p3-submit-taxonomic-classification

Submit a Taxonomic Classification Job

This script submits a Taxonomic Classification job to BV-BRC. It allows input from either read libraries or a FASTA file and uses the Kraken2 algorithm to determine the taxonomic makeup of the input.

Usage Synopsis

p3-submit-taxonomic-classification [options] output-path output-name

Start a taxonomic classification, producing output in the specified workspace path, using the specified name for the base filename of the output files.

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 classified.

  • –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.

These options modify the way reads are processed during assembly, so they should precede any library specifications to which they apply. For example,

--platform illumina --paired-end-lib S1.fq S2.fq --platform pacbio --single-end-lib ERR12345.fq  --srr-id SRR54321

means that the local files S1.fq and S2.fq are from the illumina platform, but the single-end library ERR12345.fq comes from the pacbio platform. These options only apply to FASTQ libraries, and not to libraries accessed via na NBCI ID. Thus SRR54321 above will use the default mode of having its platform inferred from the data.

  • –platform

The sequencing platform for the subsequent read library or libraries. Valid values are infer, illumina, pacbio, or <nanopore>. The default is infer.

  • –insert-size-mean

The average size of an insert in all subsequent read libraries, used for optimization.

  • –insert-size-stdev

The standard deviation of the insert sizes in all subsequent read libraries, used for optimization.

  • –read-orientation-inward

Indicates that all subsequent read libraries have the standard read orientation, with the paired ends facing inward. This is the default.

  • –read-orientation-outward

Indicates that all subseqyent read libraries have reverse read orientation, with the paired ends facing outward.

If contigs are being classified, 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 classification process.

  • –save-classified

If specified, the classified sequences will be saved in the output folder.

  • –save-unclassified

If specified, the unclassified sequences will be saved in the output folder.

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.