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ScanIndel on Biowulf

ScanIndel is a small python program that ties together a number of third party tools to detect indels. From the ScanIndel GitHub page:

ScanIndel is a python program to detect indels (insertions and deletions) from NGS data by re-align and de novo assemble soft clipped reads.

References:

  • R. Yang, A. C. Nelson, C. Henzler, B. Thyagarajan, and K. A. Silverstein. ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly. Genome Medicine 2015, 7:127. Pubmed |  PMC |  Journal
Documentation
Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

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

[user@biowulf]$ sinteractive --gres=lscratch:10 --mem=30g --cpus-per-task=8
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 scanindel
[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp -r $SCANINDEL_TEST_DATA .
[user@cn3144]$ cd example
[user@cn3144]$ mkdir hg19
[user@cn3144]$ ln -s /fdb/genomebrowser/gbdb/hg19/hg19.2bit hg19
[user@cn3144]$ cat input_data/config.txt
#name=path
bwa=/fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa
blat=hg19
freebayes=/fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/genome.fa
[user@cn3144]$ ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample.txt
...
[user@cn3144]$ ls -lh
...
-rw-r--r-- 1 user group 8.4K May 21 14:27 test.assembly.indel.vcf
-rw-r--r-- 1 user group  868 May 21 14:27 test.contigs.bam
-rw-r--r-- 1 user group  28K May 21 14:27 test.contigs.bam.bai
-rw-r--r-- 1 user group 8.4K May 21 14:27 test.mapping.indel.vcf
-rw-r--r-- 1 user group    0 May 21 14:27 test.merged.indel.vcf
-rw-r--r-- 1 user group 160K May 21 14:26 test.reads.bam
-rw-r--r-- 1 user group  29K May 21 14:26 test.reads.bam.bai

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Batch job
Most jobs should be run as batch jobs.

Create a batch input file (e.g. ScanIndel.sh) similar to the following example:

#! /bin/bash

module load scanindel/1.3 || exit 1
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample.txt

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=8 --mem=30g ScanIndel.sh
Swarm of Jobs
A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

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

ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample1.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample2.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample3.txt
ScanIndel.py -F 0 -p input_data/config.txt -i input_data/sample4.txt

Submit this job using the swarm command.

swarm -f ScanIndel.swarm -g 30 -t 8 --module ScanIndel/1.3
where
-g # Number of Gigabytes of memory required for each process (1 line in the swarm command file)
-t # Number of threads/CPUs required for each process (1 line in the swarm command file).
--module ScanIndel Loads the ScanIndel module for each subjob in the swarm