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• Module Name: stampy (see the modules page for more information)
• stampy is a multithreaded application. Please make sure to match the number of threads with the number of allocated CPUs.
• Example files in $STAMPY_TEST_DATA

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

[user@biowulf]$ sinteractive --cpus-per-task=4 --gres=lscratch:10
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 stampy samtools
[user@cn3144]$ cd /lscratch/$SLURM_JOB_ID
[user@cn3144]$ cp $STAMPY_TEST_DATA/* .
[user@cn3144]$ ls -lh
total 68M
-rw-r--r-- 1 user group 56M Jun 21 08:54 ERR458495.fastq.gz
-rwxrwxr-x 1 user group 12M Jun 21 08:54 sacCer3.fa

Build a genome and a hash file

[user@cn3144]$ stampy.py -G sacCer3 \
           --species Saccharomyces_cerevisiae \
           --assembly sacCer3 sacCer3.fa
stampy: Building genome...
stampy: Input files: ['sacCer3.fa']
stampy: Done
[user@cn3144]$ stampy.py -g sacCer3 -H sacCer3
stampy: Building hash table...
stampy: Initializing...
stampy: Counting...
stampy: Initializing hash...         
stampy: Flagging high counts...           
stampy: Creating hash...            
stampy: Writing...                  
stampy: Finished building hash table
stampy: Done

[user@cn3144]$ ls -lh
total 87M
-rw-r--r-- 1 user group  56M Jun 21 08:54 ERR458495.fastq.gz
-rwxrwxr-x 1 user group  12M Jun 21 08:54 sacCer3.fa
-rw-r--r-- 1 user group  16M Jun 21 08:58 sacCer3.sthash
-rw-r--r-- 1 user group 2.9M Jun 21 08:58 sacCer3.stidx

Align single end data

[user@cn3144]$ stampy.py -t $SLURM_CPUS_PER_TASK -g sacCer3 -h sacCer3 -M ERR458495.fastq.gz \
                      | samtools sort -@2 -T ./test -o test.bam
stampy: Mapping...
stampy: # Nucleotides (all/1/2):        52874862        52874862        0
stampy: # Variants:                     329629  329629  0
stampy: # Fraction:                     0.0062  0.0062  0.0000
stampy: Done

End the sinteractive session

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

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

#! /bin/bash

module load stampy/1.0.31 samtools/1.8 || exit 1
stampy.py -g sacCer3 -h sacCer3 -t $SLURM_CPUS_PER_TASK -M ERR458495.fastq.gz \
  | samtools sort -T /lscratch/$SLURM_JOB_ID/test -@2 -m1g -o test.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --mem=4g --gres=lscratch:10 stampy.sh

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

stampy.py -g sacCer3 -h sacCer3 -t $SLURM_CPUS_PER_TASK -M sample1.fastq.gz \
  | samtools sort -T /lscratch/$SLURM_JOB_ID/sample -@2 -m1g -o sample1.bam
stampy.py -g sacCer3 -h sacCer3 -t $SLURM_CPUS_PER_TASK -M sample2.fastq.gz \
  | samtools sort -T /lscratch/$SLURM_JOB_ID/sample -@2 -m1g -o sample2.bam
stampy.py -g sacCer3 -h sacCer3 -t $SLURM_CPUS_PER_TASK -M sample3.fastq.gz \
  | samtools sort -T /lscratch/$SLURM_JOB_ID/sample -@2 -m1g -o sample3.bam

Submit this job using the swarm command.

swarm -f stampy.swarm -g 4 -t 4 --gres=lscratch:10 --module stampy/1.0.32,samtools/1.8