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.

<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: `./`
`--run_name`	Name of the directory to hold results 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`

Nextflow Profile Parameters¶