This pipeline is designed for automated end-to-end quality control and processing of ATAC-seq or DNase-seq data. The installation mode of the pipeline on our system prevents the pipeline from running in cluster mode which means parallelization only happens within a single job - the pipeline cannot submit subjobs to slurm.
This pipeline has been deprecated and is being replaced with the WDL based Encode ATAC-seq pipeline.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem=30g --cpus-per-task=16 --gres=lscratch:100 salloc.exe: Pending job allocation 46116226 salloc.exe: job 46116226 queued and waiting for resources salloc.exe: job 46116226 has been allocated resources salloc.exe: Granted job allocation 46116226 salloc.exe: Waiting for resource configuration salloc.exe: Nodes cn3144 are ready for job [user@cn3144 ~]$ module load atac_dnase_pipelines [user@cn3144 ~]$ cd /lscratch/$SLURM_JOB_ID [user@cn3144 ~]$ cp -L ${ATAC_DNASE_PIPELINES_TEST_DATA}/*.fastq.gz . [user@cn3144 ~]$ tree . |-- ENCFF141NYG.fastq.gz `-- ENCFF566LXM.fastq.gz
These files are PE100nt ENCODE ATAC-Seq data for human thoracic aorta (sample ENCFF566LXM). After setting up the test data, run the pipeline with
[user@cn3144 ~]$ atac_dnase_pipelines -species hg19 -nth $SLURM_CPUS_PER_TASK \ -type atac-seq \ -fastq1_1 ENCFF566LXM.fastq.gz \ -fastq1_2 ENCFF141NYG.fastq.gz \ -auto_detect_adapter \ -ENCODE3 [...snip...] [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
This run will take several hours.
Create a batch input file (e.g. atac_dnase_pipelines.sh), which uses the input file 'atac_dnase_pipelines.in'. For example:
#!/bin/bash # this file is atac_test.sh module load atac_dnase_pipelines || exit 1 cd /lscratch/$SLURM_JOB_ID cp ${ATAC_DNASE_PIPELINES_TEST_DATA}/*.fastq.gz . echo "START: $(date)" atac_dnase_pipelines -species hg19 -nth $SLURM_CPUS_PER_TASK \ -type atac-seq \ -fastq1_1 ENCFF566LXM.fastq.gz \ -fastq1_2 ENCFF141NYG.fastq.gz \ -auto_detect_adapter \ -ENCODE3 echo "END: $(date)"
Submit this job using the Slurm sbatch command.
sbatch --cpus-per-task=16 --mem=40g --time=24:00:00 --gres=lscratch:50 atac_test.sh
Create a swarmfile (e.g. atac_dnase_pipelines.swarm). For example:
atac_dnase_pipelines -species hg19 -nth $SLURM_CPUS_PER_TASK \ -type atac-seq \ -fastq1_1 sample1_R1.fastq.gz \ -fastq1_2 sample1_R2.fastq.gz \ -auto_detect_adapter \ -ENCODE3 atac_dnase_pipelines -species hg19 -nth $SLURM_CPUS_PER_TASK \ -type atac-seq \ -fastq1_1 sample2_R1.fastq.gz \ -fastq1_2 sample2_R2.fastq.gz \ -auto_detect_adapter \ -ENCODE3 atac_dnase_pipelines -species hg19 -nth $SLURM_CPUS_PER_TASK \ -type atac-seq \ -fastq1_1 sample3_R1.fastq.gz \ -fastq1_2 sample3_R2.fastq.gz \ -auto_detect_adapter \ -ENCODE3
Submit this job using the swarm command.
swarm -f atac_dnase_pipelines.swarm -g 40 -t 16 --gres=lscratch:50 --time=24:00:00 --module atac_dnase_pipelines