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Bactopia Tool - gtdb

The gtdb tool uses GTDB-Tk's classify workflow to assign taxonomic classifications to your set of samples. This is done through the use of the Genome Taxonomy Database. If you are unsure of your sequences, gtdb is useful tool to help determine the taxonomy of your samples.

Example Usage

bactopia --wf gtdb \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt

Output Overview

Below is the default output structure for the gtdb tool. Where possible the file descriptions below were modified from a tools description.

gtdb/
├── bactopia-info
│   ├── gtdb-report.html
│   ├── gtdb-timeline.html
│   └── gtdb-trace.txt
└── classify
    ├── align
    │   ├── gtdb.(ar122|bac120).filtered.tsv
    │   ├── gtdb.(ar122|bac120).msa.fasta
    │   ├── gtdb.(ar122|bac120).user_msa.fasta
    │   └── intermediate_results
    │       └── gtdb.(ar122|bac120).marker_info.tsv
    ├── classify
    │   ├── gtdb.(ar122|bac120).classify.tree
    │   ├── gtdb.(ar122|bac120).summary.tsv
    │   └── intermediate_results
    │       ├── gtdb.(ar122|bac120).classification_pplacer.tsv
    │       ├── gtdb.(ar122|bac120).red_dictionary.tsv
    │       └── pplacer
    │           ├── pplacer.(ar122|bac120).json
    │           └── pplacer.(ar122|bac120).out
    ├── gtdb.(ar122|bac120).classify.tree
    ├── gtdb.(ar122|bac120).filtered.tsv
    ├── gtdb.(ar122|bac120).markers_summary.tsv
    ├── gtdb.(ar122|bac120).msa.fasta
    ├── gtdb.(ar122|bac120).summary.tsv
    ├── gtdb.(ar122|bac120).user_msa.fasta
    ├── gtdb.translation_table_summary.tsv
    └── identify
        └── intermediate_results
            └── marker_genes
                └── <SAMPLE_NAME>
                    ├── prodigal_translation_table.tsv
                    ├── <SAMPLE_NAME>_pfam_tophit.tsv
                    ├── <SAMPLE_NAME>_pfam.tsv
                    ├── <SAMPLE_NAME>_protein.{faa,fna,gff}
                    ├── <SAMPLE_NAME>_tigrfam.out
                    ├── <SAMPLE_NAME>_tigrfam_tophit.tsv
                    └── <SAMPLE_NAME>_tigrfam.tsv

Results

GTDB-Tk

Below is a description of the per-sample results from GTDB-Tk. For full details about each of the GTDB output files, see GTDB-Tk Classify Workflow page.

Filename Description
gtdb.(ar122|bac120).classify.tree Reference tree in Newick format containing query genomes placed with pplacer
gtdb.(ar122|bac120).filtered.tsv List of genomes with an insufficient number of amino acids in MSA
gtdb.(ar122|bac120).markers_summary.tsv Markers used in generation of the concatenated MSA and the order in which they were applied
gtdb.(ar122|bac120).msa.fasta FASTA file containing MSA of submitted and reference genomes
gtdb.(ar122|bac120).summary.tsv A summary of classifications provided by GTDB-Tk, see classification summary for more details
gtdb.(ar122|bac120).user_msa.fasta FASTA file containing MSA of the submitted genomes
gtdb.translation_table_summary.tsv Summary of the tranlastlation table used for each genome
gtdb.(ar122|bac120).classification_pplacer.tsv Classification of query genomes based only on their placement in the reference tree
gtdb.(ar122|bac120).red_dictionary.tsv Median RED values for taxonomic ranks
pplacer.(ar122|bac120).json Output information generated by pplacer in JSON format
pplacer.(ar122|bac120).out Output information generated by pplacer
gtdb.ar122.markers_summary.tsv Summary of unique, duplicated, and missing markers within the 122 archaeal marker set for each submitted genome
gtdb.bac120.markers_summary.tsv Summary of unique, duplicated, and missing markers within the 120 bacterial marker set for each submitted genome
gtdb.translation_table_summary.tsv The predicted translation table used for gene calling for each genome
marker_genes/ Contains individual genome results for gene calling using Prodigal and gene identification based on TIGRFAM and Pfam HMMs

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.

Logs

Each process that is executed will have a logs folder containing helpful files for you to review if the need ever arises.

Filename Description
nf-<PROCESS_NAME>.begin An empty file used to designate the process started
nf-<PROCESS_NAME>.err Contains STDERR outputs from the process
nf-<PROCESS_NAME>.log Contains both STDERR and STDOUT outputs from the process
nf-<PROCESS_NAME>.out Contains STDOUT outputs from the process
nf-<PROCESS_NAME>.run The script Nextflow uses to stage/unstage files and queue processes based on given profile
nf-<PROCESS_NAME>.sh The script executed by bash for the process
nf-<PROCESS_NAME>.trace The Nextflow Trace report for the process
versions.yml A YAML formatted file with program versions

Nextflow Reports

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

Filename Description
gtdb-dag.dot The Nextflow DAG visualisation
gtdb-report.html The Nextflow Execution Report
gtdb-timeline.html The Nextflow Timeline Report
gtdb-trace.txt The Nextflow Trace report

Program Versions

At the end of each run, each of the versions.yml files are merged into the files below.

Filename Description
software_versions.yml A complete list of programs and versions used by each process
software_versions_mqc.yml A complete list of programs and versions formatted for MultiQC

Parameters

Required Parameters

Define where the pipeline should find input data and save output data.

Parameter Description Default
--bactopia The path to bactopia results to use as inputs

Filtering Parameters

Use these parameters to specify which samples to include or exclude.

Parameter Description Default
--include A text file containing sample names (one per line) to include from the analysis
--exclude A text file containing sample names (one per line) to exclude from the analysis

GTDB Setup Parameters

Parameter Description Default
--gtdb Tarball or path of a GTDB database. If a database is not found, you must use '--download_gtdb'
--download_gtdb Download the latest GTDB database, even it exists False
--gtdb_save_as_tarball Download the latest GTDB database, and save it in a single tarball False
--skip_check Do not check the installation of GTDB database False

GTDB Classify Parameters

Parameter Description Default
--min_af Minimum alignment fraction to consider closest genome 0.65
--min_perc_aa Filter genomes with an insufficient percentage of AA in the MSA 10
--gtdb_tmp Specify alternative directory for temporary files /tmp
--gtdb_use_scratch Reduce pplacer memory usage by writing to --gtdb_tmp location (slower) False
--gtdb_debug Create intermediate files for debugging purposes False
--force_gtdb Continue processing if an error occurs on a single genome False

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter Description Default
--outdir Base directory to write results to ./
--run_name Name of the directory to hold results bactopia
--skip_compression Ouput files will not be compressed False
--keep_all_files Keeps all analysis files created False

Max Job Request Parameters

Set the top limit for requested resources for any single job.

Parameter Description Default
--max_retry Maximum times to retry a process before allowing it to fail. 3
--max_cpus Maximum number of CPUs that can be requested for any single job. 4
--max_memory Maximum amount of memory (in GB) that can be requested for any single job. 32
--max_time Maximum amount of time (in minutes) that can be requested for any single job. 120
--max_downloads Maximum number of samples to download at a time 3

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

Parameter Description Default
--nfconfig A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
--publish_dir_mode Method used to save pipeline results to output directory. copy
--infodir Directory to keep pipeline Nextflow logs and reports. ${params.outdir}/pipeline_info
--force Nextflow will overwrite existing output files. False
--cleanup_workdir After Bactopia is successfully executed, the work directory will be deleted. False

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

Parameter Description Default
--condadir Directory to Nextflow should use for Conda environments
--registry Docker registry to pull containers from. dockerhub
--singularity_cache Directory where remote Singularity images are stored.
--singularity_pull_docker_container Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead.
--force_rebuild Force overwrite of existing pre-built environments. False
--queue Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM) general,high-memory
--cluster_opts Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name'
--disable_scratch All intermediate files created on worker nodes of will be transferred to the head node. False

Helpful Parameters

Uncommonly used parameters that might be useful.

Parameter Description Default
--monochrome_logs Do not use coloured log outputs.
--nfdir Print directory Nextflow has pulled Bactopia to
--sleep_time The amount of time (seconds) Nextflow will wait after setting up datasets before execution. 5
--validate_params Boolean whether to validate parameters against the schema at runtime True
--help Display help text.
--wf Specify which workflow or Bactopia Tool to execute bactopia
--list_wfs List the available workflows and Bactopia Tools to use with '--wf'
--show_hidden_params Show all params when using --help
--help_all An alias for --help --show_hidden_params
--version Display version text.

Citations

If you use Bactopia and gtdb in your analysis, please cite the following.