Post date: Dec 27, 2016 10:5:38 PM
We now have a second assembly of the green morph genome that was generated from de novo sequencing of shotgun and Chicago libraries. This was done to improve the previous dovetail green morph assembly (see here). The new assembly and associated files are in /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_denovo. The actual genome fasta file is:
/uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_denovo/timema_green_22Dec2016_ycYxT
Summaries of the dark and green morph assemblies (provided by Victor) are here: https://drive.google.com/open?id=0Bw2usUasVLJET0ZwZFdzWXlJSTQ
I am again using Mugsy to align this to the dark morph genome (as we did here).
The comparative alignment will be here:
/uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/
The execution script is in the same directory and is mugsyDarKGreenDec16.sh. It is included below.
#!/bin/sh
#SBATCH --time=240:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=24
#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 /scratch/general/lustre/gompMugsy/
/uufs/chpc.utah.edu/common/home/u6000989/source/mugsy_x86-64-v1r2.3/mugsy --directory /scratch/general/lustre/gompMugsy --prefix mualnTcrBrwGrnDec16 /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/version3/timema_06Jun2016_RvNkF702.fasta /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/timema_green_denovo/timema_green_22Dec2016_ycYxT/timema_green_22Dec2016_ycYxT.fasta
mv ./* /uufs/chpc.utah.edu/common/home/u6000989/data/timema/tcrDovetail/MugsyComp/