XHLA

Description

From the xHLA web site: The Human Leukocyte Antigen (HLA) gene complex on human chromosome 6 is one of the most polymorphic regions in the human genome, and contributes in large part to the diversity of the immune system. Accurate typing of HLA genes with short read sequencing data has historically been difficult due to the sequence similarity between the polymorphic alleles. xHLA iteratively refines the mapping results at the amino acid level to achieve 99 to 100% 4-digit typing accuracy for both class I and II HLA genes, taking only about 3 minutes to process a 30X whole genome BAM file on a desktop computer.


Version

  • 1042017

Authorized Users

  • CIRCE account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • SC cluster

Modules

XHLA requires the following module file to run:

  • apps/xhla/1042017

Running XHLA on CIRCE/SC

The XHLA 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.

Batch Job submission

To run batch jobs on the CIRCE/SC cluster, users will need to submit their jobs to the scheduling environment if their jobs take more than 20 minutes to run on a standard PC.

For example, you can convert a FASTA file using 'diamond', and then run xHLA using python with the SLURM script below. This set is taken from the example data provided by the developer, and can be copied from the /apps/xhla/10.04.2017 directory.

#!/bin/bash
#SBATCH --job-name=test_xhla 
#SBATCH --output=output.%j.xhla-test
#SBATCH --nodes=1
#SBATCH --exclusive  ### required
#SBATCH --mem=8192
#SBATCH --time=01:00:00 


#### SLURM single node xhla test to run for 1 hour
##### using all processing cores available and 8GB of memory
##### the "--exclusive" flag is required for the multi-threaded 
##### processes to run correctly

# Unload all modules, then load the xHLA module:
module purge 
module add apps/xhla/1042017

diamond makedb --in hla.faa --db hla.dmnd

/usr/bin/time run.py --sample_id test --input_bam_path path_to_dir/test.bam --output_path test_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 ./test_xhla.sh
  • You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

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

  • XHLA Example Data
    • /apps/xhla/10.04.2017/data
    • /apps/xhla/10.04.2017/tests

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

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