phispy

Tags: prophage phage annotation bacterial archaeal bactopia-tool

Prediction of prophages in bacterial and archaeal genomes.

This Bactopia Tool uses PhiSpy to identify prophages from bacterial and archaeal genomes using machine learning approaches.

Usage

Bactopia CLI:

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

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/phispy/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs

Expected Output Files

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── phispy-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.tsv
│           ├── logs
│           │   ├── <SAMPLE_NAME>.log
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               └── <SAMPLE_NAME>_<SAMPLE_NAME>.gbk.gz
├── GCF_900478275
│   └── tools
│       └── phispy-<TIMESTAMP>
│           ├── GCF_900478275.tsv
│           ├── logs
│           │   ├── GCF_900478275.log
│           │   ├── nf.command.{begin,err,log,out,run,sh,trace}
│           │   └── versions.yml
│           └── supplemental
│               └── GCF_900478275_GCF_900478275.gbk.gz
└── bactopia-runs
    └── phispy-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── phispy-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── phispy.tsv
        └── nf-reports
            ├── phispy-dag.dot
            ├── phispy-report.html
            └── phispy-timeline.html

Per-Sample Results

File	Description
*.txt	Tab-delimited file containing prophage predictions

Merged Results

File	Description
phispy.tsv	Merged TSV file containing prophage predictions from all 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
phispy-dag.dot	The Nextflow DAG visualization
phispy-report.html	The Nextflow Execution Report
phispy-timeline.html	The Nextflow Timeline Report
phispy-trace.txt	The Nextflow Trace report

Parameters

Required Parameters

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

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

PhiSpy Parameters

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

csvtk concat Parameters

Parameter	Type	Default	Description
--csvtk_concat_opts	string		Extra csvtk concat options in quotes

Filtering Parameters

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

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

Optional Parameters

These optional parameters can be useful in certain settings.

Parameter	Type	Default	Description
--outdir	string	bactopia	Base directory to write results to
--skip_compression	boolean	false	Output files will not be compressed
--datasets	string		The path to cache datasets to
--keep_all_files	boolean	false	Keeps all analysis files created

Max Job Request Parameters

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

Parameter	Type	Default	Description
--max_retry	integer	3	Maximum times to retry a process before allowing it to fail.
--max_cpus	integer	4	Maximum number of CPUs that can be requested for any single job.
--max_memory	string	128.GB	Maximum amount of memory that can be requested for any single job.
--max_time	string	240.h	Maximum amount of time that can be requested for any single job.
--max_downloads	integer	3	Maximum number of samples to download at a time

Nextflow Configuration Parameters

Parameters to fine-tune your Nextflow setup.

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

Institutional config options

Parameters used to describe centralized config profiles. These should not be edited.

Parameter	Type	Default	Description
--custom_config_version	string	master	Git commit id for Institutional configs.
--custom_config_base	string	https://raw.githubusercontent.com/nf-core/configs/master	Base directory for Institutional configs.
--config_profile_name	string		Institutional config name.
--config_profile_description	string		Institutional config description.
--config_profile_contact	string		Institutional config contact information.
--config_profile_url	string		Institutional config URL link.

Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

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

Helpful Parameters

Uncommonly used parameters that might be useful.

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

Composition

This workflow uses the following subworkflows:

• phispy - Prediction of prophages from bacterial genomes.

Citations

If you use this 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)

• 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)

Source

View source on GitHub