Bactopia Tool - `mashdist`¶

The mashdist module uses Mash to determine the Mash distance from a given reference genome(s).

Example Usage¶

bactopia --wf mashdist \
  --bactopia /path/to/your/bactopia/results \ 
  --include includes.txt

Output Overview¶

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

mashdist/
├── <SAMPLE_NAME>
│   ├── <SAMPLE_NAME>-dist.txt
│   └── logs
│       └── mashdist
│           ├── nf-mashdist{begin,err,log,out,run,sh,trace}
│           └── versions.yml
├── logs
│   ├── csvtk_concat
│   │   ├── nf-csvtk_concat{begin,err,log,out,run,sh,trace}
│   │   └── versions.yml
│   └── custom_dumpsoftwareversions
│       ├── nf-custom_dumpsoftwareversions{begin,err,log,out,run,sh,trace}
│       └── versions.yml
├── nf-reports
│   ├── mashdist-dag.dot
│   ├── mashdist-report.html
│   ├── mashdist-timeline.html
│   └── mashdist-trace.txt
├── mashdist.tsv
├── software_versions.yml
└── software_versions_mqc.yml

Results¶

Top Level¶

Below are results that are in the base directory.

Filename	Description
mashdist.tsv	A merged TSV file with `Mash` distances against a reference from all samples

Mash¶

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

Filename	Description
<SAMPLE_NAME>-dist.txt	A tab-delimited file with `mash dist` results

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 logs folder containing helpful files for you to review if the need ever arises.

Filename	Description
nf-<PROCESS_NAME>.begin	An empty file used to designate the process started
nf-<PROCESS_NAME>.err	Contains STDERR outputs from the process
nf-<PROCESS_NAME>.log	Contains both STDERR and STDOUT outputs from the process
nf-<PROCESS_NAME>.out	Contains STDOUT outputs from the process
nf-<PROCESS_NAME>.run	The script Nextflow uses to stage/unstage files and queue processes based on given profile
nf-<PROCESS_NAME>.sh	The script executed by bash for the process
nf-<PROCESS_NAME>.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
mashdist-dag.dot	The Nextflow DAG visualisation
mashdist-report.html	The Nextflow Execution Report
mashdist-timeline.html	The Nextflow Timeline Report
mashdist-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	Default
`--bactopia`	The path to bactopia results to use as inputs

Filtering Parameters¶

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

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

mashdist Parameters¶

Parameter	Description	Default
`--mash_sketch`	The reference sequence as a Mash Sketch (.msh file)
`--mash_seed`	Seed to provide to the hash function	42
`--mash_table`	Table output (fields will be blank if they do not meet the p-value threshold)	False
`--mash_m`	Minimum copies of each k-mer required to pass noise filter for reads	1
`--mash_w`	Probability threshold for warning about low k-mer size.	0.01
`--max_p`	Maximum p-value to report.	1.0
`--max_dist`	Maximum distance to report.	1.0
`--merlin_dist`	Maximum distance to report when using Merlin .	0.1
`--full_merlin`	Go full Merlin and run all species-specific tools, no matter the Mash distance	False
`--use_fastqs`	Query with FASTQs instead of the assemblies	False

Optional Parameters¶

These optional parameters can be useful in certain settings.

Parameter	Description	Default
`--outdir`	Base directory to write results to	./
`--run_name`	Name of the directory to hold results	bactopia
`--skip_compression`	Ouput files will not be compressed	False
`--keep_all_files`	Keeps all analysis files created	False

Max Job Request Parameters¶

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

Parameter	Description	Default
`--max_retry`	Maximum times to retry a process before allowing it to fail.	3
`--max_cpus`	Maximum number of CPUs that can be requested for any single job.	4
`--max_memory`	Maximum amount of memory (in GB) that can be requested for any single job.	32
`--max_time`	Maximum amount of time (in minutes) that can be requested for any single job.	120
`--max_downloads`	Maximum number of samples to download at a time	3

Nextflow Configuration Parameters¶

Parameters to fine-tune your Nextflow setup.

Parameter	Description	Default
`--nfconfig`	A Nextflow compatible config file for custom profiles, loaded last and will overwrite existing variables if set.
`--publish_dir_mode`	Method used to save pipeline results to output directory.	copy
`--infodir`	Directory to keep pipeline Nextflow logs and reports.	${params.outdir}/pipeline_info
`--force`	Nextflow will overwrite existing output files.	False
`--cleanup_workdir`	After Bactopia is successfully executed, the `work` directory will be deleted.	False

Nextflow Profile Parameters¶