Builds a taxonomy datafile of the microbe reference
Category Metagenomics
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 PathSeqBuildKmers \ --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 | |
--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 |
[] | Undocumented option | |
--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.
--arguments_file / NA
read one or more arguments files and add them to the command line
List[File] []
--gatk-config-file / NA
A configuration file to use with the GATK.
String null
--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 [ [ -∞ ∞ ] ]
--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
--help / -h
display the help message
boolean false
--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 ] ∞ ] ]
--output / -O
Local path for the output file. By convention, the extension should be ".db"
R String null
--QUIET / NA
Whether to suppress job-summary info on System.err.
Boolean false
--reference / -R
Reference sequence file
R String null
--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
--showHidden / -showHidden
display hidden arguments
boolean false
--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
--TMP_DIR / NA
Undocumented option
List[File] []
--use-jdk-deflater / -jdk-deflater
Whether to use the JdkDeflater (as opposed to IntelDeflater)
boolean false
--use-jdk-inflater / -jdk-inflater
Whether to use the JdkInflater (as opposed to IntelInflater)
boolean false
--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
--version / NA
display the version number for this tool
boolean false
GATK version 4.0.5.1 built at 25-59-2019 01:59:53.
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