Difference between revisions of "QIIME"
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''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. | ''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. | ||
{{AppStandardHeader|1.9.1|qiime}} | |||
== Running Jobs on the Cluster == | == Running Jobs on the Cluster == | ||
{{PleaseReadUserGuide}} | |||
{{SLURMAppParams}} | |||
=== How to Submit Jobs === | === How to Submit Jobs === | ||
Use a submit script like the following to run QIIME: | |||
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;"> | <pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;"> | ||
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#SBATCH --output=output.%j.NAMD-test | #SBATCH --output=output.%j.NAMD-test | ||
#### | #### SLURM 8 processor QIIME test to run for 1 hour. | ||
module purge | module purge | ||
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*You can view the status of your job with the “squeue -u <username>” command | *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 | *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}} | |||
*QIIME Home Page | |||
**http://qiime.org/index.html | |||
* QIIME Official Documentation | * QIIME Official Documentation | ||
** http://qiime.org/documentation/index.html | ** http://qiime.org/documentation/index.html | ||
{{BKETOR}} | |||
* QIIME Scripts | * QIIME Scripts | ||
** http://qiime.org/scripts/index.html | ** http://qiime.org/scripts/index.html |
Revision as of 19:27, 29 June 2016
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.
Version
- 1.9.1
Authorized Users
CIRCE
account holdersRRA
account holdersSC
account holders
Platforms
CIRCE
clusterRRA
clusterSC
cluster
Modules
QIIME requires the following module file to run:
apps/qiime/1.9.1
- See Modules for more information.
Running Jobs on the Cluster
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 $WORK directory!
- Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
How to Submit Jobs
Use a submit script like the following to run QIIME:
#!/bin/sh #SBATCH --job-name=qiime-test #SBATCH --time=01:00:00 #SBATCH --ntasks=8 #SBATCH --output=output.%j.NAMD-test #### SLURM 8 processor QIIME test to run for 1 hour. module purge module load apps/qiime/1.9.1 mpirun parallel_align_seqs_pynast.py -i INPUT_FASTA_FP -o OUTPUT_DIR
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
[user@login0 ~]$ 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
- QIIME Home Page
- QIIME Official Documentation
Benchmarks, Known Tests, Examples, Tutorials, and Other Resources
- QIIME Scripts
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