fastQValidator on Biowulf
The fastQValidator validates the format of fastq files.
Programs Location
/usr/local/fastQValidator_biowulf/bin
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.
Submitting a single batch job
1. Create a script file. Sample batch script file
#!/bin/bash # This file is Script # #PBS -N fastqvalidator #PBS -m be #PBS -k oe cd /data/user/mydir fastqvalidator commands
2. Submit the script using the 'qsub' command on Biowulf, with, for example:
$ qsub -l nodes=1 ./script
Running an interactive job
Users may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node.
Allocate an interactive node as described below, and run the interactive job there.
biowulf% qsub -I -l nodes=1
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready
[user@pxxx]$ cd YourDir
[user@pxxx]$ fastqvalidator command here
[user@pxxx]$ exit
qsub: job 2236960.biobos completed
[user@biowulf ~]$
Documentation
