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.

QIIME Web Site

Version

1.9.1

Authorized Users

CIRCE account holders

Platforms

CIRCE cluster

Running Jobs on the Cluster

Modules

Before running a job, you must first set up your environment properly. Here are the required module files:

apps/qiime/1.9.1

To run QIIME on the cluster, ensure that you use module add prior to using any executables. See Modules for more information.

How to Submit Jobs

Make sure to run your job from your $WORK directory. 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. More information about these scripts can be found on the QIIME website, listed in the Additional Documentation section below. 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.

Additional Documentation

QIIME Official Documentation
- http://qiime.org/documentation/index.html
QIIME Scripts
- http://qiime.org/scripts/index.html
- QIIME Tutorials
- http://qiime.org/tutorials/index.html

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

QIIME

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