flexpipe

Flexible nextstrain pipeline for genomic epidemiology of pathogens.

This repository contains the essential files to create a nextstrain build. By using this pipeline users can to perform genomic epidemiology analyses and visualize phylogeographic results to track pathogen spread using genomic data and their associated metadata.

Nextstrain panel with results overview

Getting started

Learning basic UNIX commands

Familiarize yourself with basic UNIX commands for navigating and managing files and folders in a command line interface ("Terminal"). In this platform you can perform all simple tasks you usually do using mouse clicks: to copy, move, delete, access, and create files and folders. All you need to do is to type a few commands. Below you can find the main commands required to operate in a Terminal. Please access this page to learn a few more commands. Please practice the use of the commands listed below, so that you are able to navigate from/to directories ("folders") and manage files and folders in command line interfaces.

Creating, Moving and Deleting	Navigating directories	Checking content
mkdir folderX → create folderX	cd folderX → move into folderX	ls → list files and folders
mv → move files/folder from/to another directory	cd .. → go back to previous folder	head → see the first 10 lines of a file
rm → delete files/folders from a directory	pwd → check you current directory	tail → see the last 10 lines of a file

Creating a nextstrain build

Click here to download a tutorial with a step-by-step tutorial on how to prepare your working directory (files and folders), run augur, and visualize the results with auspice. Please check this webiste for more information about the distinct functionalities of nextstrain.

FAQs

1. A checkpoint issue during the rule tree prevents the flexpipe run to progress. How do I solve that?

If the workflow is executed and it fails to complete the rule tree, the previously created files will not allow iqtree to resume a new run. As a result, you may see an error message like this:

Checkpoint (results/alignments/masked.fasta.ckp.gz) indicates that a previous run successfully finished
Use `--redo` option if you really want to redo the analysis and overwrite all output files.
Use `--redo-tree` option if you want to restore ModelFinder and only redo tree search.
Use `--undo` option if you want to continue previous run when changing/adding options.

To resume the run and solve that issue you need to explicitly asks iqtree to -redo the phylogenetic inference. To do so, add an argument --redo argument in the iqtree command line in rule tree:

iqtree \
	-s {input.alignment} \
	-bb {params.bootstrap} \
	-nt {params.threads} \
	-m {params.model} \
	--redo

2. Why does rule refine display the message "ERROR: unsupported rooting mechanisms or root not found"?

This error is mostly likely caused by missing root genome(s). For example, if the phylogeny has to be rooted based on the branch leading to the genome 'JF912185', such genome must be listed among the ones in config/keep.txt. If the rooting genomes are not included in that file, they will not be included in the alignment, and this error message will be prompted:

augur refine is using TreeTime version 0.9.4
0.82        TreeTime.reroot: with method or node: JF912185

ERROR: unsupported rooting mechanisms or root not found

'JF912185' is a Yellow Fever Virus (YFV) genome. If you are not running a YFV analysis, you need to add an appropriate genome in config/keep.txt, and also change the root genome(s) listed in rule parameters of the Snakefile:

rule parameters:
	params:
		mask_5prime = 142,
		mask_3prime = 548,
		bootstrap = 1, # default = 1, but ideally it should be >= 100
		model = "GTR",
		
		root = "JF912185", # <<< set one or more genomes to root the phylogeny
		
		clock_rate = 0.0003,
		clock_std_dev = 0.0001,

Author

• Anderson Brito, Instituto Todos pela Saúde (ITpS) - Website - anderson.brito@itps.org.br

License

This project is licensed under the MIT License.