Create run_stats.sh

fst_analysis/run_stats.sh

@@ -0,0 +1,48 @@
+#Script written by Steven Van Belleghem
+
+#!/bin/bash -l 
+#SBATCH --cluster=genius 
+#SBATCH --job-name bwa 
+#SBATCH --nodes=1 
+#SBATCH --ntasks-per-node=10 
+#SBATCH --time=20:00:00 
+#SBATCH -A lp_svbelleghem
+
+# This variable will store the job array number minus 1, so we can use it to get a sample from the samples list (index starts at 0)
+ID=$((SLURM_ARRAY_TASK_ID -1))
+
+
+# Load the programs we will use
+module load Python/3.7.0-foss-2018a
+#module load tabix
+export PYTHONPATH=$PYTHONPATH:/vsc-hard-mounts/leuven-data/350/vsc35085/programs/genomics_general
+
+#REFNAME=dudPrim
+REFNAME=nieuPrim
+
+chrom=1
+
+echo "================="
+
+
+#9
+pop1=(B_NIE_T F_GUE_T P_AVE_T S_HUE_T B_HEI_2000 E_SEV_T)
+pop2=(B_DUD_S F_GUE_S P_AVE_S S_COT_S B_HEI_2018 F_CAM_S)
+
+
+#python /vsc-hard-mounts/leuven-data/350/vsc35085/programs/genomics_general/popgenWindows.py -w 50000 -s 50000 -m 500 --minData 0.1 \
+#-g /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$chrom.calls.gz \
+#-o /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$chrom.stats_$(echo "${pop1[ID]}")_$(echo "${pop2[ID]}")_w50000_s50000.csv.gz \
+#-f phased -T 8 \
+#-p $(echo "${pop1[ID]}") \
+#-p $(echo "${pop2[ID]}") \
+#--popsFile /vsc-hard-mounts/leuven-data/350/vsc35085/scripts/Pogonus_pops_batchALL.txt 
+
+python /vsc-hard-mounts/leuven-data/350/vsc35085/programs/genomics_general/popgenWindows_egglib.py -w 50000 -s 50000 --minSites 1000 --maxMissing 0.25 \
+-T 10 --windType coordinate -f phased \
+-g /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$chrom.H.calls.gz \
+--popsFile /vsc-hard-mounts/leuven-data/350/vsc35085/scripts/Pogonus_pops_batchALL.txt \
+-o /lustre1/scratch/350/vsc35085/Maria/Pogonus_reseqALL_$REFNAME.chr_$chrom.stats_$(echo "${pop1[ID]}")_$(echo "${pop2[ID]}")_w50000_s50000_eggStats.stats \
+-p $(echo "${pop1[ID]}") \
+-p $(echo "${pop2[ID]}") \
+-eggB FstWC,Dxy -eggW S,Pi,thetaW,D