Biowulf High Performance Computing at the NIH
tRNAscan-SE on Biowulf

tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database


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 trnascna-se
[+] Loading trnascan-se  2.0.0  on cn0166 

[user@cn3144 ~]$ cp /usr/local/apps/trnascan-se/TEST_DATA/ExampleSequences.fa .

[user@cn3144 ~]$ tRNAscan-SE ExampleSequences.fa

tRNAscan-SE v.2.0 (December 2017) - scan sequences for transfer RNAs
Copyright (C) 2017 Patricia Chan and Todd Lowe
                   University of California Santa Cruz
Freely distributed under the GNU General Public License (GPLv3)

Sequence file(s) to search:        ExampleSequences.fa
Search Mode:                       Eukaryotic
Results written to:                Standard output
Output format:                     Tabular
Searching with:                    Infernal First Pass->Infernal
Isotype-specific model scan:       Yes
Covariance model:                  /usr/local/apps/trnascan-se/2.0.0/lib/tRNAscan-SE/models/
Infernal first pass cutoff score:  10

Temporary directory:               /tmp

Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan
Sequence		tRNA	Bounds	tRNA	Anti	Intron Bounds	Inf	      
Name    	tRNA #	Begin	End	Type	Codon	Begin	End	Score	Note
--------	------	-----	------	----	-----	-----	----	------	------
MySeq1  	1	13 	85 	Thr	TGT	0	0	78.0	
MySeq2  	1	6  	79 	Arg	TCT	0	0	75.1	
MySeq3  	1	14 	114	Ser	CGA	51	69	71.8	
MySeq4  	1	6  	88 	Leu	AAG	0	0	65.0	
MySeq5  	1	3  	89 	SeC	TCA	0	0	146.9	
MySeq6  	1	7  	92 	Lys	CTT	0	0	72.1	

[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. For example:

set -e
module load trnascan-se
tRNAscan-SE ExampleSequences.fa

Submit this job using the Slurm sbatch command.

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. trnascan-se.swarm). For example:

tRNAscan-SE ExampleSequences1.fa > out1.txt
tRNAscan-SE ExampleSequences2.fa > out2.txt
tRNAscan-SE ExampleSequences3.fa > out3.txt

Submit this job using the swarm command.

swarm -f trnascan-se.swarm --module trnascan-se
--module trnascan-se Loads the trnascan-se module for each subjob in the swarm