All dbGaP data is stored on Isilon share mounted automatically when a user requests an interactive dbGaP session.
Step 1: Request an interactive session on Oscar on the dbGaP.
interact -q dbgap -n 20 -m 20g -t 01:00:00
Group membership fordbgap, dbg_PiLastName, dbg_import, dbg_export along with SLURM associations are required for working with dbGaP.
Step 2: Understand the dbGaP Data Hierarchy
The native GPFS file system (Home, Scratch, Data, Runtime) will be read-only access. All dbGaP related work must be done in the/dbGaProot directory. The /dbGaP directory has two sub-directories data & results . The downloaded datasets from the xfer server will be written to/dbgap/import/userand all output files will be written to the/dbgap/results/usernamedirectory. The hierarchy structure is:
psaluja@node1030:/dbGaP$ tree /dbGaP/
/dbGaP/
├── data
│ └── import
│ ├── group_1
│ ├── group_2
│ ├── user_1
| | ├── SRR10859003_1.fastq.gz
│ └── user_2
│ ├── SRR10859003_1.fastq.gz
│ ├── SRR10859003_2.fastq.gz
│ └── SRR10859003_3.fastq.gz
└── results
├── user_1
│ ├── job_script.sh
│ ├── slurm-145960.out
│ └── slurm-1445969.out
└── user_2
Step 3: Submitting a dbGaP batch jobs
Home, Scratch & Data will be in read-only mode only users must write their code files, batch scripts in their designated. Example batch script for dbGaP jobs
#!/bin/bash
# Request an hour of runtime:
#SBATCH --time=1:00:00
# Define Partition
#SBATCH -p dbgap
# Use 2 nodes with 8 tasks each, for 16 MPI tasks:
#SBATCH -N 2
#SBATCH --tasks-per-node=8
# Specify a job name:
#SBATCH -J dbGAP_analysis
# Specify an output file
#SBATCH -o /dbGaP/results/psaluja/slurm-%j.out
#SBATCH -e /dbGaP/results/psaluja/slurm-%j.err
# Run a command
module load sratoolkit/2.11.0
srun --mpi=pmix fasterq-dump --ngc your_file.ngc SRR1234567.sra
Any output files including SLURM out and err files must be written to /dbGaP/results directory.