tandem-genotypes on Biowulf

tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome.


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 input in bold):

[user@biowulf]$ sinteractive
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 tandem-genotypes

[user@cn3144 ~]$ tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/nano.maf
# tandem-genotypes /usr/local/apps/tandem-genotypes/1.9.0/tests/microsat.txt /usr/local/apps/tandem-genotypes/1.9.0/tests/nano.maf
chr22	41994883	41994923	TG	.	.	-7,-6,-4,-3,-1,0,0,2,3,4,8	-16,-14,-12,-11,-11,-11,-9,-8,-7
[user@cn3144 ~]$ 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. tandem-genotypes.sh). For example:

set -e
module load tandem-genotypes
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/nano.maf > tg.txt

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] tandem-genotypes.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. tandem-genotypes.swarm). For example:

tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample1.maf > tg1.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample2.maf > tg2.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample3.maf > tg3.txt
tandem-genotypes $TANDEMGENOTYPES_HOME/tests/microsat.txt $TANDEMGENOTYPES_HOME/tests/sample4.maf > tg4.txt

Submit this job using the swarm command.

swarm -f tandem-genotypes.swarm [-g #] [-t #] --module tandem-genotypes
-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 tandem-genotypes Loads the tandem-genotypes module for each subjob in the swarm