BAM-format files are used to store alignment information and unaligned reads from next-generation sequencing machines. This tool is intended to extract raw sequences (with qualities) from a BAM file.
module load bam2fastq cd /data/$USER/somewhereWithInputFile bam2fastq --aligned -o myfile.fastq myfile.bam
1. Create a batch script along the following lines.
#!/bin/bash echo "Running on $SLURM_CPUS_PER_TASK cores" env module load bam2fastq cd /data/$USER/somewhereWithInputFile bam2fastq --aligned -o myfile.fastq myfile.bam
2. Submit the script on Biowulf
$ sbatch myscript
Submitting a swarm of jobs
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:
bam2fastq /data/$USER/run1/myfile.bam bam2fastq /data/$USER/run2/myfile.bam bam2fastq /data/$USER/run3/myfile.bam [.....]
Submit on biowulf:
swarm -f swarmfile --module bam2fastq
-f: specify swarm file.
--module: setup bam2fastq environmental variables for each swarm command
Sometimes, bam2fastq may require that input files contain the hash or pound character '#'. If this is the case, please also include the swarm option --no-comment. Otherwise, swarm will interpret anything following the '#' character as a comment and will delete it.
If more memory is required, use -g flag:$ swarm -g 10 --module bam2fastq -f cmdfile
For more information regarding running swarm, see swarm.html
Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.
biowulf $ sinteractive [user@pXXXX]$ cd /data/$USER/myruns
[user@pxxx]$ module load bam2fastq
[user@pxxx]$ bam2fastq --aligned -o myfile.fastq myfile.bam
[user@pxxx] exit
The command 'sinteractive' has several options:
$ sinteractive -h
