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RUN_ABUNDANCE.PY(1) User Commands RUN_ABUNDANCE.PY(1)

NAME

run_abundance.py - helper script to estimate the abundance at a given taxonomic level

DESCRIPTION

usage: run_abundance.py [-h] [-v] [-A N] [-P N] [-F N] [--distance DISTANCE]

[-M DIAMETER] [-S DECOMP] [-p DIR] [-rt] [-o OUTPUT]
[-d OUTPUT_DIR] [-c CONFIG] [-t TREE] [-r RAXML] [-a ALIGN] [-f FRAG] [-m MOLECULE] [--ignore-overlap] [-x N] [-cp CHCK_FILE] [-cpi N] [-seed N] [-bt N] [-at N] [-pt N] [-g N] [-b N] [-no_trim] [-bin N] [-D] [-C N] [-G GENES]

This script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file.

optional arguments:

show this help message and exit
show program's version number and exit

DECOMPOSITION OPTIONS:

These options determine the alignment decomposition size and taxon insertion size. If None is given, then the default is to align/place at 10% of total taxa. The alignment decomosition size must be less than the taxon insertion size.
max alignment subset size of N [default: 10% of the total number of taxa or the placement subset size if given]
max placement subset size of N [default: 10% of the total number of taxa or the alignment length (whichever bigger)]
maximum fragment chunk size of N. Helps controlling memory. [default: 20000]
minimum p-distance before stopping the decomposition[default: 1]
maximum tree diameter before stopping the decomposition[default: None]
decomposition strategy [default: using tree branch length]

OUTPUT OPTIONS:

These options control output.
Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]
Remove tempfile directory. [default: disabled]
output files with prefix OUTPUT. [default: output]
output to OUTPUT_DIR directory. full-path required. [default: .]

INPUT OPTIONS:

These options control input. To run SEPP the following is required. A backbone tree (in newick format), a RAxML_info file (this is the file generated by RAxML during estimation of the backbone tree. Pplacer uses this info file to set model parameters), a backbone alignment file (in fasta format), and a fasta file including fragments. The input sequences are assumed to be DNA unless specified otherwise.
A config file, including options used to run SEPP. Options provided as command line arguments overwrite config file values for those options. [default: None]
Input tree file (newick format) [default: None]
RAxML_info file including model parameters, generated by RAxML.[default: None]
Aligned fasta file [default: None]
fragment file [default: None]
Molecule type of sequences. Can be amino, dna, or rna [default: dna]
When a query sequence has the same name as a backbone sequence, ignore the query sequences and keep the backbone sequence [default: False]

OTHER OPTIONS:

These options control how SEPP is run
Use N cpus [default: number of cpus available on the machine]
checkpoint file [default: no checkpointing]
Interval (in seconds) between checkpoint writes. Has effect only with -cp provided. [default: 3600]
random seed number. [default: 297834]

TIPP OPTIONS:

These arguments set settings specific to TIPP
Minimum query coverage for blast hit to map read to a markerThis should be a number between >0 [default : 50]
Enough alignment subsets are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
Enough placements are selected to reach a commulative probability of N. This should be a number between 0 and 1 [default: 0.95]
Classify on only the specified gene.
Blast file with fragments already binned.
Trim query sequence if it extends outside marker (BLAST only).
Use blast or hmmer for binning [default: blast]
Treat fragments as distribution
Placement probability requirement to count toward the distribution. This should be a number between 0 and 1 [default: 0.0]
Use markers or cogs genes [default: markers-v3]

SEE ALSO

run_sepp.py(1), run_tipp.py(1),

September 2021 run_abundance.py