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beast_snapp.sh
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#!/bin/bash -l
#SBATCH -D /home/dmvelasc/Projects/Prunus/Analysis/VCF_GATK/
#SBATCH -o /home/dmvelasc/Projects/Prunus/slurm-log/%j-stdout-snapp.txt
#SBATCH -e /home/dmvelasc/Projects/Prunus/slurm-log/%j-stderr-snapp.txt
#SBATCH -J snapp
#SBATCH -p med
#SBATCH -n 1
#SBATCH -c 16
#SBATCH -t 40-00:00:00
#SBATCH --mail-user=dmvelasco@ucdavis.edu
#SBATCH --mail-type=ALL
#SBATCH --mem=36G
set -e
set -u
# Load modules
module load java
# Declare directories
dir1="/home/dmvelasc/Software/beast/bin" # Beast binary directory
#dir2="/home/dmvelasc/Projects/Prunus/Analysis/VCF" # VCF directory
dir2="/home/dmvelasc/Projects/Prunus/Analysis/VCF_GATK" # VCF directory
# step 1
# convert nexus format to xml with beauti - convert locally
# could probably run beauti using srun and X11, below is command and error message
#dmvelasc@farm:~/Software/beast/bin$ ./beauti
#Exception in thread "main" java.awt.HeadlessException:
#No X11 DISPLAY variable was set, but this program performed an operation which requires it.
# at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:207)
# at java.awt.Window.<init>(Window.java:536)
# at java.awt.Frame.<init>(Frame.java:420)
# at java.awt.Frame.<init>(Frame.java:385)
# at beast.app.util.Utils6.startSplashScreen(Unknown Source)
# at beast.app.beauti.BeautiLauncher.main(Unknown Source)
# step 2
# run with beast/snapp
# attempting ingroup snippet
#"$dir1"/beast "$dir2"/snapptest_outgroup_2016-10-18.xml
# works without ingroup snippet
#"$dir1"/beast "$dir2"/snapptest_2016-10-18.xml # still works, even though snapptest_amyg_2016-10-24.xml did not
#"$dir1"/beast "$dir2"/snapptest_amyg_2016-10-24.xml
# had problems with amyg_2016-10-24 due to some issues with farm
# (patching and memory allocation)
# was producing errors that seemed java related, then apache related
# comparing xml files between snapptest_2016-10-18.xml and snapptest_amyg_2016-10-24.xml did not reveal obvious differences
#"$dir1"/beast "$dir2"/amygtest_2016-10-26.xml
# works; uses the same nexus file as snapptest_amyg_2016-10-24.xml just saved with a shorter name
# the name is somewhat perpetuated in some of the java tags, so perhaps that was the issue
# below 2016-11-03
#"$dir1"/beast "$dir2"/amyg3.xml
# below 2017-03-03
#"$dir1"/beast "$dir2"/snapp_amygtest4_final.xml
"$dir1"/beast "$dir2"/final14sept.xml