p3-submit-metagenome-binning

Submit a Metagenome Binning Job

This script submits a Metagenome Binning job to BV-BRC. It allows input from either read libraries or a FASTA file and organizes contigs into individual genomes.

Usage Synopsis

p3-submit-metagenome-binning [options] output-path output-name

Start metagenome binning, producing output in the specified workspace path, using the specified name for the output folder.

Command-Line Options

The following options are used to assist in the specification of files. Files specified in the options that are in the workspace should have a ````ws:> prefix. All others are assumed to be local.

  • –workspace-path-prefix

Base workspace directory for relative workspace paths.

  • –workspace-upload-path

Name of workspace directory to which local files should be uplaoded.

  • –overwrite

If a file to be uploaded already exists and this parameter is specified, it will be overwritten; otherwise, the script will error out.

The following options specify the reads to be binned. These are assembled internally.

  • –paired-end-lib

Two paired-end libraries containing reads. These are coded with a single invocation, e.g. --paired-end-lib left.fa right.fa. The libraries must be paired FASTQ files. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

  • –single-end-lib

A library of single reads. This must be a FASTQ file. A prefix of ws: indicates a file is in the BV-BRC workspace; otherwise they are uploaded from the local file system. This parameter may be specified multiple times.

  • –srr-id

A run ID from the NCBI sequence read archive. The run will be downloaded from the NCBI for processing. This parameter may be specified multiple times.

If contigs are being binned, specify the following parameter. All the above parameters relating to reads should not be used if contigs are specified.

  • –contigs

Input FASTA file of assembled contigs. (If specified, all options relating to assembly will be ignored. This is mutually exclusive with --paired-end-libs, --single-end-libs, and srr-ids)

The following options modify the binning process.

  • –genome-group

Group name to be assigned to the output genomes (optional).

  • –skip-indexing

If specified, the genomes created will NOT be added to the BV-BRC database.

  • –prokaryotes

If specified, bacterial/archaeal binning will be performed. This defaults to TRUE unless --viruses is specified.

  • –viruses

If specified, viral binning will be performed. This defaults to TRUE unless --prokaryotesis specified.

These options are provided for user assistance and debugging.

  • –help

Display the command-line usage and exit.

  • –dry-run

Display the JSON submission string and exit without invoking the service or uploading files.