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PHYLO_PIPELINE(1) User Commands PHYLO_PIPELINE(1)

NAME

phylo_pipeline - Phylo Pipeline of PALEOMIX suite

SYNOPSIS

paleomix phylo_pipeline <command> [options] [makefiles]

DESCRIPTION

The PALEOMIX pipelines are a set of pipelines and tools designed to aid the rapid processing of High-Throughput Sequencing (HTS) data: The BAM pipeline processes de-multiplexed reads from one or more samples, through sequence processing and alignment, to generate BAM alignment files useful in downstream analyses; the Phylogenetic pipeline carries out genotyping and phylogenetic inference on BAM alignment files, either produced using the BAM pipeline or generated elsewhere; and the Zonkey pipeline carries out a suite of analyses on low coverage equine alignments, in order to detect the presence of F1-hybrids in archaeological assemblages. In addition, PALEOMIX aids in metagenomic analysis of the extracts.

The pipelines have been designed with ancient DNA (aDNA) in mind, and includes several features especially useful for the analyses of ancient samples, but can all be for the processing of modern samples, in order to ensure consistent data processing.

phylo_pipeline is the phylo pipeline of paleomix(1).

OPTIONS

Commands

Display this message.
Copy example project to folder.
Print makefile template.
Carry out genotyping according to makefile.
Carry out multiple sequence alignment.
Carry out phylogenetic inference.

Optional arguments

show program's version number and exit
show this help message and exit
Write dependency tree to the specified dot-file.

Progress reporting

Select method for displaying the progress of the pipeline: 'running' = Display only currently running nodes; 'progress' = Display changes in state; 'summary'; one-line summary only. [Default is 'running']
Enable, disable, or force the use of color codes when printing the command-line UI. Unless forced, colors will only be printed if STDOUT is a TTY [Default is 'on']

Logging

Create the specified log-file and write any messages to this file. By default, a log-file will be generated in the folder specified using --temp-root, but only when messages are logged
Log messages to log-file at and above the specified level; one of 'info', 'warning', 'error', or 'debug' [warning]

Scheduling

Maximum number of threads to use when genotyping or building pileups [1]
Maximum number of threads to use for each instance of ExaML [1]
Maximum number of threads to use in total [4]
If passed, only a dry-run in performed, the dependency tree is printed, and no tasks are executed.

Required paths:

Location for temporary files and folders [/tmp/USERNAME/phylo_pipeline]
Location of BAM files for each sample [./data/samples]
Location of BED files containing regions of interest [./data/regions]
Location of prefixes (FASTAs) [./data/prefixes]
Location of reference sequences (FASTAs) [./data/refseqs]
The destination folder for result files [./results]

Files and executables:

List all input files used by pipeline for the makefile(s), excluding any generated by the pipeline itself.
List all output files generated by pipeline for the makefile(s).
List all executables required by the pipeline, with version requirements (if any).

Config files:

Write config using current settings to $HOME/.paleomix/phylo_pipeline.ini

SEE ALSO

paleomix(1)

AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

February 2017 phylo_pipeline 1.2.7