Optimization grid search updated with the latest version of InstaNexus

Author: marcoreverenna

grid_master.log

@@ -3,69 +3,24 @@
 ========================================
 >>> [greedy] Launching: ma1 (Chain: 'light')
 >>> [greedy] Launching: ma1 (Chain: 'heavy')
->>> [greedy] Launching: ma2 (Chain: 'light')
->>> [greedy] Launching: ma2 (Chain: 'heavy')
->>> [greedy] Launching: ma3 (Chain: 'light')
->>> [greedy] Launching: ma3 (Chain: 'heavy')
 >>> [greedy] Launching: nb1 (Chain: '')
->>> [greedy] Launching: nb2 (Chain: '')
->>> [greedy] Launching: nb3 (Chain: '')
->>> [greedy] Launching: nb4 (Chain: '')
->>> [greedy] Launching: nb5 (Chain: '')
->>> [greedy] Launching: nb6 (Chain: '')
->>> [greedy] Launching: nb7 (Chain: '')
->>> [greedy] Launching: nb8 (Chain: '')
->>> [greedy] Launching: nb9 (Chain: '')
->>> [greedy] Launching: nb10 (Chain: '')
 >>> [greedy] Launching: bsa (Chain: '')
 >>> [greedy] Launching: bind1 (Chain: '')
->>> [greedy] Launching: bind2 (Chain: '')
->>> [greedy] Launching: bind3 (Chain: '')
 ========================================
  PROCESSING MODE: dbg_weighted 
 ========================================
 >>> [dbg_weighted] Launching: ma1 (Chain: 'light')
 >>> [dbg_weighted] Launching: ma1 (Chain: 'heavy')
->>> [dbg_weighted] Launching: ma2 (Chain: 'light')
->>> [dbg_weighted] Launching: ma2 (Chain: 'heavy')
->>> [dbg_weighted] Launching: ma3 (Chain: 'light')
->>> [dbg_weighted] Launching: ma3 (Chain: 'heavy')
 >>> [dbg_weighted] Launching: nb1 (Chain: '')
->>> [dbg_weighted] Launching: nb2 (Chain: '')
->>> [dbg_weighted] Launching: nb3 (Chain: '')
->>> [dbg_weighted] Launching: nb4 (Chain: '')
->>> [dbg_weighted] Launching: nb5 (Chain: '')
->>> [dbg_weighted] Launching: nb6 (Chain: '')
->>> [dbg_weighted] Launching: nb7 (Chain: '')
->>> [dbg_weighted] Launching: nb8 (Chain: '')
->>> [dbg_weighted] Launching: nb9 (Chain: '')
->>> [dbg_weighted] Launching: nb10 (Chain: '')
 >>> [dbg_weighted] Launching: bsa (Chain: '')
 >>> [dbg_weighted] Launching: bind1 (Chain: '')
->>> [dbg_weighted] Launching: bind2 (Chain: '')
->>> [dbg_weighted] Launching: bind3 (Chain: '')
 ========================================
  PROCESSING MODE: multimodal_dbg 
 ========================================
 >>> [multimodal_dbg] Launching: ma1 (Chain: 'light')
 >>> [multimodal_dbg] Launching: ma1 (Chain: 'heavy')
->>> [multimodal_dbg] Launching: ma2 (Chain: 'light')
->>> [multimodal_dbg] Launching: ma2 (Chain: 'heavy')
->>> [multimodal_dbg] Launching: ma3 (Chain: 'light')
->>> [multimodal_dbg] Launching: ma3 (Chain: 'heavy')
 >>> [multimodal_dbg] Launching: nb1 (Chain: '')
->>> [multimodal_dbg] Launching: nb2 (Chain: '')
->>> [multimodal_dbg] Launching: nb3 (Chain: '')
->>> [multimodal_dbg] Launching: nb4 (Chain: '')
->>> [multimodal_dbg] Launching: nb5 (Chain: '')
->>> [multimodal_dbg] Launching: nb6 (Chain: '')
->>> [multimodal_dbg] Launching: nb7 (Chain: '')
->>> [multimodal_dbg] Launching: nb8 (Chain: '')
->>> [multimodal_dbg] Launching: nb9 (Chain: '')
->>> [multimodal_dbg] Launching: nb10 (Chain: '')
 >>> [multimodal_dbg] Launching: bsa (Chain: '')
 >>> [multimodal_dbg] Launching: bind1 (Chain: '')
->>> [multimodal_dbg] Launching: bind2 (Chain: '')
->>> [multimodal_dbg] Launching: bind3 (Chain: '')
 ----------------------------------------
-All grid search jobs completed.s
+All grid search jobs completed.

json/colors.json

@@ -8,8 +8,8 @@
     "scaffold": "#1f78b4"
   },
   "binders": {
-    "contig": "#FFE066",
-    "scaffold": "#E6AB02"
+    "contig": "#D8B800",
+    "scaffold": "#FFC72C"
   },
   "bsa": {
     "contig": "#fdbb84",

json/gridsearch_params.json

@@ -1,7 +1,7 @@
 {
   "greedy": {
     "fdr": [0.05, 0.10, 0.20],
-    "min_overlap": [3, 4],
+    "min_overlap": [3, 4, 5],
     "size_threshold": [0, 5, 10],
     "refine_rounds": [0, 5]
   },
@@ -10,7 +10,7 @@
     "fdr": [0.05, 0.10, 0.20],
     "kmer_size": [5, 6, 7],
     "min_weight": [2, 3],
-    "min_overlap": [3, 4],
+    "min_overlap": [3, 4, 5],
     "size_threshold": [0, 5, 10],
     "refine_rounds": [0, 5],
     "alpha_len": [1.0],