Update condenseTrees.sh

bpt26 · May 1, 2022 · 852568f · 852568f
1 parent 1247d5f
commit 852568f
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/4_simulated_data_experiments/scripts/4.8/condenseTrees.sh b/4_simulated_data_experiments/scripts/4.8/condenseTrees.sh
@@ -1,13 +1,13 @@
     usher -v ../../input/CUMULATIVE_VCFS/1.vcf -t "TREES/iteration_1/iter1.raxml.denovo.bestTree" -c -o "TREES/iteration_1/iter1.raxml.denovo.pb"
-    matUtils extract -i "TREES/iteration_1/iter1.raxml.denovo.pb" -R -O -o "TREES/iteration_1/iter1.raxml.denovo.COLLAPSED.pb" -T 15
+    matUtils extract -i "TREES/iteration_1/iter1.raxml.denovo.pb" -O -o "TREES/iteration_1/iter1.raxml.denovo.COLLAPSED.pb" -T 15
     matUtils extract -i "TREES/iteration_1/iter1.raxml.denovo.COLLAPSED.pb" -t "TREES/iteration_1/iter1.raxml.denovo.COLLAPSED.nwk" -T 15
 
 
     usher -v ../../input/CUMULATIVE_VCFS/2.vcf -t "TREES/iteration_2/iter2.raxml.denovo.lastTree.STOPPED_AFTER_2_WEEKS" -c -o "TREES/iteration_2/iter2.raxml.denovo.pb"
-    matUtils extract -i "TREES/iteration_2/iter2.raxml.denovo.pb" -R -O -o "TREES/iteration_2/iter2.raxml.denovo.COLLAPSED.pb" -T 15
+    matUtils extract -i "TREES/iteration_2/iter2.raxml.denovo.pb" -O -o "TREES/iteration_2/iter2.raxml.denovo.COLLAPSED.pb" -T 15
     matUtils extract -i "TREES/iteration_2/iter2.raxml.denovo.COLLAPSED.pb" -t "TREES/iteration_2/iter2.raxml.denovo.COLLAPSED.nwk" -T 15
 
 
     usher -v ../../input/CUMULATIVE_VCFS/3.vcf -t "TREES/iteration_3/iter3.raxml.denovo.lastTree.STOPPED_AFTER_2_WEEKS" -c -o "TREES/iteration_3/iter3.raxml.denovo.pb"
-    matUtils extract -i "TREES/iteration_3/iter3.raxml.denovo.pb" -R -O -o "TREES/iteration_3/iter3.raxml.denovo.COLLAPSED.pb" -T 15
+    matUtils extract -i "TREES/iteration_3/iter3.raxml.denovo.pb" -O -o "TREES/iteration_3/iter3.raxml.denovo.COLLAPSED.pb" -T 15
     matUtils extract -i "TREES/iteration_3/iter3.raxml.denovo.COLLAPSED.pb" -t "TREES/iteration_3/iter3.raxml.denovo.COLLAPSED.nwk" -T 15