Bactopia Tool - phispy

The phispy module uses PhiSpy to identify prophages from bacterial and archaeal genomes.

Example Usage

bactopia --wf phispy \
  --bactopia /path/to/your/bactopia/results  

Output Overview

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

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── phispy
|           ├── <SAMPLE_NAME>_prophage_information.tsv
|           ├── <SAMPLE_NAME>_bacteria.fasta
|           ├── <SAMPLE_NAME>_bacteria.gbk
|           ├── <SAMPLE_NAME>_phage.fasta
|           ├── <SAMPLE_NAME>_phage.gbk
|           ├── <SAMPLE_NAME>_prophage.gff3
|           ├── <SAMPLE_NAME>_prophage.tbl
|           └── <SAMPLE_NAME>_prophage.tsv
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── <SAMPLE_NAME>.log
│               ├── nf-phispy.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── phispy-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── phispy-concat
        │   │       ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── phispy.tsv
        └── nf-reports
            ├── phispy-dag.dot
            ├── phispy-report.html
            ├── phispy-timeline.html
            └── phispy-trace.txt

Results

Merged Results

Below are results that are concatenated into a single file.

Filename	Description
phispy.tsv	A summary of the phispy results for all samples

PhiSpy

Below is a description of the per-sample results from PhiSpy.

Filename	Description
<SAMPLE_NAME>_prophage_information.tsv	Contains prophage information for all the genes of the genome, one per line.
<SAMPLE_NAME>_bacteria.fasta	Genome with prophage regions masked with N.
<SAMPLE_NAME>_bacteria.gbk	Genome sequences identified as bacterial.
<SAMPLE_NAME>_phage.fasta	Phage sequences extracted from the genome in FASTA format.
<SAMPLE_NAME>_phage.gbk	Phage sequences extracted from the genome in GenBank format.
<SAMPLE_NAME>_prophage.gff3	Prophage information in GFF3 format.
<SAMPLE_NAME>_prophage.tbl	Prophage number and its location in the genome.
<SAMPLE_NAME>.tsv	Coordinates of each prophage identified in the genome, and their att sites (if found).

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
phispy-dag.dot	The Nextflow DAG visualisation
phispy-report.html	The Nextflow Execution Report
phispy-timeline.html	The Nextflow Timeline Report
phispy-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

PhiSpy Parameters

Parameter	Description
--phispy_number	Number of consecutive genes in a region of window size that must be prophage genes to be called Type: integer, Default: 5
--phispy_mincontigsize	Minimum contig size (in bp) to be included in the analysis. Smaller contigs will be dropped. Type: integer, Default: 5000
--phispy_windowsize	Window size of consecutive genes to look through to find phages Type: integer, Default: 30
--phispy_nonprophage_genegaps	The number of non phage genes between prophages Type: integer, Default: 10
--phispy_phage_genes	The minimum number of genes that must be identified as belonging to a phage for the region to be included Type: integer, Default: 1
--phispy_randomforest_trees	Number of trees generated by Random Forest classifier Type: integer, Default: 500
--phispy_opts	Extra options in quotes for Snippy Type: string

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 that can be requested for any single job. Type: string, Default: 128.GB
--max_time	Maximum amount of time that can be requested for any single job. Type: string, Default: 240.h
--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 phispy 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)

• PhiSpy
  Akhter S, Aziz RK, and Edwards RA PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies. Nucleic Acids Research, 40(16), e126. (2012)