Bactopia Tool - fastani
¶
The fastani
module uses FastANI to calculate the average
nucleotide identity (ANI) between your samples.
Although, sometimes you might be more interested in calculating the ANI of your samples against
a reference genome. Fortunately, using ncbi-genome-download,
the fastani
module allows you specify either a specific NCBI Assembly RefSeq accession (--accession
)
or a species name (--species
) for which to download all RefSeq genomes.
Example Usage¶
Output Overview¶
Below is the default output structure for the fastani
tool. Where possible the
file descriptions below were modified from a tools description.
<BACTOPIA_DIR>
└── bactopia-runs
└── fastani-<TIMESTAMP>
├── fastani
│ ├── <SAMPLE_NAME>.tsv
│ └── logs
│ └── <REFERENCE_NAME>
│ ├── nf-fastani.{begin,err,log,out,run,sh,trace}
│ └── versions.yml
├── merged-results
│ ├── fastani.tsv
│ └── logs
│ └── fastani-concat
│ ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
│ └── versions.yml
└── nf-reports
├── fastani-dag.dot
├── fastani-report.html
├── fastani-timeline.html
└── fastani-trace.txt
Results¶
Merged Results¶
Below are results that are concatenated into a single file.
Filename | Description |
---|---|
fastani.tsv | A merged TSV file with FastANI results from all samples |
FastANI¶
Below is a description of the per-sample results from FastANI.
Filename | Description |
---|---|
<SAMPLE_NAME>.tsv | FastANI results of all samples against a single samples |
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 folder named logs
. In this folder are helpful
files for you to review if the need ever arises.
Extension | Description |
---|---|
.begin | An empty file used to designate the process started |
.err | Contains STDERR outputs from the process |
.log | Contains both STDERR and STDOUT outputs from the process |
.out | Contains STDOUT outputs from the process |
.run | The script Nextflow uses to stage/unstage files and queue processes based on given profile |
.sh | The script executed by bash for the process |
.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 |
---|---|
fastani-dag.dot | The Nextflow DAG visualisation |
fastani-report.html | The Nextflow Execution Report |
fastani-timeline.html | The Nextflow Timeline Report |
fastani-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 |
---|---|
--bactopia |
The path to bactopia results to use as inputs Type: string |
Filtering Parameters¶
Use these parameters to specify which samples to include or exclude.
Parameter | Description |
---|---|
--include |
A text file containing sample names (one per line) to include from the analysis Type: string |
--exclude |
A text file containing sample names (one per line) to exclude from the analysis Type: string |
fastANI Parameters¶
Parameter | Description |
---|---|
--kmer |
kmer size (<= 16) for ANI calculation Type: integer , Default: 16 |
--min_fraction |
Minimum fraction of genome that must be shared for trusting ANI. Type: number , Default: 0.2 |
--frag_len |
fragment length Type: integer , Default: 3000 |
--skip_pairwise |
Only use RefSeq or local assemblies for ANI calculations Type: boolean |
Optional Parameters¶
These optional parameters can be useful in certain settings.
Parameter | Description |
---|---|
--outdir |
Base directory to write results to Type: string , Default: bactopia |
--skip_compression |
Ouput files will not be compressed Type: boolean |
--datasets |
The path to cache datasets to Type: string |
--keep_all_files |
Keeps all analysis files created Type: boolean |
Max Job Request Parameters¶
Set the top limit for requested resources for any single job.
Parameter | Description |
---|---|
--max_retry |
Maximum times to retry a process before allowing it to fail. Type: integer , Default: 3 |
--max_cpus |
Maximum number of CPUs that can be requested for any single job. Type: integer , Default: 4 |
--max_memory |
Maximum amount of memory (in GB) that can be requested for any single job. Type: integer , Default: 32 |
--max_time |
Maximum amount of time (in minutes) that can be requested for any single job. Type: integer , Default: 120 |
--max_downloads |
Maximum number of samples to download at a time Type: integer , Default: 3 |
Nextflow Configuration Parameters¶
Parameters to fine-tune your Nextflow setup.
Parameter | Description |
---|---|
--nfconfig |
A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set. Type: string |
--publish_dir_mode |
Method used to save pipeline results to output directory. Type: string , Default: copy |
--infodir |
Directory to keep pipeline Nextflow logs and reports. Type: string , Default: ${params.outdir}/pipeline_info |
--force |
Nextflow will overwrite existing output files. Type: boolean |
--cleanup_workdir |
After Bactopia is successfully executed, the work directory will be deleted. Type: boolean |
Institutional config options¶
Parameters used to describe centralized config profiles. These should not be edited.
Parameter | Description |
---|---|
--custom_config_version |
Git commit id for Institutional configs. Type: string , Default: master |
--custom_config_base |
Base directory for Institutional configs. Type: string , Default: https://raw.githubusercontent.com/nf-core/configs/master |
--config_profile_name |
Institutional config name. Type: string |
--config_profile_description |
Institutional config description. Type: string |
--config_profile_contact |
Institutional config contact information. Type: string |
--config_profile_url |
Institutional config URL link. Type: string |
Nextflow Profile Parameters¶
Parameters to fine-tune your Nextflow setup.
Parameter | Description |
---|---|
--condadir |
Directory to Nextflow should use for Conda environments Type: string |
--registry |
Docker registry to pull containers from. Type: string , Default: dockerhub |
--datasets_cache |
Directory where downloaded datasets should be stored. Type: string , Default: <BACTOPIA_DIR>/data/datasets |
--singularity_cache_dir |
Directory where remote Singularity images are stored. Type: string |
--singularity_pull_docker_container |
Instead of directly downloading Singularity images for use with Singularity, force the workflow to pull and convert Docker containers instead. Type: boolean |
--force_rebuild |
Force overwrite of existing pre-built environments. Type: boolean |
--queue |
Comma-separated name of the queue(s) to be used by a job scheduler (e.g. AWS Batch or SLURM) Type: string , Default: general,high-memory |
--cluster_opts |
Additional options to pass to the executor. (e.g. SLURM: '--account=my_acct_name' Type: string |
--container_opts |
Additional options to pass to Apptainer, Docker, or Singularityu. (e.g. Singularity: '-D pwd ' Type: string |
--disable_scratch |
All intermediate files created on worker nodes of will be transferred to the head node. Type: boolean |
Helpful Parameters¶
Uncommonly used parameters that might be useful.
Parameter | Description |
---|---|
--monochrome_logs |
Do not use coloured log outputs. Type: boolean |
--nfdir |
Print directory Nextflow has pulled Bactopia to Type: boolean |
--sleep_time |
The amount of time (seconds) Nextflow will wait after setting up datasets before execution. Type: integer , Default: 5 |
--validate_params |
Boolean whether to validate parameters against the schema at runtime Type: boolean , Default: True |
--help |
Display help text. Type: boolean |
--wf |
Specify which workflow or Bactopia Tool to execute Type: string , Default: bactopia |
--list_wfs |
List the available workflows and Bactopia Tools to use with '--wf' Type: boolean |
--show_hidden_params |
Show all params when using --help Type: boolean |
--help_all |
An alias for --help --show_hidden_params Type: boolean |
--version |
Display version text. Type: boolean |
Citations¶
If you use Bactopia and fastani
in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
csvtk
Shen, W csvtk: A cross-platform, efficient and practical CSV/TSV toolkit in Golang. (GitHub) -
FastANI
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat. Commun. 9, 5114 (2018) -
ncbi-genome-download
Blin K ncbi-genome-download: Scripts to download genomes from the NCBI FTP servers (GitHub)