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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 \ 
  --include includes.txt  

Output Overview

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

│   └── 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-report.html
            ├── phispy-timeline.html
            └── phispy-trace.txt


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


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.


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 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


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 (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:
--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


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