Bactopia Tool - `busco`¶

The busco module uses BUSCO (or Benchmarking Universal Single-Copy Orthologs) to assess the completeness of your assembly.

Example Usage¶

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

Output Overview¶

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

busco/
├── <LINEAGE>
│   ├── <SAMPLE_NAME>
│   │   ├── logs/
│   │   ├── prodigal_output/
│   │   ├── run_<LINEAGE>/
│   │   │   ├── busco_sequences
│   │   │   ├── full_table.tsv
│   │   │   ├── hmmer_output/
│   │   │   ├── missing_busco_list.tsv
│   │   │   ├── short_summary.json
│   │   │   └── short_summary.txt
│   │   ├── short_summary.specific.<LINEAGE>.<SAMPLE_NAME>.json
│   │   └── short_summary.specific.<LINEAGE>.<SAMPLE_NAME>.txt
│   ├── <LINEAGE>-summary.txt
│   └── logs
│       └── busco.log
├── logs
│   ├── busco
│   │   └── <LINEAGE>
│   │       ├── nf-busco.{begin,err,log,out,run,sh,trace}
│   │       └── versions.yml
│   ├── 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
│   ├── busco-dag.dot
│   ├── busco-report.html
│   ├── busco-timeline.html
│   └── busco-trace.txt
├── busco.tsv
├── software_versions.yml
└── software_versions_mqc.yml

Results¶

Top Level¶

Below are results that are in the base directory.

Filename	Description
busco.tsv	A merged TSV of all lineages used by BUSCO

busco¶

Below is a description of the per-lineage results from BUSCO.

Filename/Folder	Description
/-summary.txt	Tab-delimited lineage results for all samples
/logs/busco.log	Detailed information about the BUSCO run
//logs/	Log files for individual tools per-sample
//prodigal_output/	Outputs from the Prodigal gene-prediction step
//run_/busco_sequences	FASTA format file for each BUSCO gene identified
//run_/full_table.tsv	Complete results in a tab-delimited format with scores and lengths of BUSCO matches
//run_/hmmer_output	Tab-delimited output from HMMER
//run_/missing_busco_list.tsv	Tab-delimited list of missing BUSCOs
//run_/short_summary.json	A summary of BUSCO matches in JSON format
//run_/short_summary.txt	A summary of BUSCO matches
//short_summary.specific...json	A summary of BUSCO matches in JSON format per-sample
//short_summary.specific...txt	A summary of BUSCO matches per-sample

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

BUSCO Parameters¶

Parameter	Description	Default
`--busco_lineage`	Specify the name of the BUSCO lineage to be used (can separate by comma)	bacteria_odb10
`--busco_evalue`	E-value cutoff for BLAST searches. Allowed formats, 0.001 or 1e-03	1e-03
`--busco_limit`	Total candidate regions to consider per BUSCO	3
`--metaeuk_parameters`	Additional Metaeuk first-pass arguments contained within a single pair of quotation marks, separated by commas
`--metaeuk_rerun_parameters`	Additional Metaeuk second-pass arguments contained within a single pair of quotation marks, separated by commas
`--use_augustus`	Use augustus gene predictor for eukaryote runs	False
`--augustus_parameters`	Additional Augustus arguments contained within a single pair of quotation marks, separated by commas
`--augustus_species`	Specify a species for Augustus training
`--augustus_long`	Optimization Augustus self-training mode	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¶