fix hic

CSB5 · Sep 8, 2022 · 5d32b6e · 5d32b6e
1 parent 3717408
commit 5d32b6e
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Showing 6 changed files with 1,450 additions and 1,222 deletions.
diff --git a/scripts/assembly_stats.ipynb b/scripts/assembly_stats.ipynb
diff --git a/scripts/bracken_self_combine.ipynb b/scripts/bracken_self_combine.ipynb
@@ -2,8 +2,8 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 44,
-   "id": "c5001f97",
+   "execution_count": 1,
+   "id": "31811c76",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -28,8 +28,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 45,
-   "id": "66ff452f",
+   "execution_count": 2,
+   "id": "802b79c4",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -49,8 +49,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 46,
-   "id": "c016ffae",
+   "execution_count": 3,
+   "id": "45c9ecf9",
    "metadata": {},
    "outputs": [
     {
@@ -147,7 +147,7 @@
        "4       7.27   1856540    1856540    S  2820142    SPMP41_bin.4.fasta  SPMP16"
       ]
      },
-     "execution_count": 46,
+     "execution_count": 3,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -160,7 +160,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "e956df82",
+   "id": "65eea64a",
    "metadata": {},
    "source": [
     "Don't get confused here, it's normal that the SPMP label in the name is not the same than the sample name\n",
@@ -170,8 +170,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 47,
-   "id": "0ebe8e3a",
+   "execution_count": 4,
+   "id": "c6201214",
    "metadata": {},
    "outputs": [
     {
@@ -250,7 +250,7 @@
        "4  SPMP01_bin.20.fasta     Akkermansia  Akkermansia muciniphila    260"
       ]
      },
-     "execution_count": 47,
+     "execution_count": 4,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -264,8 +264,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 48,
-   "id": "e05fe53e",
+   "execution_count": 5,
+   "id": "755d1be9",
    "metadata": {},
    "outputs": [
     {
@@ -344,7 +344,7 @@
        "23  SPMP05   54    F     Malay"
       ]
      },
-     "execution_count": 48,
+     "execution_count": 5,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -361,8 +361,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 49,
-   "id": "2f10fa51",
+   "execution_count": 6,
+   "id": "57e5d736",
    "metadata": {},
    "outputs": [
     {
@@ -626,7 +626,7 @@
        "[74429 rows x 13 columns]"
       ]
      },
-     "execution_count": 49,
+     "execution_count": 6,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -640,7 +640,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "0ab9cf7f",
+   "id": "c5e88d43",
    "metadata": {},
    "source": [
     "## MaAsLin2\n",
@@ -651,17 +651,25 @@
   {
    "cell_type": "code",
    "execution_count": 7,
-   "id": "b4688cf1",
+   "id": "2c209d87",
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "mkdir: cannot create directory ‘/tmp/maaslin2’: File exists\n"
+     ]
+    }
+   ],
    "source": [
     "!mkdir /tmp/maaslin2"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 8,
-   "id": "8e604a70",
+   "id": "38398960",
    "metadata": {},
    "outputs": [
     {
@@ -1078,7 +1086,7 @@
   },
   {
    "cell_type": "markdown",
-   "id": "fcaf0cdc",
+   "id": "e6b38988",
    "metadata": {},
    "source": [
     "**MaAsLin2 is run in `maaslin3_run.ipynb`**\n",
@@ -1089,7 +1097,7 @@
   {
    "cell_type": "code",
    "execution_count": 9,
-   "id": "61f36edc",
+   "id": "1c450b3e",
    "metadata": {},
    "outputs": [
     {
@@ -1233,7 +1241,7 @@
   {
    "cell_type": "code",
    "execution_count": 10,
-   "id": "fea27a54",
+   "id": "b999ea4a",
    "metadata": {},
    "outputs": [
     {
@@ -1268,7 +1276,7 @@
   {
    "cell_type": "code",
    "execution_count": 11,
-   "id": "8ae1c9a6",
+   "id": "2ecf45d6",
    "metadata": {},
    "outputs": [
     {
@@ -1299,8 +1307,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 14,
-   "id": "e28dcb32",
+   "execution_count": 12,
+   "id": "aa80ce0d",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1349,8 +1357,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 19,
-   "id": "36f56849",
+   "execution_count": 13,
+   "id": "573de365",
    "metadata": {},
    "outputs": [
     {
@@ -1409,8 +1417,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 20,
-   "id": "ff5c0e36",
+   "execution_count": 14,
+   "id": "3fa17de6",
    "metadata": {},
    "outputs": [],
    "source": [
@@ -1420,16 +1428,16 @@
   },
   {
    "cell_type": "markdown",
-   "id": "85bd7355",
+   "id": "72ee9a17",
    "metadata": {},
    "source": [
     "## Supplementary figure 11.A"
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 21,
-   "id": "6827a3de",
+   "execution_count": 15,
+   "id": "1dcd3b81",
    "metadata": {},
    "outputs": [
     {
@@ -1449,7 +1457,7 @@
        "Name: abundance, dtype: float64"
       ]
      },
-     "execution_count": 21,
+     "execution_count": 15,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1472,8 +1480,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 22,
-   "id": "49a7147f",
+   "execution_count": 16,
+   "id": "63578781",
    "metadata": {},
    "outputs": [
     {
@@ -1522,8 +1530,8 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 39,
-   "id": "46301246",
+   "execution_count": 17,
+   "id": "8dbcd8ee",
    "metadata": {},
    "outputs": [
     {
@@ -1664,7 +1672,7 @@
        "4          Blautia_A massiliensis  "
       ]
      },
-     "execution_count": 39,
+     "execution_count": 17,
      "metadata": {},
      "output_type": "execute_result"
     }
@@ -1680,7 +1688,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "382edefe",
+   "id": "ffce3792",
    "metadata": {},
    "outputs": [],
    "source": []