• GitLab

• Module Name: tantan (see the modules page for more information)
• Example files in $TANTAN_TEST_DATA

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 tantan
[user@cn3144]$ # mask repetitive regions with lower case letters (DNA)
[user@cn3144]$ tantan $TANTAN_TEST_DATA/CM001971.fa > test.fa
[user@cn3144]$ head -n6 test.fa
>CM001971.1 Homo sapiens mitochondrion, complete sequence, whole genome shotgun sequence
CAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGT
ATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCC
GGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATT
ATTTATCGCACCTACGTTCAATATTACAGACGAACATACTTACTAAAGCG
TGTTAATtaattaaTGCTTGTAGGACATAATAATAACAATTGAATGTCTG
       |-----| masked region
[user@cn3144]$ # same, but replace with 'N' insead
[user@cn3144]$ tantan -x N $TANTAN_TEST_DATA/CM001971.fa > test.fa
[user@cn3144]$ head -n6 test.fa
>CM001971.1 Homo sapiens mitochondrion, complete sequence, whole genome shotgun sequence
CAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGT
ATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCC
GGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATT
ATTTATCGCACCTACGTTCAATATTACAGACGAACATACTTACTAAAGCG
TGTTAATNNNNNNNTGCTTGTAGGACATAATAATAACAATTGAATGTCTG
       |-----| masked region

[user@cn3144]$ # and for proteins
[user@cn3144]$ tantan -p $TANTAN_TEST_DATA/NP_002102.fa > test.fa
[user@cn3144]$ head -n3 test.fa
>NP_002102.4 huntingtin [Homo sapiens]
MATLEKLMKAFESLKSFQqqqqqqqqqqqqqqqqqqqqqqpppppppppp
pqlpqpppqaqpllpqpqppppppppppgpavaEEPLHRPKKELSATKKD

[user@cn3144]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf]$

Create a batch input file (e.g. tantan.sh) similar to the following example:

#! /bin/bash

module load tantan/13 || exit 1
tantan -p human_genome.fa > human_genome_masked.fa

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=2 --mem=4g tantan.sh

Create a swarmfile (e.g. tantan.swarm). For example:

tantan -p seq1.fa > seq1_masked.fa
tantan -p seq2.fa > seq2_masked.fa
tantan -p seq3.fa > seq3_masked.fa

Submit this job using the swarm command.

swarm -f tantan.swarm -g 2 -t 1 -p 2 --module tantan/13