QIIME

Description

From the QIIME home page: QIIME stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics.

Versions

  • Qiime 1.9.1
  • Qiime2 2019.10 (available on RHEL7 nodes only)

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

  • apps/qiime/1.9.1

or

  • apps/qiime2/2019.10

Running QIIME on CIRCE/SC

The QIIME user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.


Using Qiime2 with Q2Studio

In order to use Qiime2 Studio, you will need to start a SLURM Interactive session on a partition node with RHEL7. Follow the below example in order to get an srun session with X11 capabilities.

[user@itn0 ~]$ echo $DISPLAY
itn1.rc.usf.edu:121.0
[user@itn0 ~]$ srun --time=24:00:00 -p bgfsqdr --mem=16384 --nodes=1 --ntasks-per-node=8 --pty /bin/bash
[user@svc-3024-9-24 ~]$ export DISPLAY=itn1:121.0
[user@svc-3024-9-24 ~]$ module load apps/qiime2/2019.10
[user@svc-3024-9-24 ~]$ source activate qiime2-2019.10
(qiime2-2017.8) [user@svc-3024-9-24 ~]$ npm start --prefix /apps/qiime2/q2studio-2019.10.0

This will get start a session with 8 cpu cores on a single node with 16 GB of shared memory for 24 hours, and allow you to use the Qiime2 Studio interface.


How to Submit Jobs

The following directions pertain to Qiime 1.X. Similar batch job submissions are possible with Qiime2 as well. Please consult the Qiime2 User Guide (https://docs.qiime2.org/2019.10/) for command line options applicable to your job workflow.

Use a submit script like the following to run QIIME:

#!/bin/sh
#
#SBATCH --job-name=qiime-test
#SBATCH --time=01:00:00
#SBATCH --ntasks=8
#SBATCH --output=output.%j.NAMD-test

#### SLURM 8 processor QIIME test to run for 1 hour.

module purge
module load apps/qiime/1.9.1

mpirun parallel_align_seqs_pynast.py  -i INPUT_FASTA_FP -o OUTPUT_DIR

 
Next, you can change to your job’s directory, and run the sbatch command to submit the job:

[user@login0 ~]$ cd my/jobdir
[user@login0 jobdir]$ sbatch ./qiime-test.sh
  • You can view the status of your job with the “squeue -u <username>” command
  • Your submit scripts will vary depending on your individual needs. QIIME consists of many different python scripts. Additionally, using the “-h” flag after the script name will provide some information about it’s use. Only scripts with the “parallel_” prefix can be used with more than 1 processor. For all other scripts, the “mpirun” command can be removed from the above example.

Documentation

Home Page, User Guides, and Manuals

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with QIIME to the IT Help Desk: rc-help@usf.edu