QIIME2-Sapelo2 - Revision history

Shtsai at 01:24, 5 April 2026

2026-04-05T01:24:20Z

← Older revision		Revision as of 21:24, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2		2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2

	=== Author / Distributor ===		== Author / Distributor ==

	[https://qiime2.org/ QIIME2]		[https://qiime2.org/ QIIME2]

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

	More details are at [https://qiime2.org/ QIIME2]		More details are at [https://qiime2.org/ QIIME2]

	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	</pre>		</pre>

	=== Documentation ===		== Documentation ==


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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation ===		== Installation ==

	source code from [https://qiime2.org/ QIIME2]		source code from [https://qiime2.org/ QIIME2]

	=== System ===		== System ==
	64-bit Linux		64-bit Linux

Chelsea: /* Documentation */

2024-05-14T12:28:24Z

Documentation

← Older revision		Revision as of 08:28, 14 May 2024
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	<pre class="gcommand">		<pre class="gcommand">
	ml QIIME2/~~2020~~.11		[cft07037@b1-24 singularity-images]$ ml QIIME2/2023.2
	qiime --help		[cft07037@b1-24 singularity-images]$ qiime --help

	Usage: qiime [OPTIONS] COMMAND [ARGS]...		Usage: qiime [OPTIONS] COMMAND [ARGS]...

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	your .zshrc:		your .zshrc:

	autoload ~~bashcompinit~~ && bashcompinit && source tab-qiime		autoload -Uz compinit && compinit
			autoload bashcompinit && bashcompinit
			source tab-qiime

	Options:		Options:
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	cutadapt Plugin for removing adapter sequences, primers, and		cutadapt Plugin for removing adapter sequences, primers, and
	other unwanted sequence from sequence data.		other unwanted sequence from sequence data.

	dada2 Plugin for sequence quality control with DADA2.		dada2 Plugin for sequence quality control with DADA2.
	deblur Plugin for sequence quality control with Deblur.		deblur Plugin for sequence quality control with Deblur.
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	fragment-insertion Plugin for extending phylogenies.		fragment-insertion Plugin for extending phylogenies.
	gneiss Plugin for building compositional models.		gneiss Plugin for building compositional models.
			greengenes2 Methods for interaction with Greengenes2
	longitudinal Plugin for paired sample and time series analyses.		longitudinal Plugin for paired sample and time series analyses.
	metadata Plugin for working with Metadata.		metadata Plugin for working with Metadata.
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	sample-classifier Plugin for machine learning prediction of sample		sample-classifier Plugin for machine learning prediction of sample
	metadata.		metadata.

	taxa Plugin for working with feature taxonomy annotations.		taxa Plugin for working with feature taxonomy annotations.
	vsearch Plugin for clustering and dereplicating with vsearch.		vsearch Plugin for clustering and dereplicating with vsearch.

Chelsea: /* Version */

2024-05-14T12:26:14Z

Version

← Older revision		Revision as of 08:26, 14 May 2024
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	=== Version ===		=== Version ===

	~~2019~~.10, ~~2020~~.2, ~~2020~~.6, ~~2020~~.11		2020.6, 2023.2, 2023.5.1, 2023.7, 2023.9, 2024.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	*Version 2019.10 installed as a conda environment at /apps/eb/QIIME2/2019.10
	*Version 2020.2 installed as a conda environment at /apps/eb/QIIME2/2020.2
	*Version 2020.6 installed as a conda environment at /apps/eb/QIIME2/2020.6		*Version 2020.6 installed as a conda environment at /apps/eb/QIIME2/2020.6
	*Version ~~2020~~.11 installed as a conda environment at /apps/eb/QIIME2/~~2020~~.11		*Version 2023.2 installed as a conda environment at /apps/eb/QIIME2/2023.2
			*Version 2023.5.1 installed as a conda environment at /apps/eb/QIIME2/2023.5.1-foss-2022a
			*Version 2023.7 installed as a conda environment at /apps/eb/QIIME2/2023.7

	To use version ~~2019~~.10, please first load the module with		To use version 2020.6, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2019~~.10		module load QIIME2/2020.6
	</pre>		</pre>

	To use ~~version 2020~~.2, please first load the module with		To use version2023.2, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2020~~.2		module load QIIME2/2023.2
	</pre>		</pre>

	To use version ~~2020~~.6, please first load the module with		To use version 2023.5.1, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2020~~.6		module load QIIME2/2023.5.1-foss-2022a
	</pre>		</pre>

	To use version ~~2020~~.11, please first load the module with		To use version 2023.7, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2020~~.11		module load QIIME2/2023.7
	</pre>		</pre>


	Example of a shell script sub.sh to run QIIME2 ~~2020~~.11 at the batch queue:		Example of a shell script sub.sh to run QIIME2 2023.7 at the batch queue:
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml QIIME2/~~2020~~.11		ml QIIME2/2023.7

	echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc		echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc

Moses at 20:55, 7 May 2021

2021-05-07T20:55:42Z

← Older revision		Revision as of 16:55, 7 May 2021
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	=== Documentation ===		=== Documentation ===


	<pre class="gcommand">		<pre class="gcommand">
	ml QIIME2/2020.11		ml QIIME2/2020.11

Moses at 20:48, 7 May 2021

2021-05-07T20:48:28Z

← Older revision		Revision as of 16:48, 7 May 2021
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	#SBATCH --job-name=j_qiime2 # Job name		#SBATCH --job-name=j_qiime2 # Job name
	#SBATCH --partition=batch # Partition (queue) name		#SBATCH --partition=batch # Partition (queue) name
	#SBATCH --ntasks=1 # Run on a single CPU		#SBATCH --ntasks=1 # Run on a single CPU by default
			#SBATCH --cpus-per-task=1 # Number of CPU cores per task
	#SBATCH --mem=20gb # Job memory request		#SBATCH --mem=20gb # Job memory request
	#SBATCH --time=02:00:00 # Time limit hrs:min:sec		#SBATCH --time=48:00:00 # Time limit hrs:min:sec
	#SBATCH --output=~~testserial~~.%j.out # Standard output log		#SBATCH --output=log.%j.out # Standard output log
	#SBATCH --error=~~testserial~~.%j.err # Standard error log		#SBATCH --error=log.%j.err # Standard error log

	#SBATCH --mail-type=~~END,FAIL~~ # Mail events (NONE, BEGIN, END, FAIL, ALL)		#SBATCH --mail-type=ALL # Mail events (NONE, BEGIN, END, FAIL, ALL)
	#SBATCH --mail-user=username@uga.edu # Where to send mail		#SBATCH --mail-user=username@uga.edu # Where to send mail

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	~~module load~~ QIIME2/2020.11		ml QIIME2/2020.11

	echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc		echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
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	Example of job submission		Example of job submission
	<pre class="gcommand">		<pre class="gcommand">
	sbatch ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>

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	<pre class="gcommand">		<pre class="gcommand">
	~~module load~~ QIIME2/~~2018~~.8		ml QIIME2/2020.11
	qiime		qiime --help

	Usage: qiime [OPTIONS] COMMAND [ARGS]...		Usage: qiime [OPTIONS] COMMAND [ARGS]...

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

	Commands:		Commands:
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	cutadapt Plugin for removing adapter sequences, primers, and		cutadapt Plugin for removing adapter sequences, primers, and
	other unwanted sequence from sequence data.		other unwanted sequence from sequence data.

	dada2 Plugin for sequence quality control with DADA2.		dada2 Plugin for sequence quality control with DADA2.
	deblur Plugin for sequence quality control with Deblur.		deblur Plugin for sequence quality control with Deblur.
	demux Plugin for demultiplexing & viewing sequence quality.		demux Plugin for demultiplexing & viewing sequence quality.
	diversity Plugin for exploring community diversity.		diversity Plugin for exploring community diversity.
			diversity-lib Plugin for computing community diversity.
	emperor Plugin for ordination plotting with Emperor.		emperor Plugin for ordination plotting with Emperor.
	feature-classifier Plugin for taxonomic classification.		feature-classifier Plugin for taxonomic classification.
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	sample-classifier Plugin for machine learning prediction of sample		sample-classifier Plugin for machine learning prediction of sample
	metadata.		metadata.

	taxa Plugin for working with feature taxonomy annotations.		taxa Plugin for working with feature taxonomy annotations.
	vsearch Plugin for clustering and dereplicating with vsearch.		vsearch Plugin for clustering and dereplicating with vsearch.
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	source code from [https://qiime2.org/ QIIME2]		source code from [https://qiime2.org/ QIIME2]

	~~source code from [https://github.com/biocore/q2-fragment-insertion q2-fragment-insertion]~~

	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Moses at 20:45, 7 May 2021

2021-05-07T20:45:14Z

← Older revision		Revision as of 16:45, 7 May 2021
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	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
	#SBATCH --job-name=j_qiime2 # Job name		#SBATCH --job-name=j_qiime2 # Job name
	#SBATCH --partition=batch # Partition (queue) name		#SBATCH --partition=batch # Partition (queue) name
	#SBATCH --ntasks=1 # Run on a single CPU		#SBATCH --ntasks=1 # Run on a single CPU
	#SBATCH --mem=~~1gb~~ # Job memory request
			#SBATCH --mem=20gb # Job memory request
	#SBATCH --time=02:00:00 # Time limit hrs:min:sec		#SBATCH --time=02:00:00 # Time limit hrs:min:sec
	#SBATCH --output=testserial.%j.out # Standard output log		#SBATCH --output=testserial.%j.out # Standard output log

Moses at 20:44, 7 May 2021

2021-05-07T20:44:01Z

← Older revision		Revision as of 16:44, 7 May 2021
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	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
			#SBATCH --job-name=j_qiime2 # Job name
			#SBATCH --partition=batch # Partition (queue) name
			#SBATCH --ntasks=1 # Run on a single CPU
			#SBATCH --mem=1gb # Job memory request
			#SBATCH --time=02:00:00 # Time limit hrs:min:sec
			#SBATCH --output=testserial.%j.out # Standard output log
			#SBATCH --error=testserial.%j.err # Standard error log

	#~~PBS~~ -~~N j_qiime2~~		#SBATCH --mail-type=END,FAIL # Mail events (NONE, BEGIN, END, FAIL, ALL)
	~~#PBS~~ -~~q batch~~		#SBATCH --mail-user=username@uga.edu # Where to send mail
	~~#PBS~~ -~~l nodes~~=~~1:ppn=1~~
	#~~PBS~~ -~~l walltime~~=~~24:00:00~~
	#~~PBS -l mem=10gb~~

	cd $~~PBS_O_WORKDIR~~		cd $SLURM_SUBMIT_DIR

			module load QIIME2/2020.11

	~~module load QIIME2/2020.6~~
	echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc		echo "backend: Agg" > ~/.config/matplotlib/matplotlibrc
	qiime [OPTIONS] COMMAND [ARGS]...		qiime [OPTIONS] COMMAND [ARGS]...
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	Example of job submission		Example of job submission
	<pre class="gcommand">		<pre class="gcommand">
	~~qsub~~ ./sub.sh		sbatch ./sub.sh
	</pre>		</pre>

Moses at 20:42, 7 May 2021

2021-05-07T20:42:11Z

← Older revision		Revision as of 16:42, 7 May 2021
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	*Version 2020.11 installed as a conda environment at /apps/eb/QIIME2/2020.11		*Version 2020.11 installed as a conda environment at /apps/eb/QIIME2/2020.11

	To use version ~~2018~~.8, please first load the module with		To use version 2019.10, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2018~~.8		module load QIIME2/2019.10
	</pre>		</pre>

	To use version ~~2018~~.11, please first load the module with		To use version 2020.2, please first load the module with

	<pre class="gscript">		<pre class="gscript">
	module load QIIME2/~~2018~~.11		module load QIIME2/2020.2
	~~</pre>~~

	~~To use version 2019.7, please first load the module with~~

	~~<pre class="gscript">~~
	~~module load qiime2/2019.7_conda~~
	</pre>		</pre>

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	</pre>		</pre>

			To use version 2020.11, please first load the module with

	~~Example of a shell script sub.sh to run qiime v2018.11 at the batch queue:~~
	~~<pre class="gscript">~~
	~~#!/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]...~~
	~~</pre>~~

	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:~~
	<pre class="gscript">		<pre class="gscript">
	~~#!/bin/bash~~		module load QIIME2/2020.11

	~~#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~~
	</pre>		</pre>

	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:		Example of a shell script sub.sh to run QIIME2 2020.11 at the batch queue:
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash

Moses at 20:38, 7 May 2021

2021-05-07T20:38:14Z

← Older revision		Revision as of 16:38, 7 May 2021
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
	~~Also refer to [[Running_Jobs_on_Sapelo2#Running_an_X-windows_application \| Run X window Jobs]] and~~
	~~[[Running_Jobs_on_Sapelo2#Running_an_Interactive_Job \| 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

			*Version 2019.10 installed as a conda environment at /apps/eb/QIIME2/2019.10
			*Version 2020.2 installed as a conda environment at /apps/eb/QIIME2/2020.2
			*Version 2020.6 installed as a conda environment at /apps/eb/QIIME2/2020.6
			*Version 2020.11 installed as a conda environment at /apps/eb/QIIME2/2020.11

	To use version 2018.8, please first load the module with		To use version 2018.8, please first load the module with

Moses at 20:33, 7 May 2021

2021-05-07T20:33:42Z

← Older revision		Revision as of 16:33, 7 May 2021
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	=== Version ===		=== Version ===

	~~v2019~~.10, ~~v2020~~.2 2020.6, ~~v2020~~.11		2019.10, 2020.2, 2020.6, 2020.11

	=== Author / Distributor ===		=== Author / Distributor ===