Description

From the LUMPY Home Page: A probabilistic framework for structural variant discovery.

Version

• 0.2.11

Authorized Users

• CIRCE account holders
• RRA account holders
• SC account holders

Platforms

• CIRCE cluster
• RRA cluster
• SC cluster

Modules

LUMPY requires the following module file to run:

• apps/lumpy/0.2.11

• See Modules for more information.

Running LUMPY on CIRCE/SC

The LUMPY 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.

Interactive Mode

Next, use the following commands to open an SRUN Interactive Session, load the module for LUMPY, and execute the LUMPY binary:

[user@login0 ~]$ srun --time=48:00:00 --nodes=1 --ntasks-per-node=1 --pty /bin/bash
[user@wh-520-4-1 ~]$ module load apps/lumpy/0.2.11
[user@wh-520-4-1 ~]$ lumpy \
    -mw 4 \
    -tt 0 \
    -pe id:sample,bam_file:sample.discordants.bam,histo_file:sample.lib1.histo,mean:500,stdev:50,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,min_mapping_threshold:20 \
    -sr id:sample,bam_file:sample.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20 \
    > sample.vcf

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.

If, for example, you wish to run lumpy with paired-end and split-reads, you would set up a submit script to use lumpy like this

#!/bin/bash
#
#SBATCH --job-name=lumpy-test
#SBATCH --time=01:00:00
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=output.%j.lumpy-test

#### SLURM 1 processor LUMPY test to run for 1 hours.

# Load the LUMPY module:
module load apps/lumpy/0.2.11

# Start LUMPY
lumpy \
  -mw 4 \
  -tt 0 \
  -pe id:sample,bam_file:sample.discordants.bam,histo_file:sample.lib1.histo,mean:500,stdev:50,read_length:101,min_non_overlap:101,discordant_z:5,back_distance:10,weight:1,min_mapping_threshold:20 \
  -sr id:sample,bam_file:sample.splitters.bam,back_distance:10,weight:1,min_mapping_threshold:20 \
  > sample.vcf

 
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 ./lumpy-test.sh

• You can view the status of your job with the “squeue -u <username>” command

Documentation

Home Page, User Guides, and Manuals

• LUMPY Home Page:
  • https://github.com/arq5x/lumpy-sv

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

• LUMPY scripts:
  • /apps/lumpy/0.2.11/script - script such as pairend_distro.py (make sure to add a python module when using this Python script)

More Job Information

See the following for more detailed job submission information:

• SLURM User’s Guide
• Scheduling and Dispatch Policies
• Advanced Submit Techniques

Reporting Bugs

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