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Long Ranger

Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants.

Long Ranger is available as a module on Apocrita.

Usage

To run the default installed version of Long Ranger, simply load the longranger module:

$ module load longranger
$ longranger
longranger (<VERSION>)
Copyright (c) 2017 10x Genomics, Inc.  All rights reserved.
-------------------------------------------------------------------------------

Usage:
    longranger mkfastq
    longranger demux
...

For more information regarding each analysis pipeline, pass the --help switch after the pipeline sub-command (i.e. longranger wgs --help).

Example jobs

Running Long Ranger in cluster mode

To run Long Ranger jobs on Apocrita, pass the --jobmode=sge switch. This will make the underlying Martian pipeline framework launch each stage through the scheduler qsub command.

As stages' jobs are queued, launched, and completed, the pipeline framework will track their states using the metadata files that each stage maintains in the pipeline output directory.

We have configured a template (located at: /share/apps/centos7/longranger/<VERSION>/martian-cs/2.1.2/jobmanagers/ sge.template) with the default settings:

  • Bash Shell -S "/bin/bash"
  • Single Machine Processing PE -pe smp
  • 240 hours run time -l h_rt=240:0:0
  • Execution in the current working directory -cwd

The above settings will be used per job, so each stage will have a 240 hour runtime.

Core Requests and Consumption

The number of cores required is determined by the pipeline framework stage however, Martian jobs will run with only 1 thread.

Memory Requests and Consumption

To specify the memory-per-core resource (h_vmem), pass the --mempercore switch. This value will be used at all pipeline framework stages.

Serial job

Here is an example job running with 1 core and 1GB of memory, to submit each stage (with 4GB per core):

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load longranger

longranger wgs --id 1234 --fastqs raw_data.fastq \
               --reference /share/apps/centos7/longranger/<VERSION>/reference_data/GRCh38 \
               --sample 1234 \
               --jobmode=sge --mempercore=4

Long Ranger can also be submitted from within a qlogin session; replace <COMMAND> with the actual command to be executed (see example above).

qlogin -pe smp 1 -l h_vmem=1G -l h_rt=1:0:0 -j y
module load longranger
longranger <COMMAND>

Chromium references

Chromium references are available at: /share/apps/centos7/longranger/<VERSION>/reference_data.

Reference