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.
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
[user@biowulf]$ module avail bam2fastq ----------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------- bam2fastq/1.1.0 [user@biowulf]$ module load bam2fastq [user@biowulf]$ module list Currently Loaded Modulefiles: 1) bam2fastq/1.1.0 [user@biowulf]$ module unload bam2fastq [user@biowulf]$ module load bam2fastq/1.1.0 [user@biowulf]$ module list Currently Loaded Modulefiles: 1) bam2fastq/1.1.0 [user@biowulf]$ module show bam2fastq ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/bam2fastq/1.1.0: module-whatis Sets up bam2fastq 1.1.0 prepend-path PATH /usr/local/bam2fastq -------------------------------------------------------------------
1. Create a batch script along the following lines.
#!/bin/bash # This file is runbam2fastq # #PBS -N bam2fastq #PBS -m be #PBS -k oe module load bam2fastq cd /data/$USER/somewhereWithInputFile bam2fastq --aligned -o myfile.fastq myfile.bam
2. Submit the script using the 'qsub' command on Biowulf
Useful commands:
freen: see http://biowulf.nih.gov/user_guide.html#freen
qstat: search for 'qstat' on http://biowulf.nih.gov/user_guide.html for it's usage.
jobload: search for 'jobload' on http://biowulf.nih.gov/user_guide.html for it's usage.
Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.
Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:
bam2fastq /data/$USER/run1/myfile.bam bam2fastq /data/$USER/run2/myfile.bam bam2fastq /data/$USER/run3/myfile.bam [.....]
There are one flag of swarm that's required '-f'
By default, each line of the commands above will be executed on '1' processor core of a node and uses 1GB of memory. If this is not what you want, you will need to specify '-g' flags when you submit the job on biowulf.
Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:
[user@biowulf]$ swarm -g 10 --module bam2fastq -f cmdfile
--module: setup bam2fastq environmental variables for each swarm command
For more information regarding running swarm, see swarm.html
User 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.
[user@biowulf] $ qsub -I -l nodes=1
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready
[user@pXXX]$ cd /data/$USER/myruns
[user@pXXX]$ bam2fastq myfile.bam...........
[user@pXXX] exit
qsub: job 2236960.biobos completed
[user@biowulf]$ User may add property of node in the qsub command to request specific interactive node. For example, if you need a node with 24gb of memory to run job interactively, do this:
