---
name: "run_tipp.py"
section: "1"
platform: "linux"
package: "sepp"
version: "4.3.10+dfsg-5"
release: "Debian 11 (Bullseye)"
platforms: ["linux"]
url: "https://new.carta.tech/run_tipp.py"
---

# run\_tipp.py(1)

an identification and phylogenetic profiling tool

## NAME

run\_tipp.py - an identification and phylogenetic profiling tool

## DESCRIPTION

usage: run\_tipp.py \[-h\] \[-v\] \[-A N\] \[-P N\] \[-F N\] \[--distance DISTANCE\]

-

  \[-M DIAMETER\] \[-S DECOMP\] \[-p DIR\] \[-o OUTPUT\] \[-d OUTPUT\_DIR\] \[-t TREE\] \[-r RAXML\] \[-a ALIGN\] \[-f FRAG\] \[-m MOLECULE\] \[-x N\] \[-cp CHCK\_FILE\] \[-cpi N\] \[-seed N\] \[-R N\] \[-at N\] \[-D\] \[-pt N\] \[-PD N\] \[-tx TAXONOMY\] \[-txm MAPPING\] \[-adt TREE\] \[-C N\]

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://github.com/tandyw/tipp-reference/releases/download/v2.0.0/tipp.zip**

If the local administrator has not set the path to this reference dataset in /etc/sepp/tipp.config, you should copy this file to ~/.sepp/ and put the path to the dataset in the **reference** section of the configuration file, see [**tipp.config**(5)](/tipp.config/5.md).

### 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. \[default: /tmp/sepp\]

- **-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.

- **-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 \[default: dna\]

### 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)](/run_sepp.py/1.md), [**tipp.config**(5)](/tipp.config/5.md)