usage: gottcha2.py [-h] [-i [FASTQ] [[FASTQ] ...]] [-s [SAMFILE]]
                   [-d [MINIMAP2_INDEX]] [-l [LEVEL]] [-ti [FILE]] [-np]
                   [-pm <INT>] [-e [TAXID]] [-fm [STR]] [-r [FIELD]]
                   [-t <INT>] [-o [DIR]] [-p <STR>] [-xm <STR>] [-mc <FLOAT>]
                   [-mr <INT>] [-ml <INT>] [-mz <FLOAT>] [-nc] [-c] [-v]
                   [--silent] [--debug]

Genomic Origin Through Taxonomic CHAllenge (GOTTCHA) is an annotation-
independent and signature-based metagenomic taxonomic profiling tool that has
significantly smaller FDR than other profiling tools. This program is a
wrapper to map input reads to pre-computed signature databases using minimap2
and/or to profile mapped reads in SAM format. (VERSION: 2.1.5 BETA)

optional arguments:
  -h, --help            show this help message and exit
  -i [FASTQ] [[FASTQ] ...], --input [FASTQ] [[FASTQ] ...]
                        Input one or multiple FASTQ/FASTA file(s). Use space
                        to separate multiple input files.
  -s [SAMFILE], --sam [SAMFILE]
                        Specify the input SAM file. Use '-' for standard
                        input.
  -d [MINIMAP2_INDEX], --database [MINIMAP2_INDEX]
                        The path of signature database. The database can be in
                        FASTA format or minimap2 index (5 files).
  -l [LEVEL], --dbLevel [LEVEL]
                        Specify the taxonomic level of the input database. You
                        can choose one rank from "superkingdom", "phylum",
                        "class", "order", "family", "genus", "species" and
                        "strain". The value will be auto-detected if the input
                        database ended with levels (e.g. GOTTCHA_db.species).
  -ti [FILE], --taxInfo [FILE]
                        Specify the path of taxonomy information file
                        (taxonomy.tsv). GOTTCHA2 will try to locate this file
                        when user doesn't specify a path. If '--database'
                        option is used, the program will try to find this file
                        in the directory of specified database. If not, the
                        'database' directory under the location of gottcha.py
                        will be used as default.
  -np, --nanopore       Adjust options for Nanopore reads. The 'mismatch'
                        option will be ignored. [-xm map-ont -mr 1]
  -pm <INT>, --mismatch <INT>
                        Mismatch penalty for the aligner. [default: 10]
  -e [TAXID], --extract [TAXID]
                        Extract reads mapping to a specific TAXID. [default:
                        None]
  -fm [STR], --format [STR]
                        Format of the results; available options include tsv,
                        csv or biom. [default: tsv]
  -r [FIELD], --relAbu [FIELD]
                        The field will be used to calculate relative
                        abundance. You can specify one of the following
                        fields: "LINEAR_LENGTH", "TOTAL_BP_MAPPED",
                        "READ_COUNT" and "LINEAR_DOC". [default: ROLLUP_DOC]
  -t <INT>, --threads <INT>
                        Number of threads [default: 1]
  -o [DIR], --outdir [DIR]
                        Output directory [default: .]
  -p <STR>, --prefix <STR>
                        Prefix of the output file [default:
                        <INPUT_FILE_PREFIX>]
  -xm <STR>, --presetx <STR>
                        The preset option (-x) for minimap2. Default value
                        'sr' for short reads. [default: sr]
  -mc <FLOAT>, --minCov <FLOAT>
                        Minimum linear coverage to be considered valid in
                        abundance calculation [default: 0.005]
  -mr <INT>, --minReads <INT>
                        Minimum number of reads to be considered valid in
                        abundance calculation [default: 3]
  -ml <INT>, --minLen <INT>
                        Minimum unique length to be considered valid in
                        abundance calculation [default: 60]
  -mz <FLOAT>, --maxZscore <FLOAT>
                        Maximum estimated zscore of depths of mapped region
                        [default: 10]
  -nc, --noCutoff       Remove all cutoffs. This option is equivalent to use
                        [-mc 0 -mr 0 -ml 0].
  -c, --stdout          Write on standard output.
  -v, --version         Print version number.
  --silent              Disable all messages.
  --debug               Debug mode. Provide verbose running messages and keep
                        all temporary files.

usage: pull_database.py [-h] [-u URL] [-r RANK]

This script will pull the latest version of the Gottcha2 database.

optional arguments:
  -h, --help            show this help message and exit
  -u URL, --url URL     specify a URL to pull from (will override the default)
  -r RANK, --rank RANK  taxonomic rank of the database (superkingdom, phylum, class, order, famiily, genus, species)