Biowulf High Performance Computing at the NIH
TransDecoder on Biowulf

TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.

TransDecoder identifies likely coding sequences based on the following criteria:

Documentation
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@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 TransDecoder
[user@cn3144 ~]$ cp $TRANSDECODERHOME/sample_data/* .
[user@cn3144 ~]$ ./runMe.sh

[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. TransDecoder.sh). For example:

#!/bin/bash
module load TransDecoder
cufflinks_gtf_genome_to_cdna_fasta.pl transcripts.gtf test.genome.fasta > transcripts.fasta

Submit this job using the Slurm sbatch command.

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

TransDecoder.LongOrfs -t target_transcripts1.fasta
TransDecoder.LongOrfs -t target_transcripts2.fasta
TransDecoder.LongOrfs -t target_transcripts3.fasta
TransDecoder.LongOrfs -t target_transcripts4.fasta

Submit this job using the swarm command.

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