Builds a taxonomy datafile of the microbe reference

Category Metagenomics

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Overview

Build an annotated taxonomy datafile for a given microbe reference. The output file from this tool is required to run the PathSeq pipeline.

The tool reads the list of sequence accessions from the given reference. For each accession, it looks up the NCBI taxonomic ID of the corresponding organism and builds a taxonomic tree containing only organisms that are represented in the reference. The reference should only contain sequences from NCBI RefSeq and/or Genbank databases.

Input

• An indexed microbe reference in FASTA format (NCBI RefSeq/Genbank sequences)
• Downloaded NCBI RefSeq (and/or GenBank) catalog archive file(s)
• Downloaded NCBI taxonomy archive file

See argument documentation for information about where to download the archive files.

Output

• A binary file containing reference taxonomy information

Usage examples

 gatk PathSeqBuildReferenceTaxonomy \
   --reference microbe_reference.fasta \
   --output taxonomy.db \
   --refseq-catalog RefSeq-releaseXX.catalog.gz \
   --tax-dump taxdump.tar.gz \
   --min-non-virus-contig-length 2000
 

Notes

Often there are inconsistencies between the reference sequences, NCBI catalog, and taxonomy archive. To minimize this issue, ensure that the input files are retrieved on the same date.

PathSeqBuildReferenceTaxonomy specific arguments

This table summarizes the command-line arguments that are specific to this tool. For more details on each argument, see the list further down below the table or click on an argument name to jump directly to that entry in the list.

Argument name(s)	Default value	Summary
Required Arguments
--output  -O	null	Local path for the output file. By convention, the extension should be ".db"
--reference  -R	null	Reference sequence file
--tax-dump  -TD	null	Local path to taxonomy dump tarball (taxdump.tar.gz available at ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)
Optional Tool Arguments
--arguments_file	[]	read one or more arguments files and add them to the command line
--gcs-max-retries  -gcs-retries	20	If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection
--gcs-project-for-requester-pays	""	Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.
--genbank-catalog  -GC	null	Local path to Genbank catalog file (gbXXX.catalog.XXX.txt.gz at ftp://ftp.ncbi.nlm.nih.gov/genbank/catalog/)
--help  -h	false	display the help message
--min-non-virus-contig-length	0	Minimum reference contig length for non-viruses
--refseq-catalog  -RC	null	Local path to catalog file (RefSeq-releaseXX.catalog.gz available at ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/)
--version	false	display the version number for this tool
Optional Common Arguments
--gatk-config-file	null	A configuration file to use with the GATK.
--QUIET	false	Whether to suppress job-summary info on System.err.
--tmp-dir	null	Temp directory to use.
--use-jdk-deflater  -jdk-deflater	false	Whether to use the JdkDeflater (as opposed to IntelDeflater)
--use-jdk-inflater  -jdk-inflater	false	Whether to use the JdkInflater (as opposed to IntelInflater)
--verbosity	INFO	Control verbosity of logging.
Advanced Arguments
--showHidden	false	display hidden arguments

Argument details

Arguments in this list are specific to this tool. Keep in mind that other arguments are available that are shared with other tools (e.g. command-line GATK arguments); see Inherited arguments above.

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--arguments_file / NA

read one or more arguments files and add them to the command line

List[File]  []

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--gatk-config-file / NA

A configuration file to use with the GATK.

String  null

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--gcs-max-retries / -gcs-retries

If the GCS bucket channel errors out, how many times it will attempt to re-initiate the connection

int  20  [ [ -∞  ∞ ] ]

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--gcs-project-for-requester-pays / NA

Project to bill when accessing "requester pays" buckets. If unset, these buckets cannot be accessed.

String  ""

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--genbank-catalog / -GC

Local path to Genbank catalog file (gbXXX.catalog.XXX.txt.gz at ftp://ftp.ncbi.nlm.nih.gov/genbank/catalog/)
This may be supplied alone or in addition to the RefSeq catalog in the case that sequences from GenBank are present in the reference.

String  null

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--help / -h

display the help message

boolean  false

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--min-non-virus-contig-length / -min-non-virus-contig-length

Minimum reference contig length for non-viruses
Sequences from non-virus organisms less than this length will be filtered out such that any reads aligning to them will be ignored. This is a quality control measure to remove shorter sequences from draft genomes that are likely to contain sequencing artifacts such as cross-species contamination or sequencing adapters. Note this may remove some bacteria plasmid sequences.

int  0  [ [ 0  [ 500  10,000 ]  ∞ ] ]

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--output / -O

Local path for the output file. By convention, the extension should be ".db"

R String  null

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--QUIET / NA

Whether to suppress job-summary info on System.err.

Boolean  false

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--reference / -R

Reference sequence file

R String  null

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--refseq-catalog / -RC

Local path to catalog file (RefSeq-releaseXX.catalog.gz available at ftp://ftp.ncbi.nlm.nih.gov/refseq/release/release-catalog/)

String  null

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--showHidden / -showHidden

display hidden arguments

boolean  false

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--tax-dump / -TD

Local path to taxonomy dump tarball (taxdump.tar.gz available at ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/)

R String  null

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--tmp-dir / NA

Temp directory to use.

GATKPathSpecifier  null

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--use-jdk-deflater / -jdk-deflater

Whether to use the JdkDeflater (as opposed to IntelDeflater)

boolean  false

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--use-jdk-inflater / -jdk-inflater

Whether to use the JdkInflater (as opposed to IntelInflater)

boolean  false

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--verbosity / -verbosity

Control verbosity of logging.

The --verbosity argument is an enumerated type (LogLevel), which can have one of the following values:

ERROR

WARNING

INFO

DEBUG

LogLevel  INFO

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--version / NA

display the version number for this tool

boolean  false

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GATK version 4.1.6.0-SNAPSHOT built at Thu, 2 Apr 2020 14:54:17 -0400.