Provided by: tipp_1.0+dfsg-2_amd64 
NAME
run_tipp.py - an identification and phylogenetic profiling tool
DESCRIPTION
usage: run_tipp.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] [-R N] [-at N] [-D] [-pt N] [-PD N] [-tx TAXONOMY] [-txm MAPPING] [-adt TREE] [-C N]
This script runs the SEPP algorithm on an input tree, alignment, fragment file, and RAxML info file. It
uses a reference dataset which has to be downloaded from
https://obj.umiacs.umd.edu/tipp/tipp2-refpkg.tar.gz
If the local administrator has not set the path to this reference dataset in /etc/tipp/tipp.config, you
should copy this file to ~/.tipp/ and put the path to the dataset in the reference section of the
configuration file, see tipp.config(5).
optional arguments:
-h, --help
show this help message and exit
-v, --version
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.
-A N, --alignmentSize N
max alignment subset size of N [default: 10% of the total number of taxa or the placement subset
size if given]
-P N, --placementSize N
max placement subset size of N [default: 10% of the total number of taxa or the alignment length
(whichever bigger)]
-F N, --fragmentChunkSize N
maximum fragment chunk size of N. Helps controlling memory. [default: 20000]
--distance DISTANCE
minimum p-distance before stopping the decomposition[default: 1]
-M DIAMETER, --diameter DIAMETER
maximum tree diameter before stopping the decomposition[default: None]
-S DECOMP, --decomp_strategy DECOMP
decomposition strategy [default: using tree branch length]
OUTPUT OPTIONS:
These options control output.
-p DIR, --tempdir DIR
Tempfile files will be written to DIR. Full-path required. [default: /tmp/sepp]
-rt, --remtemp
Remove template directory. [default: disabled]
-o OUTPUT, --output OUTPUT
output files with prefix OUTPUT. [default: output]
-d OUTPUT_DIR, --outdir OUTPUT_DIR
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.
-c CONFIG, --config CONFIG
A config file, including options used to run SEPP. Options provided as command line arguments
overwrite config file values for those options. [default: None]
-t TREE, --tree TREE
Input tree file (newick format) [default: None]
-r RAXML, --raxml RAXML
RAxML_info file including model parameters, generated by RAxML.[default: None]
-a ALIGN, --alignment ALIGN
Aligned fasta file [default: None]
-f FRAG, --fragment FRAG
fragment file [default: None]
-m MOLECULE, --molecule MOLECULE
Molecule type of sequences. Can be amino, dna, or rna [default: dna]
--ignore-overlap
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
-x N, --cpu N
Use N cpus [default: number of cpus available on the machine]
-cp CHCK_FILE, --checkpoint CHCK_FILE
checkpoint file [default: no checkpointing]
-cpi N, --interval N
Interval (in seconds) between checkpoint writes. Has effect only with -cp provided. [default:
3600]
-seed N, --randomseed N
random seed number. [default: 297834]
TIPP OPTIONS:
These arguments set settings specific to TIPP
-R N, --reference_pkg N
Use a pre-computed reference package [default: None]
-at N, --alignmentThreshold N
Enough alignment subsets are selected to reach a commulative probability of N. This should be a
number between 0 and 1 [default: 0.95]
-D, --dist
Treat fragments as distribution
-pt N, --placementThreshold N
Enough placements are selected to reach a commulative probability of N. This should be a number
between 0 and 1 [default: 0.95]
-PD N, --push_down N
Whether to classify based on children below or above insertion point. [default: True]
-tx TAXONOMY, --taxonomy TAXONOMY
A file describing the taxonomy. This is a commaseparated text file that has the following fields:
taxon_id,parent_id,taxon_name,rank. If there are other columns, they are ignored. The first line
is also ignored.
-txm MAPPING, --taxonomyNameMapping MAPPING
A comma-separated text file mapping alignment sequence names to taxonomic ids. Formats (each
line): sequence_name,taxon_id. If there are other columns, they are ignored. The first line is
also ignored.
-adt TREE, --alignmentDecompositionTree TREE
A newick tree file used for decomposing taxa into alignment subsets. [default: the backbone tree]
-C N, --cutoff N
Placement probability requirement to count toward the distribution. This should be a number
between 0 and 1 [default: 0.0]
SEE ALSO
run_sepp.py(1), tipp.config(5)
run_tipp.py September 2021 RUN_TIPP.PY(1)