QIIME2-Sapelo2

Category

Bioinformatics

Program On

Sapelo2

Version

2019.10, 2020.2, 2020.6, 2020.11

Author / Distributor

QIIME2

Description

QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed."

More details are at QIIME2

Running Program

Also refer to Running Jobs on Sapelo2 Also refer to Run X window Jobs and Run interactive Jobs

• Version 2018.8, installed at /usr/local/apps/eb/QIIME2/2018.8; Plug-in q2-fragment-insertion is installed under same location.
• Version 2018.11, installed at /usr/local/apps/eb/QIIME2/2018.11
• Version 2019.7, installed as a conda virtual environment at /usr/local/apps/gb/qiime2/2019.7
• Version 2020.6, installed at /usr/local/apps/eb/QIIME2/2020.6

To use version 2018.8, please first load the module with

module load QIIME2/2018.8

To use version 2018.11, please first load the module with

module load QIIME2/2018.11

To use version 2019.7, please first load the module with

module load qiime2/2019.7_conda

To use version 2020.6, please first load the module with

module load QIIME2/2020.6

Example of a shell script sub.sh to run qiime v2018.11 at the batch queue:

#!/bin/bash

#PBS -N j_qiime2
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=24:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load QIIME2/2018.11
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
qiime [OPTIONS] COMMAND [ARGS]...

where [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

Example of a shell script sub.sh to run qiime v2019.7 at the batch queue:

#!/bin/bash

#PBS -N j_qiime2
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=24:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load qiime2/2019.7_conda
source activate ${ROOT_qiime2}
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
qiime [OPTIONS] COMMAND [ARGS]...
conda deactivate

where ROOT_qiime2 is the environment variable storing QIIME2/2019.7 installation path, i.e./usr/local/apps/gb/qiime2/2019.7; [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

Example of a shell script sub.sh to run qiime v2020.6 at the batch queue:

#!/bin/bash

#PBS -N j_qiime2
#PBS -q batch
#PBS -l nodes=1:ppn=1
#PBS -l walltime=24:00:00
#PBS -l mem=10gb

cd $PBS_O_WORKDIR

module load QIIME2/2020.6
echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
qiime [OPTIONS] COMMAND [ARGS]...

where [OPTIONS], COMMAND, and [ARGS] need to be replaced by the options, command, and arguments you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number cores per node, and the job name need to be modified appropriately as well.

Example of job submission

qsub  ./sub.sh 

Documentation

module load QIIME2/2018.8
qiime
Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload bashcompinit && bashcompinit && source tab-qiime

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  info                Display information about current deployment.
  tools               Tools for working with QIIME 2 files.
  dev                 Utilities for developers and advanced users.
  alignment           Plugin for generating and manipulating alignments.
  composition         Plugin for compositional data analysis.
  cutadapt            Plugin for removing adapter sequences, primers, and
                      other unwanted sequence from sequence data.
  dada2               Plugin for sequence quality control with DADA2.
  deblur              Plugin for sequence quality control with Deblur.
  demux               Plugin for demultiplexing & viewing sequence quality.
  diversity           Plugin for exploring community diversity.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  fragment-insertion  Plugin for extending phylogenies.
  gneiss              Plugin for building compositional models.
  longitudinal        Plugin for paired sample and time series analyses.
  metadata            Plugin for working with Metadata.
  phylogeny           Plugin for generating and manipulating phylogenies.
  quality-control     Plugin for quality control of feature and sequence data.
  quality-filter      Plugin for PHRED-based filtering and trimming.
  sample-classifier   Plugin for machine learning prediction of sample
                      metadata.
  taxa                Plugin for working with feature taxonomy annotations.
  vsearch             Plugin for clustering and dereplicating with vsearch.

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Installation

source code from QIIME2

source code from q2-fragment-insertion

System

64-bit Linux