Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Allocate an interactive session and run the program. Sample session:
[user@biowulf]$ sinteractive --mem 5g 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 trf [+] Loading trf, version 4.09... [user@cn3144 ~]$ trf \ /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \ 2 `# match weight` \ 7 `# mismatch penalty` \ 7 `# indel penalty` \ 80 `# match probability` \ 10 `# indel probability` \ 50 `# minimum alignment score to report` \ 500 `# maximum period size to report` \ -f `# record flanking sequence` \ -d `# produce detailed data file` \ -m `# generate a masked sequence file` \ -l 6 `# longest tandem repeat array expected (in Mbp)` Tandem Repeats Finder, Version 4.09 Copyright (C) Dr. Gary Benson 1999-2012. All rights reserved. Loading sequence... Allocating Memory... Initializing data structures... Computing TR Model Statistics... Scanning Sequence 1... Freeing Memory... Resolving output... Done. Loading sequence file... Allocating Memory... Initializing data structures... Computing TR Model Statistics... ... .................... ..................... ..................... [user@cn3144 ~]$ exit salloc.exe: Relinquishing job allocation 46116226 [user@biowulf ~]$
Create a batch input file (e.g. trf.sh). For example:
#!/bin/sh module load trf || exit 1 trf \ /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \ 2 `# match weight` \ 7 `# mismatch penalty` \ 7 `# indel penalty` \ 80 `# match probability` \ 10 `# indel probability` \ 50 `# minimum alignment score to report` \ 500 `# maximum period size to report` \ -f `# record flanking sequence` \ -d `# produce detailed data file` \ -m `# generate a masked sequence file` \ -l 6 `# longest tandem repeat array expected (in Mbp)`
Submit this job using the Slurm sbatch command.
sbatch --mem 5g --time 4:00:00 trf.sh
Create a swarmfile (e.g. trf.swarm). For example:
cd sample1 && trf sample1.fa 2 7 7 80 10 50 500 -f -d -m cd sample2 && trf sample2.fa 2 7 7 80 10 50 500 -f -d -m cd sample3 && trf sample3.fa 2 7 7 80 10 50 500 -f -d -m cd sample4 && trf sample4.fa 2 7 7 80 10 50 500 -f -d -m
Submit this job using the swarm command.
swarm -f trf.swarm [-g #] [-t #] --module trfwhere
| -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 trf | Loads the trf module for each subjob in the swarm |