-directory** *PATH*
Symlink representative genomes into this directory.
**\--output-representative-fasta-directory-copy** *PATH*
Copy representative genomes into this directory.
**\--output-representative-list** *PATH*
Print newline separated list of paths to representatives into this
file.
# GENERAL PARAMETERS
**-t**, **\--threads** *INT*
Number of threads. [default: `1`]
**-v**, **\--verbose**
Print extra debugging information
**-q**, **\--quiet**
Unless there is an error, do not print log messages
**-h**, **\--help**
Output a short usage message.
**\--full-help**
Output a full help message and display in \'man\'.
**\--full-help-roff**
Output a full help message in raw ROFF format for conversion to
other formats.
# EXIT STATUS
**0**
Successful program execution.
**1**
Unsuccessful program execution.
**101**
The program panicked.
# AUTHOR
> Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>