checkpoint before clock modelling in BEAST

ktmeaton · Feb 17, 2021 · ff71d89 · ff71d89
1 parent 1471e40
commit ff71d89
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Showing 3 changed files with 14 additions and 3 deletions.
diff --git a/docs/results/latest/snippy_multi/constant_sites.txt b/docs/results/latest/snippy_multi/constant_sites.txt
@@ -0,0 +1 @@
+1118602,1006722,1017783,1115293
diff --git a/docs/results/latest/treemmer/treemmer_rtl.png b/docs/results/latest/treemmer/treemmer_rtl.png
diff --git a/workflow/notebooks/2_treemmer.py.ipynb b/workflow/notebooks/2_treemmer.py.ipynb
@@ -904,18 +904,27 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 9,
+   "execution_count": 18,
    "id": "armed-petersburg",
    "metadata": {},
    "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "DEPRECATED: `should_run_async` will not call `transform_cell` automatically in the future. Please pass the result to `transformed_cell` argument and any exception that happen during thetransform in `preprocessing_exc_tuple` in IPython 7.17 and above.\n",
+      "\n"
+     ]
+    },
     {
      "name": "stdout",
      "output_type": "stream",
      "text": [
       "keep:\t 247\n",
       "tree:\t 247\n",
       "df:\t 247\n",
-      "align:\t 247\n"
+      "align taxa:\t 247\n",
+      "align taxa: 4207\n"
      ]
     }
    ],
@@ -969,7 +978,8 @@
     "# Tree might have a bit more for retained internal nodes = OK\n",
     "print(\"tree:\\t\",len(tree.get_terminals()))\n",
     "print(\"df:\\t\", len(tree_df))\n",
-    "print(\"align:\\t\", len(treemmer_align))\n"
+    "print(\"align taxa:\\t\", len(treemmer_align))\n",
+    "print(\"align taxa:\", len(treemmer_align[0]))\n"
    ]
   },
   {