Post date: Jun 29, 2016 10:55:35 PM
I am using mugsy to align the genomes (this is what I used for Lycaeides too). The submission script (below) and results are in (will be in) /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp.
#!/bin/sh
#SBATCH --time=120:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=30
#SBATCH --account=gompert-kp
#SBATCH --partition=gompert-kp
#SBATCH --job-name=mugsy
#SBATCH --mail-type=FAIL
#SBATCH --mail-user=zach.gompert@usu.edu
echo ------------------------------------------------------
echo ------------------------------------------------------
echo SLURM: job identifier is $SLURM_JOBID
echo SLURM: job name is $SLURM_JOB_NAME
echo ------------------------------------------------------
bash
source /uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsyenv.sh
cd /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp
/uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsy --directory /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/ --prefix mualnTcr /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version2/timema_06Jun2016_RvNkF.fasta /uufs/chpc.utah.edu/common/home/u6000989/data/timema/draft_genome/draft0.1/timemaGenome.fasta
early()
{
echo ' '
echo ' ############ WARNING: EARLY TERMINATION ############# '
echo ' '
}
exit