The nci-dragen partition as of January 2024 includes one dragen server. It has been funded by NCI/CBIIT until the end of FY 2027
Notes:
nci_dragen_turbo
QOS
or 8h (other users)/staging
disk partition./staging/human
Create a batch script similar to the following:
#! /bin/bash # set up paths etc source /etc/profile.d/edico.sh RUNPATH=/fdb/app_testdata/fastq/Homo_sapiens RUNFOLDER=SRR24373805 ANALYSIS="/staging/${RUNFOLDER}-$(date +%s)" METRICS=${ANALYSIS}/Results/MetricsOutput.tsv RESULTPATH=${PWD}/${RUNFOLDER}-dragen-results # clean up after run trap 'rm -rf "/staging/${RUNFOLDER}" "${ANALYSIS}"' EXIT cp -r "${RUNPATH}/${RUNFOLDER}" /staging || exit 100 mkdir -p "${ANALYSIS}" || exit 101 #load reference for your analysis, for DNA, RNA, CNV, and HLA analysis, use dragen -l -r /staging/human/hg38 #for Methylation analysis, use #dragen -l -r /staging/human/hg38/hg38.fa.single_pass.Methylation # Running a RNA pipeline with dragen dragen -r /staging/human/hg38 \ -1 /staging/${RUNFOLDER}/SRR24373805_1.fastq.gz \ -2 /staging/${RUNFOLDER}/SRR24373805_2.fastq.gz \ -a /staging/human/hg38/genes.gtf \ --output-dir ${ANALYSIS} \ --output-file-prefix RNA_test \ --enable-rna true \ --enable-rna-gene-fusion true \ --RGID rg \ --RGSM sm \ --enable-rna-quantification=true # copy results back to working directory cp -r "${ANALYSIS}" "${RESULTPATH}" || exit 103
And submit with
[user@biowulf]$ sbatch --mem=0 --partition nci-dragen --qos=nci_dragen_turbo dragen.sh 12345678
Note that the $ANALYSIS
folder is lager than the input
with Logs_Intermediates
taking up most the space. The script
above could be modified to only transfer a subset of files back to shared
storage.
Please send questions and comments to staff@hpc.nih.gov