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checkm-software

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CheckM

CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. It provides robust estimates of genome completeness and contamination by using collocated sets of genes that are ubiquitous and single-copy within a phylogenetic lineage.

Information

Usage

See which versions of checkm are available:

$ module avail checkm

Load one version into your environment and run it:

$ module load checkm/1.1.2
$ drep

Installation

Notes from the sysadmin during installation:

$ sudo mkdir -p /export/apps/checkm/1.1.2
$ sudo chown aorth /export/apps/checkm/1.1.2
$ python3.6 -m venv /export/apps/checkm/1.1.2
$ source /export/apps/checkm/1.1.2/bin/activate
$ pip install --upgrade pip setuptools
$ pip install checkm-genome==1.1.2
$ wget https://data.ace.uq.edu.au/public/CheckM_databases/checkm_data_2015_01_16.tar.gz
$ mkdir -p /export/apps/checkm/1.1.2/data
$ tar xf checkm_data_2015_01_16.tar.gz -C /export/apps/checkm/1.1.2/data
$ find /export/apps/checkm/1.1.2/data -type d -exec chmod 755 {} \;
$ find /export/apps/checkm/1.1.2/data -type f -exec chmod 644 {} \;
$ checkm data setRoot /export/apps/checkm/1.1.2/data
$ sudo chown -R root:root /export/apps/checkm/1.1.2

Test the installation with:

$ checkm test /tmp/test-checkm
checkm-software.txt · Last modified: 2020/03/12 19:45 by aorth