Complete CLI reference
Generated by python scripts/generate_cli_docs.py. Run metapathways COMMAND --help for the help of your installed revision.
prepare_test
usage: metapathways [-h] -o OUTPUT_DIR
Copy the bundled test inputs and reference seeds into a writable workspace.
options:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
workspace for cami-test/ inputs and MPDB/ reference seeds
run
usage: Metapathways run [options]
Minimum REQUIRED Command:
MetaPathways run -i INPUT_FILE -o OUTPUT_DIR -d REFDB_DIR
options:
-h, --help show this help message and exit
--dryrun show the execution plan without running tasks
Minimum Required Arguments:
-i INPUT_FILE, --input_file INPUT_FILE
path to the input fasta file/input dir [REQUIRED]
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to the output directory [REQUIRED]
-d REFDB_DIR, --refdb_dir REFDB_DIR
path to the reference DB [REQUIRED]
Quality Controls Arguments:
--input_format {fasta,fasta-amino}
Input format, FASTA support only [fasta]
--qc_min_length QC_MIN_LENGTH
Minimum length for quality control [180]
--qc_delete_replicates {yes,no}
Delete replicates in quality control [yes]
ORF Prediction Arguments:
--orf_strand {pos,neg,both}
Strand for ORF prediction [both]
--orf_algorithm ORF_ALGORITHM
Algorithm for ORF prediction, Prodigal support only [prodigal]
--orf_min_length ORF_MIN_LENGTH
Minimum ORF length [60]
--orf_translation_table ORF_TRANSLATION_TABLE
Translation table for ORF prediction, see Prodigal for translation tables [11]
--orf_mode {single,meta}
Mode for ORF prediction [meta]
Functional Annotation Arguments:
--annotation_algorithm {FAST,BLAST}
Algorithm for ORF annotation [FAST]
--annotation_dbs ANNOTATION_DBS [ANNOTATION_DBS ...]
Database(s) for annotation, space-separated list [swissprot]
--annotation_min_bsr ANNOTATION_MIN_BSR
Minimum BSR for annotation [0.4]
--annotation_max_evalue ANNOTATION_MAX_EVALUE
Maximum e-value for annotation [0.000001]
--annotation_min_score ANNOTATION_MIN_SCORE
Minimum score for annotation [20]
--annotation_min_length ANNOTATION_MIN_LENGTH
Minimum length for annotation [45]
--annotation_max_hits ANNOTATION_MAX_HITS
Maximum hits for annotation [5]
--annotation_run_mode {default,pervol}
Run mode for annotation, FAST only [pervol]
rRNA Annotation Arguments:
--rRNA_refdbs RRNA_REFDBS [RRNA_REFDBS ...]
Reference databases for rRNA annotation, space-separated list
[SILVA_138.1_LSURef_NR99_tax_silva_trunc SILVA_138.1_SSURef_NR99_tax_silva_trunc]
--rRNA_max_evalue RRNA_MAX_EVALUE
Maximum e-value for rRNA annotation [0.000001]
--rRNA_min_identity RRNA_MIN_IDENTITY
Minimum identity for rRNA annotation [20]
--rRNA_min_bitscore RRNA_MIN_BITSCORE
Minimum bitscore for rRNA annotation [50]
Read Mapping Arguments (single sample support only):
-1 FWD_FASTQ, --fastq FWD_FASTQ
location of the raw fastq file, either forward or interleaved
-2 REV_FASTQ, --rev_fastq REV_FASTQ
location of the raw reverse fastq file, if separate paired-end
--interleaved if paired-end is interleaved [False]
Pipeline Step Arguments:
--PREPROCESS_INPUT {yes,skip,redo}
Step: PREPROCESS_INPUT [yes]
--ORF_PREDICTION {yes,skip,redo}
Step: ORF_PREDICTION [yes]
--FILTER_AMINOS {yes,skip,redo}
Step: FILTER_AMINOS [yes]
--SCAN_rRNA {yes,skip,redo}
Step: SCAN_rRNA [yes]
--SCAN_tRNA {yes,skip,redo}
Step: SCAN_tRNA [yes]
--FUNC_SEARCH {yes,skip,redo}
Step: FUNC_SEARCH [yes]
--PARSE_FUNC_SEARCH {yes,skip,redo}
Step: PARSE_FUNC_SEARCH [yes]
--ANNOTATE_ORFS {yes,skip,redo}
Step: ANNOTATE_ORFS [yes]
--GENBANK_FILE {yes,skip,redo}
Step: GENBANK_FILE [yes]
--CREATE_ANNOT_REPORTS {yes,skip,redo}
Step: CREATE_ANNOT_REPORTS [yes]
--PATHOLOGIC_INPUT {yes,skip,redo}
Step: PATHOLOGIC_INPUT [yes]
--COMPUTE_TPM {yes,skip,redo}
Step: COMPUTE_TPM [yes]
--force_redo Redo all steps [False]
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [16 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget; Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
Miscellaneous Arguments:
-s SAMPLES [SAMPLES ...], --samples SAMPLES [SAMPLES ...]
process only specific samples, space-separated list
-t THREADS, --threads THREADS
threads per capable tool [8], capped by --max_cpus; serial stages use one CPU
-v, --verbose print more information on the stdout
--test use test values for all arguments
analysis_wf
usage: Metapathways analysis_wf [options]
Annotate multiple metagenomes, split MAGs, build PGDBs and generate a combined report.
options:
-h, --help show this help message and exit
--dryrun show the execution plan without running tasks
--manifest MANIFEST TSV with sample_id, assembly, read_layout, reads_1, reads_2, mag_map
--reads_dir READS_DIR
Flat reads directory; -i then names the assemblies directory
--mag_maps_dir MAG_MAPS_DIR
Flat contig-to-MAG map directory; -i then names the assemblies directory
--no_reads Explicitly omit read mapping during automatic discovery
--no_mags Explicitly omit MAG splitting during automatic discovery
--skip_ptools Omit community and MAG PGDB construction
--compact_results Use task scratch, archive PGDBs/diagnostics, and remove completed sample intermediates
--scratch_dir SCRATCH_DIR
Worker-local scratch directory for compact mode [Slurm: SLURM_TMPDIR; local: system temporary directory]
--image IMAGE Pathway Tools SIF [registered by build_pt]
--taxon_id TAXON_ID Override PGDB NCBI taxon in private inputs; applies to every selected entity
--taxonomic_scope {all,bacteria,archaea,eukaryotes}
Named PGDB taxon override; all means cellular life; euks aliases eukaryotes. Taxonomic pruning is enabled by default. Default: all (cellular life).
--no_transport_inference
Disable TIP transport inference
--taxprune Enable taxonomic pruning [default]
--no_taxprune Disable taxonomic pruning and perform unpruned rescoring
--ptools_memory PTOOLS_MEMORY
Optional PGDB memory override [same as --memory]
Minimum Required Arguments:
-i INPUT_FILE, --input_file INPUT_FILE
dataset root, or assemblies directory with --reads_dir/--mag_maps_dir; alternative: --manifest
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path to the output directory [REQUIRED]
-d REFDB_DIR, --refdb_dir REFDB_DIR
path to the reference DB [REQUIRED]
Quality Controls Arguments:
--input_format {fasta,fasta-amino}
Input format, FASTA support only [fasta]
--qc_min_length QC_MIN_LENGTH
Minimum length for quality control [180]
--qc_delete_replicates {yes,no}
Delete replicates in quality control [yes]
ORF Prediction Arguments:
--orf_strand {pos,neg,both}
Strand for ORF prediction [both]
--orf_algorithm ORF_ALGORITHM
Algorithm for ORF prediction, Prodigal support only [prodigal]
--orf_min_length ORF_MIN_LENGTH
Minimum ORF length [60]
--orf_translation_table ORF_TRANSLATION_TABLE
Translation table for ORF prediction, see Prodigal for translation tables [11]
--orf_mode {single,meta}
Mode for ORF prediction [meta]
Functional Annotation Arguments:
--annotation_algorithm {FAST,BLAST}
Algorithm for ORF annotation [FAST]
--annotation_dbs ANNOTATION_DBS [ANNOTATION_DBS ...]
Database(s) for annotation, space-separated list [swissprot]
--annotation_min_bsr ANNOTATION_MIN_BSR
Minimum BSR for annotation [0.4]
--annotation_max_evalue ANNOTATION_MAX_EVALUE
Maximum e-value for annotation [0.000001]
--annotation_min_score ANNOTATION_MIN_SCORE
Minimum score for annotation [20]
--annotation_min_length ANNOTATION_MIN_LENGTH
Minimum length for annotation [45]
--annotation_max_hits ANNOTATION_MAX_HITS
Maximum hits for annotation [5]
--annotation_run_mode {default,pervol}
Run mode for annotation, FAST only [pervol]
rRNA Annotation Arguments:
--rRNA_refdbs RRNA_REFDBS [RRNA_REFDBS ...]
Reference databases for rRNA annotation, space-separated list
[SILVA_138.1_LSURef_NR99_tax_silva_trunc SILVA_138.1_SSURef_NR99_tax_silva_trunc]
--rRNA_max_evalue RRNA_MAX_EVALUE
Maximum e-value for rRNA annotation [0.000001]
--rRNA_min_identity RRNA_MIN_IDENTITY
Minimum identity for rRNA annotation [20]
--rRNA_min_bitscore RRNA_MIN_BITSCORE
Minimum bitscore for rRNA annotation [50]
Pipeline Step Arguments:
--PREPROCESS_INPUT {yes,skip,redo}
Step: PREPROCESS_INPUT [yes]
--ORF_PREDICTION {yes,skip,redo}
Step: ORF_PREDICTION [yes]
--FILTER_AMINOS {yes,skip,redo}
Step: FILTER_AMINOS [yes]
--SCAN_rRNA {yes,skip,redo}
Step: SCAN_rRNA [yes]
--SCAN_tRNA {yes,skip,redo}
Step: SCAN_tRNA [yes]
--FUNC_SEARCH {yes,skip,redo}
Step: FUNC_SEARCH [yes]
--PARSE_FUNC_SEARCH {yes,skip,redo}
Step: PARSE_FUNC_SEARCH [yes]
--ANNOTATE_ORFS {yes,skip,redo}
Step: ANNOTATE_ORFS [yes]
--GENBANK_FILE {yes,skip,redo}
Step: GENBANK_FILE [yes]
--CREATE_ANNOT_REPORTS {yes,skip,redo}
Step: CREATE_ANNOT_REPORTS [yes]
--PATHOLOGIC_INPUT {yes,skip,redo}
Step: PATHOLOGIC_INPUT [yes]
--COMPUTE_TPM {yes,skip,redo}
Step: COMPUTE_TPM [yes]
--force_redo Redo all steps [False]
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [16 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget; Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
Miscellaneous Arguments:
-t THREADS, --threads THREADS
threads per capable tool [8], capped by --max_cpus; serial stages use one CPU
-v, --verbose print more information on the stdout
build_db
usage: metapathways [-h] [-d PATH] [--func [CATEGORICAL ...]] [-a ALIGNER] [--skip_pt_screen]
[--screen_image SCREEN_IMAGE] [--metacyc_source METACYC_SOURCE] [-t INT]
[--dryrun] [--snakemake [SNAKEMAKE ...]] [--test] [--max_cpus MAX_CPUS]
[--memory MEMORY] [--max_memory MAX_MEMORY] [--max_tasks MAX_TASKS]
[--executor {local,slurm}] [--account ACCOUNT] [--partition PARTITION]
[--qos QOS] [--reservation RESERVATION] [--time_limit TIME_LIMIT]
[--submit_rate SUBMIT_RATE] [--work_dir WORK_DIR] [--conda_cache CONDA_CACHE]
[--keep_work]
automated database install
options:
-h, --help show this help message and exit
-t INT, --threads INT
total database-build CPU budget [available CPUs]
--dryrun show the database execution plan without running tasks
--snakemake [SNAKEMAKE ...]
legacy compatibility flags; use the resource flags for new runs
--test build test SwissProt/SILVA references; use -d for the prepared MPDB
directory
database arguments:
-d PATH, --refdb_dir PATH
path to save the reference DB, [DEFAULT "./"]
--func [CATEGORICAL ...]
functional references, select any combination from ['swissprot', 'cazy',
'eggnog', 'uniref50', 'uniref90', 'metacyc'], [DEFAULT ['swissprot']]
-a ALIGNER, --aligner ALIGNER
local aligner to index for, select one of ['fast', 'blast'], [DEFAULT
fast]
--skip_pt_screen Skip default PTools reaction compatibility screening for MetaCyc
--screen_image SCREEN_IMAGE
PTools SIF for screening a MetaCyc directory [registered SIF]
--metacyc_source METACYC_SOURCE
licensed MetaCyc data directory or Pathway Tools SIF [registered SIF when
--func includes metacyc]
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [16 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget;
Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
mag_split
usage: Metapathways mag_split [options]
Minimum REQUIRED Command:
Metapathways mag_split -o output_dir -m contig_mag_map
options:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path where MP output was saved [REQUIRED]
-m MAG_MAP, --contig_mag_map MAG_MAP
TSV file that contains contig-to-MAG mapping [REQUIRED]
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [16 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget; Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
build_pt
usage: metapathways build_pt [-h] -i INSTALLER [--ptools_version PTOOLS_VERSION] [-d REFDB_DIR]
[--skip_pt_screen] [-a {fast,blast}] [-o OUTPUT_DIR] [-t THREADS]
[--dryrun] [--max_cpus MAX_CPUS] [--memory MEMORY]
[--max_memory MAX_MEMORY] [--max_tasks MAX_TASKS]
[--executor {local,slurm}] [--account ACCOUNT]
[--partition PARTITION] [--qos QOS] [--reservation RESERVATION]
[--time_limit TIME_LIMIT] [--submit_rate SUBMIT_RATE]
[--work_dir WORK_DIR] [--conda_cache CONDA_CACHE] [--keep_work]
Build a Pathway Tools SIF from a local Linux installer using Nextflow and Apptainer.
options:
-h, --help show this help message and exit
-i INSTALLER, --installer INSTALLER
local Pathway Tools Linux x86-64 installer
--ptools_version PTOOLS_VERSION
release number if the installer was renamed; otherwise inferred from its
filename
-d REFDB_DIR, --refdb_dir REFDB_DIR
also export and prepare the licensed MetaCyc reference in this MPDB after
building the SIF
--skip_pt_screen Skip default reaction compatibility screening when building MetaCyc with
-d
-a {fast,blast}, --aligner {fast,blast}
MetaCyc reference index format with -d [fast]
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
container directory [~/.local/share/metapathways/containers]
-t THREADS, --threads THREADS
CPUs for image compression [2]; Pathway Tools uses one CPU
--dryrun write and show the build plan without building or registering
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [4 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget;
Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
screen_pt
usage: metapathways [-h] -d REFDB_DIR -o OUTPUT_DIR [--image IMAGE] [--publish]
[--reactions REACTIONS [REACTIONS ...]] [--batch_size BATCH_SIZE]
[--max_tasks MAX_TASKS] [--confirm_runs CONFIRM_RUNS] [--timeout TIMEOUT]
[--scratch_dir SCRATCH_DIR]
Screen explicit MPDB reaction assignments against a licensed PTools SIF
options:
-h, --help show this help message and exit
-d REFDB_DIR, --refdb_dir REFDB_DIR
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
--image IMAGE PTools SIF [registered build_pt image]
--publish Save a completed full screen compatibility list in the MPDB
--reactions REACTIONS [REACTIONS ...]
Optional reaction IDs for a targeted screen
--batch_size BATCH_SIZE
--max_tasks MAX_TASKS
Concurrent isolated containers [1]
--confirm_runs CONFIRM_RUNS
--timeout TIMEOUT Seconds per build [1800]; timeout is inconclusive
--scratch_dir SCRATCH_DIR
Local temporary storage for private PGDB builds
ptools
usage: Metapathways ptools [options]
Minimum REQUIRED Command:
Metapathways ptools -o output_dir
options:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
path where MP output was saved [REQUIRED]
--tag TAG Custom name for ePGDB [optional]
--container Flag only used in containerized env [special flag]
--taxprune Enable taxonomic pruning [default]
--no_taxprune Disable taxonomic pruning and perform unpruned rescoring
--taxon_id TAXON_ID Override PGDB NCBI taxon in private inputs; applies to every selected entity
--taxonomic_scope {all,bacteria,archaea,eukaryotes}
Named PGDB taxon override; all means cellular life; euks aliases eukaryotes. Taxonomic pruning is enabled by default. Default: all (cellular life).
--no_transport_inference
Disable TIP transport inference (SIF only)
--entity ENTITY Build only community or the specified MAG ID
--image IMAGE Pathway Tools SIF [registered by build_pt]
Execution Resources:
--max_cpus MAX_CPUS total CPU budget [local: available CPUs; Slurm: no aggregate cap]
--memory MEMORY memory reservation per task [4 GB]
--max_memory MAX_MEMORY
total memory budget [local: available memory; Slurm: no aggregate cap]
--max_tasks MAX_TASKS
maximum submitted tasks, including queued/running [local: CPU budget; Slurm: 4]
--executor {local,slurm}
execution backend [local]; Slurm uses your logged-in cluster identity
--account ACCOUNT Slurm allocation/account
--partition PARTITION
Slurm partition [cluster default]
--qos QOS Slurm quality of service
--reservation RESERVATION
Slurm reservation
--time_limit TIME_LIMIT
Slurm walltime per task [24h]
--submit_rate SUBMIT_RATE
maximum Slurm submissions per minute [6]
--work_dir WORK_DIR custom Nextflow work directory; retained after the run
--conda_cache CONDA_CACHE
custom Conda cache directory; retained after the run
--keep_work retain automatically allocated work/cache directories
report
usage: metapathways [-h] -o OUTPUT_DIR [--serve] [--no-rebuild] [--port PORT] [--no-browser]
Build a navigable report from existing MP outputs; no analyses are rerun.
options:
-h, --help show this help message and exit
-o OUTPUT_DIR, --output_dir OUTPUT_DIR
sample output or parent containing sample outputs
--serve open the local searchable portal and serve until Ctrl-C
--no-rebuild use an existing report snapshot
--port PORT local port [automatically selected]
--no-browser print the local URL without opening a browser