Bactopia Tool - `ariba`¶

The ariba module uses ARIBA to rapidly identify genes in a database by creating local assemblies.

Example Usage¶

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

Output Overview¶

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

ariba/
├── <DATABASE>
│   └── <SAMPLE_NAME>
│       ├── card
│       │   ├── assembled_genes.fa.gz
│       │   ├── assembled_seqs.fa.gz
│       │   ├── assemblies.fa.gz
│       │   ├── debug.report.tsv
│       │   ├── log.clusters.gz
│       │   ├── report.tsv
│       │   ├── summary.csv
│       │   └── version_info.txt
│       └── logs
│           └── ariba
│               ├── nf-ariba.{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
│   ├── ariba-dag.dot
│   ├── ariba-report.html
│   ├── ariba-timeline.html
│   └── ariba-trace.txt
├── ariba-report.tsv
├── ariba-summary.csv
├── software_versions.yml
└── software_versions_mqc.yml

Directory structure might be different

ariba is available as a standalone Bactopia Tool, as well as from the main Bactopia workflow (e.g. through Staphopia or Merlin). If executed from Bactopia, the ariba directory structure might be different, but the output descriptions below still apply.

Results¶

Top Level¶

Below are results that are in the base directory.

Filename	Description
ariba-report.tsv	A merged TSV file with `ARIBA` results from all samples
ariba-summary.csv	A merged CSV file created with `ariba summary`

ARIBA¶

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

Filename	Description
assembled_genes.fa.gz	All the assembled genes
assembled_seqs.fa.gz	All the assembled sequences that match the reference
assemblies.fa.gz	All the raw local assembles
debug.report.tsv	Contains the results from `report.tsv` in addition to synonymous mutations
log.clusters.gz	A log of the ARIBA analysis
report.tsv	A report of the ARIBA analysis results
summary.csv	A summary of the report created using `ariba summary`
version_info.txt	Containes info on the versions of ARIBA and its dependencies

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

Ariba GetRef Parameters¶

Parameter	Description	Default
`--ariba_dir`	Path to save or retrieve Ariba databases
`--ariba_db`	A database to query, if unavailable it will be downloaded to the path given by --ariba_dir

Ariba Run Parameters¶

Parameter	Description	Default
`--nucmer_min_id`	Minimum alignment identity (delta-filter -i)	90
`--nucmer_min_len`	Minimum alignment identity (delta-filter -i)	20
`--nucmer_breaklen`	Value to use for -breaklen when running nucmer	200
`--assembly_cov`	Target read coverage when sampling reads for assembly	50
`--min_scaff_depth`	Minimum number of read pairs needed as evidence for scaffold link between two contigs	10
`--spades_options`	Extra options to pass to Spades assembler
`--assembled_threshold`	If proportion of gene assembled (regardless of into how many contigs) is at least this value then the flag gene_assembled is set	0.95
`--gene_nt_extend`	Max number of nucleotides to extend ends of gene matches to look for start/stop codons	30
`--unique_threshold`	If proportion of bases in gene assembled more than once is <= this value, then the flag unique_contig is set	0.03
`--ariba_no_clean`	Do not clean up intermediate files created by Ariba.

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¶