Bactopia Tool - `mashtree`¶

The mashtree module uses Mashtree to create a tree of your samples using Mash distances.

You can also use --species or -accessions to see how your samples compare to completed genomes. If used, ncbi-genome-download will download available completed genomes available from RefSeq and they will be included in your tree.

Example Usage¶

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

Output Overview¶

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

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

Results¶

Top Level¶

Below are results that are in the base directory.

Filename	Description
mashtree.dnd	A Newick formatted tree file
mashtree.tsv	A TSV matrix of pair-wise Mash distances

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

Mashtree Parameters¶

Parameter	Description	Default
`--trunclength`	How many characters to keep in a filename	250
`--sortorder`	For neighbor-joining, the sort order can make a difference.	ABC
`--genomesize`	Genome size of the input samples	5000000
`--mindepth`	If mindepth is zero, then it will be chosen in a smart but slower method, to discard lower-abundance kmers.	5
`--kmerlength`	Hashes will be based on strings of this many nucleotides	21
`--sketchsize`	Each sketch will have at most this many non-redundant min-hashes	10000

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¶