HTGTS represents High-Throughput Genome-Wide Translocation Sequencing pipeline - provided by the Alt Lab

• http://robinmeyers.github.io/transloc_pipeline/thedocs.html

• Module Name: htgts (see the modules page for more information)
• Multithreaded

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive --mem=20g --cpus-per-task=6
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 htgts
[user@cn3144 ~]$ GENOME_DB=/fdb/htgts/genomes
[user@cn3144 ~]$ BOWTIE2_INDEXES=/fdb/htgts/genomes/bowtie2_indexes/hg19
[user@cn3144 ~]$ SPECIES=hg19
[user@cn3144 ~]$ cp -r /usr/local/apps/htgts/tutorial_data/ /data/$USER/
[user@cn3144 ~]$ cd /data/$USER/tutorial_data
[user@cn3144 ~]$ TranslocPreprocess.pl tutorial_metadata.txt preprocess/ --threads $SLURM_CPUS_PER_TASK --read1 pooled_R1.fastq.gz --read2 pooled_R2.fastq.gz
[user@cn3144 ~]$ TranslocWrapper.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK
[user@cn3144 ~]$ TranslocFilter.pl results/RAG1A_IR_SRep1/RAG1A_IR_SRep1.tlx results/RAG1A_IR_SRep1/RAG1A_IR_SRep1_filtered.tlx --filters "f.unaligned=1"
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. batch.sh). For example:

#!/bin/bash
set -e
module load htgts
TranslocPreprocess.pl tutorial_metadata.txt preprocess/ --threads $SLURM_CPUS_PER_TASK --read1 poole\
d_R1.fastq.gz --read2 pooled_R2.fastq.gz                                                                                     TranslocWrapper.pl tutorial_metadata.txt preprocess/ results/ --threads $SLURM_CPUS_PER_TASK
TranslocFilter.pl results/RAG1A_IR_SRep1/RAG1A_IR_SRep1.tlx results/RAG1A_IR_SRep1/RAG1A_IR_SRep1_fi\
ltered.tlx --filters "f.unaligned=1"

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=6 --mem=20g batch.sh

Create a swarmfile (e.g. job.swarm). For example:

cd dir1; TranslocPreprocess.pl...;TranslocWrapper.pl...;TranslocFilter.pl...
cd dir2; TranslocPreprocess.pl...;TranslocWrapper.pl...;TranslocFilter.pl...
cd dir3; TranslocPreprocess.pl...;TranslocWrapper.pl...;TranslocFilter.pl...

Submit this job using the swarm command.

swarm -f job.swarm -g 20 -t 6 --module htgts