Difference between revisions of "QIIME"

From arccwiki
Jump to: navigation, search
 
Line 13: Line 13:
 
* We are still learning to what extent qiime2 is parallelized. At this moment we ''believe'' that it can only run on a single node. ''Some'' plugins can make use of multiple cores on that node, which can be found by reading the documentation relating to that plugin. Since there is no consistent syntax across the plugins on how to make use of this, if you can not work it out yourself please contact ARCC and we'll be happy to help.
 
* We are still learning to what extent qiime2 is parallelized. At this moment we ''believe'' that it can only run on a single node. ''Some'' plugins can make use of multiple cores on that node, which can be found by reading the documentation relating to that plugin. Since there is no consistent syntax across the plugins on how to make use of this, if you can not work it out yourself please contact ARCC and we'll be happy to help.
 
* If the usage of the software increases and the demand warrants the managing of central reference database then ARCC is happy to discuss and explore.
 
* If the usage of the software increases and the demand warrants the managing of central reference database then ARCC is happy to discuss and explore.
 +
* The version of qiime2 installed on Teton has been built using the Singularity container and NOT Conda. Moving forward, we will explore updating new versions with Conda which is inline with the ''typical'' Conda installation process. The current implication is that any online articles that talk about using Conda will NOT work.
 
* If and when things change, we will update this page.
 
* If and when things change, we will update this page.
  

Latest revision as of 14:11, 7 November 2019

QIIME Quantitative Insights Into Microbial Ecology

  • Automatically track your analyses with decentralized data provenance — no more guesswork on what commands were run!
  • Interactively explore your data with beautiful visualizations that provide new perspectives.
  • Easily share results with your team, even those members without QIIME 2 installed.
  • Plugin-based system — your favorite microbiome methods all in one place.

Manual: 2019.1

Notes:

  • ARCC currently does not monitor current/latest versions of software. If you require an update to a version please remember to put a request in.
  • Qiime2 does have a collection of plugins. The ones available can be seen by typing qiime from the command line once the module has been loaded, as shown below. If you require a plugin not listed please put a request into ARCC and we can explore how best to make this available.
  • We are still learning to what extent qiime2 is parallelized. At this moment we believe that it can only run on a single node. Some plugins can make use of multiple cores on that node, which can be found by reading the documentation relating to that plugin. Since there is no consistent syntax across the plugins on how to make use of this, if you can not work it out yourself please contact ARCC and we'll be happy to help.
  • If the usage of the software increases and the demand warrants the managing of central reference database then ARCC is happy to discuss and explore.
  • The version of qiime2 installed on Teton has been built using the Singularity container and NOT Conda. Moving forward, we will explore updating new versions with Conda which is inline with the typical Conda installation process. The current implication is that any online articles that talk about using Conda will NOT work.
  • If and when things change, we will update this page.

Module: Example

[]$ [salexan5@tlog1 ~]$ module spider qiime2

-----------------------------------
  qiime2:
-----------------------------------
     Versions:
        qiime2/2017.10
        qiime2/2019.1

-----------------------------------
  For detailed information about a specific "qiime2" module (including how to load the modules) use the module's full name.
  For example:
-----------------------------------
<pre>
[]$ module load qiime2/2019.1

[]$ 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.

Using:

After logging onto teton either:
1) Create an interactive session: In the example below change arcc to your project name, and modify the time you think you need, the example below is set for 60 minutes.

[...@tlog1 qiime2]$ salloc --account=arcc --time=60:00
salloc: Granted job allocation 3489587

[...@m067 qiime2]$ 
[...@m067 qiime2]$ module load qiime2/2019.1

[...@m067 qiime2]$ qiime feature-table filter-samples \
        --i-table data/R1-5_table_forwards.qza \
        --m-metadata-file data/metadata_R1-5.txt \
        --p-where "GroupStatus='JLinfected' OR GroupStatus='JLcontrol'" \
        --o-filtered-table data/output_results.qza


2) Submit a job: Below is an example of a batch file:

#!/bin/bash
#SBATCH --account=arcc
#SBATCH --time=00:30:00
#SBATCH --nodes=1
#SBATCH --mem=0
#SBATCH --output=qiime_%A.out
#SBATCH --chdir=/project/arcc/salexan5/qiime2

module load qiime2/2019.1

qiime feature-table filter-samples \
        --i-table data/R1-5_table_forwards.qza \
        --m-metadata-file data/metadata_R1-5.txt \
        --p-where "GroupStatus='JLinfected' OR GroupStatus='JLcontrol'" \
        --o-filtered-table data/output_results.qza

wait


Back to HPC Installed Software