MetaCerberus Options

Important

If the MetaCerberus environment is not used, make sure the dependencies are in PATH or specified in the config file.

• Run metacerberus.py with the options required for your project.

Usage of metacerberus.py:

Note

The following are different options/arguments to modify the execution of MetaCerberus.

Setup arguments:

Argument/Option	Function [Default]	Usage Format	Accepted format	Example (Type as one line)
--setup	Setup additional dependencies [False]	--setup	N/A	metacerberus.py --setup
--update	Update downloaded databases [False]	--update	N/A	metacerberus.py --update
--list-db	List available and downloaded databases [False]	--list-db	N/A	metacerberus.py --list-db
--download	Downloads selected HMMs. Use the option --list-db for a list of available databases, default is to download all available databases	--download [DOWNLOAD ...]	--download [.HMM FILE]	--download path/to/example/directory.hmm
--uninstall	Remove downloaded databases and FragGeneScan+ [False]	--uninstall	N/A	metacerberus.py --uninstall

Input File Arguments:

Important

At least one sequence is required.

Accepted formats: [.fastq, .fq, .fasta, .fa, .fna, .ffn, .faa]

Example:

• metacerberus.py --prodigal file1.fasta

• metacerberus.py --config file.config

If a sequence is given in [.fastq, .fq] format, one of --nanopore, --illumina, or --pacbio is required.:

Option format interpretation:

• --setup = accepts no additional options

• --download DOWNLOAD = accepts one option, (represented by capitalized command ‘DOWNLOAD’)

• --fraggenescan FRAGGENESCAN [FRAGGENESCAN...] = accepts one or greater options (represented by capitalized commands)

Argument/Option	Function	Usage Format	Accepted format	# Options Accepted	Example (Type as one line)
-c or --config	Path to config file, command line takes priority	-c CONFIG or --config CONFIG	Path to config file	1	metacerberus.py -c path/to/config/file
--prodigal	Prokaryote nucleotide sequence (includes microbes, bacteriophage)	--prodigal PRODIGAL [PRODIGAL ...]	Sequence file	=>1	metacerberus.py --prodigal FILE1 FILE2...
--fraggenescan	Eukaryote nucleotide sequence (includes other viruses, works all around for everything)	--fraggenescan FRAGGENESCAN [FRAGGENESCAN ...]	Sequence file	=>1	metacerberus.py --fraggenescan FILE1 FILE2...
--super	Runs sequence in both –prodigal and –fraggenescan modes	--super SUPER [SUPER ...]	Sequence file	=>1	metacerberus.py --super FILE1 FILE2...
--prodigalgv	Giant virus nucleotide sequence	--prodigalgv PRODIGALGV [PRODIGALGV ...]	Sequence file	=>1	metacerberus.py --prodigalgv FILE1 FILE2...
--phanotate	Phage sequence	--phanotate PHANOTATE [PHANOTATE ...]	Sequence file	=>1	metacerberus.py --phanotate  FILE1 FILE2...
--protein or --amino	Protein Amino Acid sequence	--protein PROTEIN [PROTEIN ...] or --amino PROTEIN [PROTEIN ...]	Sequence file	=>1	metacerberus.py --protein FILE1 FILE2... or metacerberus.py --amino FILE1 FILE2...
--hmmer-tsv	Annotations tsv file from HMMER (experimental)	--hmmer-tsv HMMER_TSV [HMMER_TSV ...]	Sequence file	=>1	metacerberus.py --hmmer-tsv FILE1 FILE2...
--class	path to a tsv file which has class information for the samples. If this file is included, scripts will be included to run Pathview in R	--class CLASS	Path to TSV file	1	metacerberus.py --class TSV_FILE1
--illumina	Specifies that the given FASTQ files are from Illumina	--illumina	N/A	N/A	metacerberus.py --illumina
--nanopore	Specifies that the given FASTQ files are from Nanopore	--nanopore	N/A	N/A	metacerberus.py --nanopore
--pacbio	Specifies that the given FASTQ files are from PacBio	--pacbio	N/A	N/A	metacerberus.py --pacbio

Output options:

Argument/Option	Function [DEFAULT]	Usage Format	Accepted format	# Options Accepted	Example (Type as one line)
--dir-out	path to output directory, defaults to “results-metacerberus” in current directory. [./results-`]	--dir-out DIR_OUT	output file path	1	--dir-out path/to/output/file
--replace	Flag to replace existing files. [False]	--replace	metacerberus.py option	N/A	metacerberus.py --replace
--keep	Flag to keep temporary files. [False]	--keep	metacerberus.py option	N/A	metacerberus.py --keep
--tmpdir	Temp directory for RAY (experimental) [system tmp dir]	--tmpdir TMPDIR	metacerberus.py option	1	metacerberus.py --tmpdir TEMPFILE1

Database options:

Argument/Option	Function [DEFAULT]	Usage Format	Accepted format	# Options Accepted	Example (Type as one line)
--hmm	A list of databases for HMMER. Use the option --list-db for a list of available databases [KOFam_all]	--hmm HMM [HMM ...]	metacerberus.py option	=>1	metacerberus.py --hmm DATABASE1 DATABASE2...
--db-path	Path to folder of databases [Default: under the library path of metacerberus]	--db-path DB_PATH	path to databases folder	1	--db-path path/to/databases/folder

Optional Arguments:

Argument/Option	Function [DEFAULT]	Usage Format	Accepted format	# Options Accepted	Example (Type as one line)
--meta	Metagenomic nucleotide sequences (for prodigal) [False]	--meta	metacerberus.py option	N/A	metacerberus.py --meta
--scaffolds	Sequences are treated as scaffolds [False]	--scaffolds	metacerberus.py option	N/A	metacerberus.py --scaffolds
--minscore	Score cutoff for parsing HMMER results [60]	--minscore MINSCORE	whole integer value	1	metacerberus.py --minscore 50
--evalue	E-value cutoff for parsing HMMER results [1e-09]	--evalue EVALUE	E-value	1	metacerberus.py --evalue [E-value]
--skip-decon	Skip decontamination step. [False]	--skip-decon	metacerberus.py option	N/A	metacerberus.py --skip-decon
--skip-pca	Skip PCA. [False]	--skip-pca	metacerberus.py option	N/A	metacerberus.py --skip-pca
--cpus	Number of CPUs to use per task. System will try to detect available CPUs if not specified [Auto Detect]	--cpus CPUS	whole integer value	1	metacerberus.py --cpus 16
--chunker	Split files into smaller chunks, in Megabytes [Disabled by default]	--chunker CHUNKER	whole integer value	1	metacerberus.py --chunker 300
--grouped	Group multiple fasta files into a single file before processing. When used with –chunker (see above) can improve speed	--grouped	metacerberus.py option	N/A	metacerberus.py --grouped
--version or -v	show the version number and exit	--version or -v	metacerberus.py option	N/A	metacerberus.py --version
-h or --help	show this help message and exit	-h or --help	metacerberus.py option	N/A	metacerberus.py -h
--adapters	FASTA File containing adapter sequences for trimming	--adapters ADAPTERS	FASTA file	1	metacerberus.py --adapters /path/to/FASTA/file
--qc_seq	FASTA File containing control sequences for decontamination	--qc_seq QC_SEQ	FASTA file	1	metacerberus.py --qc_seq /path/to/FASTA/file

Note

Arguments/options that start with -- can also be set in a config file (specified via -c). Config file syntax allows: key=value, flag=true, stuff=[a,b,c] (for details, see syntax. In general, command-line values override config file values which override defaults.