tandem-genotypes on Biowulf
tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome.
References:
- Mitsuhashi, S., Frith, M.C., Mizuguchi, T. et al. Tandem-genotypes: robust detection of tandem repeat expansions from long DNA reads. Genome Biol 20, 58 (2019).
Documentation
Important Notes
- Module Name: tandem-genotypes (see the modules page for more information)
- This application produces plots via the tandem-genotypes-plot command. You can use hpcdrive to view them on your local workstation.
- Environment variables set
- TANDEMGENOTYPES_HOME
- Example files in $TANDEMGENOTYPES_HOME/tests
Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.
Allocate an interactive session and run the program.
Sample session (user input in bold):
[user@biowulf]$ 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:
#!/bin/bash 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-genotypeswhere
| -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 |