diff --git a/.gitignore b/.gitignore
index abe11b1..fb27253 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,5 +1,5 @@
 data/
-
+executions/
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
diff --git a/compute1/launch_notebook.sh b/compute1/launch_notebook.sh
new file mode 100644
index 0000000..d9db527
--- /dev/null
+++ b/compute1/launch_notebook.sh
@@ -0,0 +1,4 @@
+export LSF_DOCKER_VOLUMES="/storage1/fs1/dinglab:/storage1/fs1/dinglab /scratch1/fs1/dinglab:/scratch1/fs1/dinglab /home/estorrs:/home/estorrs"
+export PATH="/miniconda/envs/ancestry/bin:$PATH"
+
+LSF_DOCKER_PORTS='8282:8888' bsub -R 'select[mem>10GB,port8282=1] rusage[mem=10GB] span[hosts=1]' -M 11GB -q general-interactive -G compute-dinglab -Is -a 'docker(estorrs/ancestry-pipeline:0.0.1)' 'jupyter notebook --port 8888 --no-browser --ip=0.0.0.0'
diff --git a/notebooks/make_test_data.ipynb b/notebooks/make_test_data.ipynb
new file mode 100644
index 0000000..1078006
--- /dev/null
+++ b/notebooks/make_test_data.ipynb
@@ -0,0 +1,596 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "a63150d1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import re\n",
+    "\n",
+    "import pandas as pd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "accd9693",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th># sample_name</th>\n",
+       "      <th>case</th>\n",
+       "      <th>disease</th>\n",
+       "      <th>experimental_strategy</th>\n",
+       "      <th>sample_type</th>\n",
+       "      <th>data_path</th>\n",
+       "      <th>filesize</th>\n",
+       "      <th>data_format</th>\n",
+       "      <th>reference</th>\n",
+       "      <th>UUID</th>\n",
+       "      <th>system</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>29</th>\n",
+       "      <td>C1230738.WXS.T.ADNA_eb44394c.hg38</td>\n",
+       "      <td>C1230738</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>34561898412</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>f6c72dde-4426-4a98-9716-e4490b425df3</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>31</th>\n",
+       "      <td>C1230738.WXS.T.hg38</td>\n",
+       "      <td>C1230738</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>34971128893</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>b06c50fe-383f-4cce-a9b0-9f70f118d5e0</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>51</th>\n",
+       "      <td>C1245129.WXS.T.ADNA_f4f0a623.hg38</td>\n",
+       "      <td>C1245129</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>37402084587</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>9e05a653-da61-49f4-b2a7-b58f4781e760</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>53</th>\n",
+       "      <td>C1245129.WXS.T.hg38</td>\n",
+       "      <td>C1245129</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>39273198570</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>923cea70-4973-4a54-ad99-151028fe7669</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>81</th>\n",
+       "      <td>C204057.WXS.T.ADNA_fb79d37d.hg38</td>\n",
+       "      <td>C204057</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>36138400689</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>6a93dee0-802a-47cc-90a5-37f686a9aebf</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7190</th>\n",
+       "      <td>C761370.WXS.T.ADNA_260f1df4.hg38</td>\n",
+       "      <td>C761370</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>44821987147</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>fd66e1f9-ce3b-4a76-9e48-23bf78568f41</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7192</th>\n",
+       "      <td>C761370.WXS.T.hg38</td>\n",
+       "      <td>C761370</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>34824648092</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>8541768d-a439-4abf-987e-d08039a4ec1d</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7214</th>\n",
+       "      <td>C827913.WXS.T.hg38</td>\n",
+       "      <td>C827913</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>31571237792</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>295d757c-a37e-49f5-9d26-65dff2dbbf13</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7238</th>\n",
+       "      <td>C846363.WXS.T.ADNA_51dcc4a3.hg38</td>\n",
+       "      <td>C846363</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>47361689745</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>83a989e8-836e-42b2-a240-f87f0858d189</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7240</th>\n",
+       "      <td>C846363.WXS.T.hg38</td>\n",
+       "      <td>C846363</td>\n",
+       "      <td>GBM</td>\n",
+       "      <td>WXS</td>\n",
+       "      <td>tumor</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "      <td>22124861490</td>\n",
+       "      <td>BAM</td>\n",
+       "      <td>hg38</td>\n",
+       "      <td>e3e1eeb8-e749-4520-83e2-3ae1091a7207</td>\n",
+       "      <td>storage1</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>137 rows × 11 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                          # sample_name      case disease  \\\n",
+       "29    C1230738.WXS.T.ADNA_eb44394c.hg38  C1230738     GBM   \n",
+       "31                  C1230738.WXS.T.hg38  C1230738     GBM   \n",
+       "51    C1245129.WXS.T.ADNA_f4f0a623.hg38  C1245129     GBM   \n",
+       "53                  C1245129.WXS.T.hg38  C1245129     GBM   \n",
+       "81     C204057.WXS.T.ADNA_fb79d37d.hg38   C204057     GBM   \n",
+       "...                                 ...       ...     ...   \n",
+       "7190   C761370.WXS.T.ADNA_260f1df4.hg38   C761370     GBM   \n",
+       "7192                 C761370.WXS.T.hg38   C761370     GBM   \n",
+       "7214                 C827913.WXS.T.hg38   C827913     GBM   \n",
+       "7238   C846363.WXS.T.ADNA_51dcc4a3.hg38   C846363     GBM   \n",
+       "7240                 C846363.WXS.T.hg38   C846363     GBM   \n",
+       "\n",
+       "     experimental_strategy sample_type  \\\n",
+       "29                     WXS       tumor   \n",
+       "31                     WXS       tumor   \n",
+       "51                     WXS       tumor   \n",
+       "53                     WXS       tumor   \n",
+       "81                     WXS       tumor   \n",
+       "...                    ...         ...   \n",
+       "7190                   WXS       tumor   \n",
+       "7192                   WXS       tumor   \n",
+       "7214                   WXS       tumor   \n",
+       "7238                   WXS       tumor   \n",
+       "7240                   WXS       tumor   \n",
+       "\n",
+       "                                              data_path     filesize  \\\n",
+       "29    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  34561898412   \n",
+       "31    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  34971128893   \n",
+       "51    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  37402084587   \n",
+       "53    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  39273198570   \n",
+       "81    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  36138400689   \n",
+       "...                                                 ...          ...   \n",
+       "7190  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  44821987147   \n",
+       "7192  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  34824648092   \n",
+       "7214  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  31571237792   \n",
+       "7238  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  47361689745   \n",
+       "7240  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  22124861490   \n",
+       "\n",
+       "     data_format reference                                  UUID    system  \n",
+       "29           BAM      hg38  f6c72dde-4426-4a98-9716-e4490b425df3  storage1  \n",
+       "31           BAM      hg38  b06c50fe-383f-4cce-a9b0-9f70f118d5e0  storage1  \n",
+       "51           BAM      hg38  9e05a653-da61-49f4-b2a7-b58f4781e760  storage1  \n",
+       "53           BAM      hg38  923cea70-4973-4a54-ad99-151028fe7669  storage1  \n",
+       "81           BAM      hg38  6a93dee0-802a-47cc-90a5-37f686a9aebf  storage1  \n",
+       "...          ...       ...                                   ...       ...  \n",
+       "7190         BAM      hg38  fd66e1f9-ce3b-4a76-9e48-23bf78568f41  storage1  \n",
+       "7192         BAM      hg38  8541768d-a439-4abf-987e-d08039a4ec1d  storage1  \n",
+       "7214         BAM      hg38  295d757c-a37e-49f5-9d26-65dff2dbbf13  storage1  \n",
+       "7238         BAM      hg38  83a989e8-836e-42b2-a240-f87f0858d189  storage1  \n",
+       "7240         BAM      hg38  e3e1eeb8-e749-4520-83e2-3ae1091a7207  storage1  \n",
+       "\n",
+       "[137 rows x 11 columns]"
+      ]
+     },
+     "execution_count": 3,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df = pd.read_csv('/storage1/fs1/dinglab/Active/Projects/estorrs/CPTAC3.catalog/BamMap/storage1.BamMap.dat',\n",
+    "                sep='\\t')\n",
+    "df = df[df['data_format']=='BAM']\n",
+    "df = df[df['reference']=='hg38']\n",
+    "df = df[df['experimental_strategy']=='WXS']\n",
+    "df = df[df['disease']=='GBM']\n",
+    "df = df[df['sample_type']=='tumor']\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "c4da7ec6",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>sample_id</th>\n",
+       "      <th>filepath</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>29</th>\n",
+       "      <td>C1230738.WXS.T.ADNA_eb44394c.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>31</th>\n",
+       "      <td>C1230738.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>51</th>\n",
+       "      <td>C1245129.WXS.T.ADNA_f4f0a623.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>53</th>\n",
+       "      <td>C1245129.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>81</th>\n",
+       "      <td>C204057.WXS.T.ADNA_fb79d37d.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7190</th>\n",
+       "      <td>C761370.WXS.T.ADNA_260f1df4.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7192</th>\n",
+       "      <td>C761370.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7214</th>\n",
+       "      <td>C827913.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7238</th>\n",
+       "      <td>C846363.WXS.T.ADNA_51dcc4a3.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7240</th>\n",
+       "      <td>C846363.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>137 rows × 2 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                              sample_id  \\\n",
+       "29    C1230738.WXS.T.ADNA_eb44394c.hg38   \n",
+       "31                  C1230738.WXS.T.hg38   \n",
+       "51    C1245129.WXS.T.ADNA_f4f0a623.hg38   \n",
+       "53                  C1245129.WXS.T.hg38   \n",
+       "81     C204057.WXS.T.ADNA_fb79d37d.hg38   \n",
+       "...                                 ...   \n",
+       "7190   C761370.WXS.T.ADNA_260f1df4.hg38   \n",
+       "7192                 C761370.WXS.T.hg38   \n",
+       "7214                 C827913.WXS.T.hg38   \n",
+       "7238   C846363.WXS.T.ADNA_51dcc4a3.hg38   \n",
+       "7240                 C846363.WXS.T.hg38   \n",
+       "\n",
+       "                                               filepath  \n",
+       "29    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "31    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "51    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "53    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "81    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "...                                                 ...  \n",
+       "7190  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7192  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7214  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7238  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7240  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "\n",
+       "[137 rows x 2 columns]"
+      ]
+     },
+     "execution_count": 4,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df = df[['# sample_name', 'data_path']]\n",
+    "df.columns = ['sample_id', 'filepath']\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "a9e97e74",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>sample_id</th>\n",
+       "      <th>filepath</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>29</th>\n",
+       "      <td>C1230738.WXS.T.ADNA_eb44394c.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>31</th>\n",
+       "      <td>C1230738.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>51</th>\n",
+       "      <td>C1245129.WXS.T.ADNA_f4f0a623.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>53</th>\n",
+       "      <td>C1245129.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>81</th>\n",
+       "      <td>C204057.WXS.T.ADNA_fb79d37d.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7190</th>\n",
+       "      <td>C761370.WXS.T.ADNA_260f1df4.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7192</th>\n",
+       "      <td>C761370.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7214</th>\n",
+       "      <td>C827913.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7238</th>\n",
+       "      <td>C846363.WXS.T.ADNA_51dcc4a3.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>7240</th>\n",
+       "      <td>C846363.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>69 rows × 2 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                              sample_id  \\\n",
+       "29    C1230738.WXS.T.ADNA_eb44394c.hg38   \n",
+       "31                  C1230738.WXS.T.hg38   \n",
+       "51    C1245129.WXS.T.ADNA_f4f0a623.hg38   \n",
+       "53                  C1245129.WXS.T.hg38   \n",
+       "81     C204057.WXS.T.ADNA_fb79d37d.hg38   \n",
+       "...                                 ...   \n",
+       "7190   C761370.WXS.T.ADNA_260f1df4.hg38   \n",
+       "7192                 C761370.WXS.T.hg38   \n",
+       "7214                 C827913.WXS.T.hg38   \n",
+       "7238   C846363.WXS.T.ADNA_51dcc4a3.hg38   \n",
+       "7240                 C846363.WXS.T.hg38   \n",
+       "\n",
+       "                                               filepath  \n",
+       "29    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "31    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "51    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "53    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "81    /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "...                                                 ...  \n",
+       "7190  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7192  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7214  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7238  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "7240  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "\n",
+       "[69 rows x 2 columns]"
+      ]
+     },
+     "execution_count": 8,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "mask = [True if os.path.exists(fp) else False for fp in df['filepath']]\n",
+    "df = df[mask]\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "55bd3c7c",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "df.to_csv('../executions/cptac_test/gbm_sample_to_bam.txt', sep='\\t', index=False)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "2639b817",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}
diff --git a/notebooks/run_ancestry.ipynb b/notebooks/run_ancestry.ipynb
new file mode 100644
index 0000000..bac7bec
--- /dev/null
+++ b/notebooks/run_ancestry.ipynb
@@ -0,0 +1,903 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 58,
+   "id": "a971c34e",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "import os\n",
+    "import re\n",
+    "import subprocess\n",
+    "from pathlib import Path\n",
+    "\n",
+    "import pandas as pd\n",
+    "\n",
+    "from wombat.bsub import batch_bsub_commands, write_command_file, DEFAULT_ARGS\n",
+    "from wombat.utils import listfiles"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 59,
+   "id": "3860ecd6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "run_dir = '/scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test'\n",
+    "Path(run_dir).mkdir(parents=True, exist_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8d3fdc26",
+   "metadata": {},
+   "source": [
+    "## define inputs"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "db1ae8ea",
+   "metadata": {},
+   "source": [
+    "thousand genomes sample panel used for training"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 60,
+   "id": "80e694dd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "thousand_genomes_panel = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/integrated_call_samples_v3.20130502.ALL.panel'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "b78b039d",
+   "metadata": {},
+   "source": [
+    "reference genome (preferably the same reference used to align the .bams that are having ancestry called on them)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 61,
+   "id": "fa48babe",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "reference_fasta = '/storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "593b4c00",
+   "metadata": {},
+   "source": [
+    "vcf and bed file for thousand genomes project samples.\n",
+    "\n",
+    "make sure to use the correct vcf/bed file depending on your reference (hg19 vs hg38) and whether the genome coordinates start with \"chr\" or not\n",
+    "\n",
+    "you can find different versions of these files here\n",
+    "\n",
+    "hg38 and genome coordinates start with chr\n",
+    "+ thousand_genomes_vcf = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.vcf'\n",
+    "+ thousand_genomes_bed = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed'\n",
+    "\n",
+    "hg38 and genome coordinates do not start with chr\n",
+    "+ thousand_genomes_vcf = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.vcf'\n",
+    "+ thousand_genomes_bed = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.bed'\n",
+    "\n",
+    "hg19 and genome coordinates start with chr\n",
+    "+ thousand_genomes_vcf = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg19/all.coding.sorted.02maf.snps.chr.vcf'\n",
+    "+ thousand_genomes_bed = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg19/all.coding.sorted.02maf.snps.chr.bed'\n",
+    "\n",
+    "hg19 and genome coordinates do not start with chr\n",
+    "+ thousand_genomes_vcf = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg19/all.coding.sorted.02maf.snps.vcf'\n",
+    "+ thousand_genomes_bed = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg19/all.coding.sorted.02maf.snps.bed'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 62,
+   "id": "898bc4bd",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "thousand_genomes_vcf = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.vcf'\n",
+    "thousand_genomes_bed = '/storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed'"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "fe406ed2",
+   "metadata": {},
+   "source": [
+    "sample bam locations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 63,
+   "id": "a11b763d",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>sample_id</th>\n",
+       "      <th>filepath</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>C1230738.WXS.T.ADNA_eb44394c.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>1</th>\n",
+       "      <td>C1230738.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>2</th>\n",
+       "      <td>C1245129.WXS.T.ADNA_f4f0a623.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>3</th>\n",
+       "      <td>C1245129.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>4</th>\n",
+       "      <td>C204057.WXS.T.ADNA_fb79d37d.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>...</th>\n",
+       "      <td>...</td>\n",
+       "      <td>...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>64</th>\n",
+       "      <td>C761370.WXS.T.ADNA_260f1df4.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>65</th>\n",
+       "      <td>C761370.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>66</th>\n",
+       "      <td>C827913.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>67</th>\n",
+       "      <td>C846363.WXS.T.ADNA_51dcc4a3.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "    <tr>\n",
+       "      <th>68</th>\n",
+       "      <td>C846363.WXS.T.hg38</td>\n",
+       "      <td>/storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "<p>69 rows × 2 columns</p>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "                            sample_id  \\\n",
+       "0   C1230738.WXS.T.ADNA_eb44394c.hg38   \n",
+       "1                 C1230738.WXS.T.hg38   \n",
+       "2   C1245129.WXS.T.ADNA_f4f0a623.hg38   \n",
+       "3                 C1245129.WXS.T.hg38   \n",
+       "4    C204057.WXS.T.ADNA_fb79d37d.hg38   \n",
+       "..                                ...   \n",
+       "64   C761370.WXS.T.ADNA_260f1df4.hg38   \n",
+       "65                 C761370.WXS.T.hg38   \n",
+       "66                 C827913.WXS.T.hg38   \n",
+       "67   C846363.WXS.T.ADNA_51dcc4a3.hg38   \n",
+       "68                 C846363.WXS.T.hg38   \n",
+       "\n",
+       "                                             filepath  \n",
+       "0   /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "1   /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "2   /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "3   /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "4   /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "..                                                ...  \n",
+       "64  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "65  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "66  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "67  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "68  /storage1/fs1/dinglab/Active/Primary/CPTAC3.sh...  \n",
+       "\n",
+       "[69 rows x 2 columns]"
+      ]
+     },
+     "execution_count": 63,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "df = pd.read_csv('/storage1/fs1/dinglab/Active/Projects/estorrs/ancestry-pipeline/executions/cptac_test/gbm_sample_to_bam.txt',\n",
+    "                sep='\\t')\n",
+    "df"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "08cf2f19",
+   "metadata": {},
+   "source": [
+    "sanity check to make sure genome coordinates match, in this test case we expect \"chr\" to prepend all genome coordinates"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 64,
+   "id": "c3d88215",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/html": [
+       "<div>\n",
+       "<style scoped>\n",
+       "    .dataframe tbody tr th:only-of-type {\n",
+       "        vertical-align: middle;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe tbody tr th {\n",
+       "        vertical-align: top;\n",
+       "    }\n",
+       "\n",
+       "    .dataframe thead th {\n",
+       "        text-align: right;\n",
+       "    }\n",
+       "</style>\n",
+       "<table border=\"1\" class=\"dataframe\">\n",
+       "  <thead>\n",
+       "    <tr style=\"text-align: right;\">\n",
+       "      <th></th>\n",
+       "      <th>0</th>\n",
+       "      <th>1</th>\n",
+       "      <th>2</th>\n",
+       "    </tr>\n",
+       "  </thead>\n",
+       "  <tbody>\n",
+       "    <tr>\n",
+       "      <th>0</th>\n",
+       "      <td>chr1</td>\n",
+       "      <td>13273</td>\n",
+       "      <td>13273</td>\n",
+       "    </tr>\n",
+       "  </tbody>\n",
+       "</table>\n",
+       "</div>"
+      ],
+      "text/plain": [
+       "      0      1      2\n",
+       "0  chr1  13273  13273"
+      ]
+     },
+     "execution_count": 64,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pd.read_csv(thousand_genomes_bed, sep='\\t', header=None, nrows=1)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 65,
+   "id": "ac29eb22",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'chr1'"
+      ]
+     },
+     "execution_count": 65,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "fp = df['filepath'][0]\n",
+    "cmd = f'samtools view {fp} | head -n 1'\n",
+    "out = subprocess.check_output(cmd, shell=True) # chromosome coordinate is in third column\n",
+    "out.decode().split('\\t')[2]"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "6dff02a7",
+   "metadata": {},
+   "source": [
+    "## setting bsub related parameters"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "8efa5eb7",
+   "metadata": {},
+   "source": [
+    "## step 1: extract readcounts with bam-readcount"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 66,
+   "id": "b65deb39",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "execution_dir = os.path.join(run_dir, '1.slate')\n",
+    "log_dir = os.path.join(execution_dir, 'logs')\n",
+    "result_dir = os.path.join(execution_dir, 'results')\n",
+    "Path(log_dir).mkdir(parents=True, exist_ok=True)\n",
+    "Path(result_dir).mkdir(parents=True, exist_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 67,
+   "id": "247b5e2a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_slate_command(input_bam_fp, readcount_fp, trimmed_bam_fp):\n",
+    "    return f'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 \\\n",
+    "--fasta {reference_fasta} --positions {thousand_genomes_bed} \\\n",
+    "--readcount-output {readcount_fp} --filtered-bam-output {trimmed_bam_fp} {input_bam_fp}'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 68,
+   "id": "ef02a722",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'mem': 10,\n",
+       " 'n_processes': 1,\n",
+       " 'max_mem': None,\n",
+       " 'docker': 'python:3.8',\n",
+       " 'queue': 'dinglab',\n",
+       " 'gpu_model': 'TeslaV100_SXM2_32GB',\n",
+       " 'gpu_mem': '30',\n",
+       " 'gpu_num': 1,\n",
+       " 'use_gpu': False,\n",
+       " 'group': 'compute-dinglab',\n",
+       " 'group_name': None,\n",
+       " 'n_concurrent': 10,\n",
+       " 'interactive': False,\n",
+       " 'username': 'estorrs'}"
+      ]
+     },
+     "execution_count": 68,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "volumes = ['/storage1/fs1/dinglab', '/scratch1/fs1/dinglab', '/home/estorrs'] # compute1 needs to know which directories to map, replace /home/<username> if you are not me\n",
+    "exports = ['/miniconda/bin'] # need to override compute1 PATH defaults\n",
+    "args = DEFAULT_ARGS.copy()\n",
+    "args"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 69,
+   "id": "926f080b",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['mkdir -p /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs',\n",
+       " 'export LSF_DOCKER_VOLUMES=\"/storage1/fs1/dinglab:/storage1/fs1/dinglab /scratch1/fs1/dinglab:/scratch1/fs1/dinglab /home/estorrs:/home/estorrs /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs:/scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs\"',\n",
+       " 'bgadd -L 100 /estorrs/ancestry_slate',\n",
+       " 'export PATH=\"/opt/java/openjdk/bin:/miniconda/bin:$PATH\"',\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C1230738.WXS.T.ADNA_eb44394c.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C1230738.WXS.T.ADNA_eb44394c.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1230738.WXS.T.ADNA_eb44394c.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1230738.WXS.T.ADNA_eb44394c.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/f6c72dde-4426-4a98-9716-e4490b425df3/062a4cb7-1a73-4382-9f16-fdd891218a97_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C1230738.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C1230738.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1230738.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1230738.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/b06c50fe-383f-4cce-a9b0-9f70f118d5e0/aee72b24-81c3-47b5-856d-35ff22208f84_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C1245129.WXS.T.ADNA_f4f0a623.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C1245129.WXS.T.ADNA_f4f0a623.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1245129.WXS.T.ADNA_f4f0a623.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1245129.WXS.T.ADNA_f4f0a623.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/9e05a653-da61-49f4-b2a7-b58f4781e760/5b739159-0dff-476e-932e-8198cb3c76e4_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C1245129.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C1245129.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1245129.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C1245129.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/923cea70-4973-4a54-ad99-151028fe7669/fb858b07-76dc-48b4-9096-adb0aed38c31_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C204057.WXS.T.ADNA_fb79d37d.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C204057.WXS.T.ADNA_fb79d37d.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C204057.WXS.T.ADNA_fb79d37d.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C204057.WXS.T.ADNA_fb79d37d.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/6a93dee0-802a-47cc-90a5-37f686a9aebf/b1b62bc9-91c7-416b-92c8-35f6e197980a_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C204057.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C204057.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C204057.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C204057.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/a3e622c4-b84b-41a3-810a-97bf521ba9a9/73fbc689-0c62-4ccb-8aaf-6d3697fc06e1_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C207624.WXS.T.ADNA_8ab52100.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C207624.WXS.T.ADNA_8ab52100.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C207624.WXS.T.ADNA_8ab52100.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C207624.WXS.T.ADNA_8ab52100.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/370da836-9a04-4ad5-9b4f-11270f994e3c/fd0af1cc-2bd5-4433-b288-a8f95f0f4eb9_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C207624.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C207624.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C207624.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C207624.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/1252d351-fbb5-4716-b862-028f33399922/0af3abb3-d73f-47f4-9f8a-9ac41d230bca_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C208854.WXS.T.ADNA_15b44502.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C208854.WXS.T.ADNA_15b44502.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.ADNA_15b44502.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.ADNA_15b44502.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/18f09f19-5cc3-413d-968f-a574a8a6084d/eb327532-25bd-4c10-a414-185474bdb7ef_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C208854.WXS.T.ADNA_93ae1041.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C208854.WXS.T.ADNA_93ae1041.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.ADNA_93ae1041.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.ADNA_93ae1041.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/af9ba009-d30c-4629-98a5-80c96e605e94/9c504d59-e2a4-492c-ae3a-993e3f802cef_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C208854.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C208854.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C208854.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/20773aad-0e5f-4b6d-8542-6981c9bf31a9/39d0b9dc-ead3-409f-87fc-484fee59f592_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C217710.WXS.T.ADNA_e91fb26d.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C217710.WXS.T.ADNA_e91fb26d.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C217710.WXS.T.ADNA_e91fb26d.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C217710.WXS.T.ADNA_e91fb26d.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/8bbd9c83-206a-4547-93fb-1dbc329c4128/cdfb6ee2-5d43-478c-8f60-80c3c5ef589e_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C217710.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C217710.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C217710.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C217710.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/1d5ad431-811e-436c-8f11-dc1badb61be6/49aea928-c7da-432e-aa39-ec92de5d9f00_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C219555.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C219555.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C219555.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C219555.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/1d6f28a8-c2fe-4259-b1ed-b59d4b65d934/b8cc75d6-b8c2-4e04-8808-9c99797b2115_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C224106.WXS.T.ADNA_4208c7cd.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C224106.WXS.T.ADNA_4208c7cd.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224106.WXS.T.ADNA_4208c7cd.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224106.WXS.T.ADNA_4208c7cd.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/68b960fe-389d-45f1-a5b1-4500a8670c48/03758b31-f5e1-4bea-8001-a5147945dafa_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C224106.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C224106.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224106.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224106.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/3345bb07-d0be-4306-be6e-ea632f8c5fc8/a5fb9d82-568c-4f92-9d20-ff80d6bce284_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C224967.WXS.T.ADNA_ef1b8e33.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C224967.WXS.T.ADNA_ef1b8e33.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224967.WXS.T.ADNA_ef1b8e33.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224967.WXS.T.ADNA_ef1b8e33.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/406c1599-e9aa-41f3-95d8-3126dece3c82/75069e02-ca1b-4e5d-bd9a-7e0996430dec_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C224967.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C224967.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224967.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C224967.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/63f77087-cd4f-4b87-a777-57a55abe245f/aac08359-e9fe-4cf7-b5e1-12cc6dfa6cf4_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C229764.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C229764.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C229764.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C229764.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/0858e1ec-6d27-4654-9a9d-ac8d08173e1a/ac8d4e2a-cbf6-4679-b022-ab0518e1ae21_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C231855.WXS.T.ADNA_40a9c1b9.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C231855.WXS.T.ADNA_40a9c1b9.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C231855.WXS.T.ADNA_40a9c1b9.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C231855.WXS.T.ADNA_40a9c1b9.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/aea7e706-e796-4b1f-bb99-40a333b400e9/8b5d164f-881e-476b-ad10-84e8b23a9601_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C231855.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C231855.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C231855.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C231855.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/f12a807d-d1e9-4c32-a4ac-798ff0359c82/ca322924-b07a-4fbb-8634-78e26e197671_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C234192.WXS.T.ADNA_a92ddca1.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C234192.WXS.T.ADNA_a92ddca1.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C234192.WXS.T.ADNA_a92ddca1.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C234192.WXS.T.ADNA_a92ddca1.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/391bf1c9-43e5-4e52-b602-a8014c059dbc/4eae5599-7c20-444f-8253-fc4a0195d96f_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C234192.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C234192.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C234192.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C234192.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/00d428d0-e8fc-4662-a0fa-cabc09e83c20/d774c07e-df68-4037-983e-1b21d267226b_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C2415597.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C2415597.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C2415597.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C2415597.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/d7016be0-b5fd-4b35-bfcb-b9f68116a669/bc166e0c-63e2-409c-a09f-7100fc4d0399_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C243048.WXS.T.ADNA_94a7b89d.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C243048.WXS.T.ADNA_94a7b89d.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243048.WXS.T.ADNA_94a7b89d.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243048.WXS.T.ADNA_94a7b89d.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/ba5c13e9-a560-4436-90f2-011d77ee7531/e4e6f65e-c590-48d7-8fba-1bfc0f10d029_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C243048.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C243048.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243048.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243048.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/8bdfe531-ae92-49f4-87c0-02ee2ad09779/6c5fd8de-99ba-4d63-8dd6-7587d7e72478_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C243909.WXS.T.ADNA_74725183.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C243909.WXS.T.ADNA_74725183.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243909.WXS.T.ADNA_74725183.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243909.WXS.T.ADNA_74725183.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/fff94d78-afc1-4c90-9e46-7d90e2f05b5f/d013c55d-d3bd-488f-95cd-6c6e9228d817_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C243909.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C243909.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243909.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C243909.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/c7bd5850-d12c-44e5-ab30-20b39a264488/87b93eca-6649-48fe-8311-56853e65a862_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C247230.WXS.T.ADNA_0aa190bd.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C247230.WXS.T.ADNA_0aa190bd.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C247230.WXS.T.ADNA_0aa190bd.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C247230.WXS.T.ADNA_0aa190bd.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/f79420a5-f8b3-4853-85e4-8103a56fc3f9/44d33820-4b25-4059-b10b-6f7b9038ed39_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C247230.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C247230.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C247230.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C247230.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/94b2e77b-dacb-475b-bbef-febab3c064c2/eafce93e-0fd9-44bb-942d-7820b6f68744_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C259161.WXS.T.ADNA_5c7e3295.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C259161.WXS.T.ADNA_5c7e3295.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C259161.WXS.T.ADNA_5c7e3295.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C259161.WXS.T.ADNA_5c7e3295.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/942805cd-2142-4c93-b3d2-a8980b14e829/71aff02e-d6dd-4292-8627-d33c7d95fea5_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C259161.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C259161.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C259161.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C259161.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/2fe9a9b8-b5c4-4e72-8fb7-71cac06dd773/c72c1846-16af-4899-a429-9f5b7c954a58_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C266664.WXS.T.ADNA_5dbc58a2.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C266664.WXS.T.ADNA_5dbc58a2.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C266664.WXS.T.ADNA_5dbc58a2.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C266664.WXS.T.ADNA_5dbc58a2.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/ad1b5b7b-5c70-44e1-aa5c-f1e397fbb55a/670c02b3-383c-4ca4-9a0d-2fc479296d0c_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C266664.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C266664.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C266664.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C266664.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/7fa81b59-b344-463c-91a7-3bf91763635f/3af09701-86aa-4741-aa59-9aed8b02f2bf_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C283515.WXS.T.ADNA_16970afa.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C283515.WXS.T.ADNA_16970afa.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C283515.WXS.T.ADNA_16970afa.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C283515.WXS.T.ADNA_16970afa.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/fb59bee7-446d-4669-bd78-6234196d0153/2a1d8b76-daf0-4068-8ad2-61c163e545a3_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C283515.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C283515.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C283515.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C283515.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/5aa549bf-6059-4691-9a1a-dc2e334019b0/e251ee1d-1c35-4852-89fe-50fc2a4ac948_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C287328.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C287328.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C287328.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C287328.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/bc0a38db-f504-49c1-b50f-25b1cc7af943/198d468f-807f-4fbc-80c3-db5d8d0b859f_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C289419.WXS.T.ADNA_ebf29e44.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C289419.WXS.T.ADNA_ebf29e44.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C289419.WXS.T.ADNA_ebf29e44.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C289419.WXS.T.ADNA_ebf29e44.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/56d4c848-6cf4-4228-ad97-d3ab5056812d/4d704111-c691-4670-b26a-c087157c5729_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C289419.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C289419.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C289419.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C289419.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/7ca5f822-55be-4e81-81e4-5542cf2b6fe1/1db3a7f3-a22c-4898-82e3-8957c1238080_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C298152.WXS.T.ADNA_cb6d6363.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C298152.WXS.T.ADNA_cb6d6363.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C298152.WXS.T.ADNA_cb6d6363.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C298152.WXS.T.ADNA_cb6d6363.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/96617688-1ee2-4e4a-b128-6e170cee9966/2359e710-f546-4a7d-9b12-c9c3028c8b92_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C298152.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C298152.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C298152.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C298152.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/83633780-d4aa-48d6-bf32-90efafb8eb91/45164d3a-0a7f-498f-a025-eae34981591f_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C317832.WXS.T.ADNA_4b7f0398.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C317832.WXS.T.ADNA_4b7f0398.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C317832.WXS.T.ADNA_4b7f0398.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C317832.WXS.T.ADNA_4b7f0398.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/5b5d151b-3c7f-423a-9684-a301d78e9be5/a8de32a7-4eaf-498c-8b3f-17a2c36aba44_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C317832.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C317832.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C317832.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C317832.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/a3eb79f6-7744-45d2-b66f-8ab2c0a4a670/88fc297c-04d4-4bbe-885c-794e65593177_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C330255.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C330255.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C330255.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C330255.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/1342f51b-95be-4e96-9d04-5ce16089b486/cad8ffba-1e4f-4f8f-9378-0bd507f2444a_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C383391.WXS.T.ADNA_4db2e37f.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C383391.WXS.T.ADNA_4db2e37f.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C383391.WXS.T.ADNA_4db2e37f.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C383391.WXS.T.ADNA_4db2e37f.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/7341902c-8501-419d-a4a6-d88859d9a8d8/0d5862af-2f59-42b9-b6d8-5c1d84d662e9_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C383391.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C383391.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C383391.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C383391.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/cff641f8-776b-4b10-8983-71008ed827f4/f7d2db47-e553-4569-b883-51d139f98ef5_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-04081.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-04081.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-04081.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-04081.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/4f239bb8-5070-4cf0-b14c-599bbb7bfd94/fef12b13-bc4b-49fe-8975-9e7b25380154_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-05481.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-05481.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-05481.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-05481.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/e6b33d67-a8b0-42ce-8994-6e3e5e782da4/a8b62182-6e82-446f-bd1f-e829cf7979c7_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-06625.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-06625.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-06625.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-06625.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/926f6d61-0f53-4923-96cf-73626b0e0fe7/41fbd2d6-fccb-42f0-ae30-f26011c2e96e_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-07202.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-07202.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07202.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07202.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/5c4c8930-d564-4e1a-97bd-5971d536af18/ce1dba67-d732-46e3-9e72-096f6f0b75b9_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-07213.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-07213.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07213.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07213.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/57461fc1-881f-4b14-9c8c-6c795a225e1f/63cdc123-6efd-4d15-a5cb-4c8205b9eefe_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3L-07611.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3L-07611.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07611.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3L-07611.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/66ea66b9-4620-4c09-a59d-f9b1c0bcb09f/f135e074-b46a-473b-8015-439c78e8f6fd_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3N-01197.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3N-01197.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-01197.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-01197.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/813f42ab-91e9-4dbc-8d09-bf15289946f8/8a4a56fd-dd41-4555-b2ac-8f80c06a75e4_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3N-04113.WXS.T.RDNA_o25vvXX.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3N-04113.WXS.T.RDNA_o25vvXX.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-04113.WXS.T.RDNA_o25vvXX.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-04113.WXS.T.RDNA_o25vvXX.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/e4493502-3425-4529-96af-414aae684e99/1ac39c4d-4742-4eea-ac1a-074503b7b5a4_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C3N-05991.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C3N-05991.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-05991.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C3N-05991.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/7c48aae6-c19b-46e4-a8aa-205117088f07/0ca72fda-2cdf-415a-b5a4-53470bf3af60_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C464694.WXS.T.ADNA_7319b796.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C464694.WXS.T.ADNA_7319b796.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C464694.WXS.T.ADNA_7319b796.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C464694.WXS.T.ADNA_7319b796.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/00eb9000-e8b4-4b57-8f08-45b92aaba916/737a37b7-31a5-4187-a4fa-5e7171bb6569_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C464694.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C464694.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C464694.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C464694.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/44dd95c6-0058-43cc-8f40-781d00ea6f46/31b51dd4-c4fe-4d97-ae09-698217519667_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C524103.WXS.T.ADNA_aee3de0f.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C524103.WXS.T.ADNA_aee3de0f.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C524103.WXS.T.ADNA_aee3de0f.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C524103.WXS.T.ADNA_aee3de0f.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/35d02b21-b274-4b7c-ac81-9f4a5dd1176d/4c95a675-d17a-40a7-b77f-a2389895f7fe_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C524103.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C524103.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C524103.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C524103.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/2b0b81ce-7556-4be8-bf5f-6f359239cc39/ffd6163a-085f-4213-89e4-5bbc68bca404_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C621273.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C621273.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C621273.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C621273.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/4daf5e7f-6a2a-4c49-a2cb-abb712bacfae/3f83ce79-0cd9-4e7e-9352-726042aff7c8_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C685110.WXS.T.ADNA_224ab8cc.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C685110.WXS.T.ADNA_224ab8cc.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C685110.WXS.T.ADNA_224ab8cc.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C685110.WXS.T.ADNA_224ab8cc.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/0da7ee04-c471-488a-900b-44c538d9b274/9cd89b80-7f2d-4caf-9599-4457c80de4cd_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C685110.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C685110.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C685110.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C685110.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/533ec6cf-ac77-4d87-ad54-c8f34025c447/1e2e1134-2810-4845-91cb-feed8c0cb7af_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C760878.WXS.T.ADNA_b1ddc47c.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C760878.WXS.T.ADNA_b1ddc47c.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C760878.WXS.T.ADNA_b1ddc47c.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C760878.WXS.T.ADNA_b1ddc47c.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/dae070e2-2c6a-49ba-ae92-6f2319325e2a/9efda7a7-d54a-492b-9158-88f2644e909f_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C760878.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C760878.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C760878.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C760878.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/5495a6ee-951b-4613-b9d3-3344fe76a916/ad3ce926-8ffc-46c4-87c9-64fba596ac12_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C761370.WXS.T.ADNA_260f1df4.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C761370.WXS.T.ADNA_260f1df4.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C761370.WXS.T.ADNA_260f1df4.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C761370.WXS.T.ADNA_260f1df4.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/fd66e1f9-ce3b-4a76-9e48-23bf78568f41/59ba09c2-abf4-46dd-b566-c703d8da80e5_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C761370.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C761370.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C761370.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C761370.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/8541768d-a439-4abf-987e-d08039a4ec1d/94dc4f39-5f41-450e-bc88-b5efb574ab4b_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C827913.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C827913.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C827913.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C827913.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/295d757c-a37e-49f5-9d26-65dff2dbbf13/04ca4248-176f-4eda-89af-30230af7817d_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C846363.WXS.T.ADNA_51dcc4a3.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C846363.WXS.T.ADNA_51dcc4a3.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C846363.WXS.T.ADNA_51dcc4a3.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C846363.WXS.T.ADNA_51dcc4a3.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/83a989e8-836e-42b2-a240-f87f0858d189/9dd34d93-e75b-4bc5-b49a-b095ba8daf3e_wxs_gdc_realn.bam'\",\n",
+       " \"bsub -R 'select[mem>5GB] rusage[mem=5GB] span[hosts=1]' -M 6GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/slate:0.0.2)' -g /estorrs/ancestry_slate -J C846363.WXS.T.hg38 -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/logs/C846363.WXS.T.hg38.txt 'python /slate/slate/slate.py --min-base-quality 20 --min-mapping-quality 20 --fasta /storage1/fs1/dinglab/Active/Projects/PECGS/ref_genome/GRCh38.d1.vd1.fa --positions /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.bed --readcount-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C846363.WXS.T.hg38.readcount --filtered-bam-output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results/C846363.WXS.T.hg38.filtered.bam /storage1/fs1/dinglab/Active/Primary/CPTAC3.share/CPTAC3-GDC/GDC_import/data/e3e1eeb8-e749-4520-83e2-3ae1091a7207/d895aa40-8999-4f0b-be15-694f1bdb380c_wxs_gdc_realn.bam'\"]"
+      ]
+     },
+     "execution_count": 69,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "args['username'] = 'estorrs' # change username if you arent me :) \n",
+    "args['docker'] = 'estorrs/slate:0.0.2'\n",
+    "args['queue'] = 'general'\n",
+    "args['n_concurrent'] = 100\n",
+    "args['mem'] = 5\n",
+    "args['group_name'] = 'ancestry_slate' # job group name\n",
+    "\n",
+    "commands = []\n",
+    "for s_id, fp in zip(df['sample_id'], df['filepath']):\n",
+    "\n",
+    "    command = get_slate_command(fp,\n",
+    "                                os.path.join(result_dir, f'{s_id}.readcount'),\n",
+    "                                os.path.join(result_dir, f'{s_id}.filtered.bam'))\n",
+    "\n",
+    "    commands.append(command)\n",
+    "                     \n",
+    "bsub_commands = batch_bsub_commands(commands, df['sample_id'].to_list(), log_dir, args,\n",
+    "                                    volumes=volumes, exports=exports)\n",
+    "bsub_commands"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 71,
+   "id": "289b3d04",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/run_slate.sh'"
+      ]
+     },
+     "execution_count": 71,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "fp = os.path.join(execution_dir, 'run_slate.sh')\n",
+    "write_command_file(bsub_commands, fp)\n",
+    "fp"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ddbb0f74",
+   "metadata": {},
+   "source": [
+    "sanity check to make sure all runs completed successfully"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 73,
+   "id": "5e551369",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "(69, 69)"
+      ]
+     },
+     "execution_count": 73,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "fps = sorted(listfiles(log_dir, regex=r'.txt$'))\n",
+    "count = 0\n",
+    "for fp in fps:\n",
+    "    f = open(fp)\n",
+    "    if 'Successfully completed.' in f.read():\n",
+    "        count += 1\n",
+    "    f.close()\n",
+    "len(fps), count"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "d2b5b012",
+   "metadata": {},
+   "source": [
+    "After running, make sure to clean up slate directory, it produces trim bammed as an output and they take up a lot of space. run the below command to delete the unecessary fiels"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 75,
+   "id": "e032d66d",
+   "metadata": {
+    "scrolled": true
+   },
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "69"
+      ]
+     },
+     "execution_count": 75,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "fps = sorted(listfiles(result_dir, regex=r'.filtered.bam$'))\n",
+    "len(fps)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 76,
+   "id": "0120524a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "for fp in fps:\n",
+    "    os.remove(fp)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2a539285",
+   "metadata": {},
+   "source": [
+    "## step 2: run genotype caller"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 77,
+   "id": "ddd42f42",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "execution_dir = os.path.join(run_dir, '2.genotype_caller')\n",
+    "log_dir = os.path.join(execution_dir, 'logs')\n",
+    "result_dir = os.path.join(execution_dir, 'results')\n",
+    "Path(log_dir).mkdir(parents=True, exist_ok=True)\n",
+    "Path(result_dir).mkdir(parents=True, exist_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 78,
+   "id": "f5dc8982",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_genotype_calling_command(script, readcount_dir, output_fp):\n",
+    "    return f'python  {script} \\\n",
+    "--readcount-dir {readcount_dir} --genomes-vcf {thousand_genomes_vcf} \\\n",
+    "--output {output_fp}'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 79,
+   "id": "82996a39",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "{'mem': 10,\n",
+       " 'n_processes': 1,\n",
+       " 'max_mem': None,\n",
+       " 'docker': 'python:3.8',\n",
+       " 'queue': 'dinglab',\n",
+       " 'gpu_model': 'TeslaV100_SXM2_32GB',\n",
+       " 'gpu_mem': '30',\n",
+       " 'gpu_num': 1,\n",
+       " 'use_gpu': False,\n",
+       " 'group': 'compute-dinglab',\n",
+       " 'group_name': None,\n",
+       " 'n_concurrent': 10,\n",
+       " 'interactive': False,\n",
+       " 'username': 'estorrs'}"
+      ]
+     },
+     "execution_count": 79,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "volumes = ['/storage1/fs1/dinglab', '/scratch1/fs1/dinglab', '/home/estorrs'] # compute1 needs to know which directories to map, replace /home/<username> if you are not me\n",
+    "exports = ['/miniconda/envs/ancestry/bin'] # need to override compute1 PATH defaults\n",
+    "args = DEFAULT_ARGS.copy()\n",
+    "args"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 81,
+   "id": "3819a903",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "['mkdir -p /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/logs',\n",
+       " 'export LSF_DOCKER_VOLUMES=\"/storage1/fs1/dinglab:/storage1/fs1/dinglab /scratch1/fs1/dinglab:/scratch1/fs1/dinglab /home/estorrs:/home/estorrs /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/logs:/scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/logs\"',\n",
+       " 'export PATH=\"/opt/java/openjdk/bin:/miniconda/envs/ancestry/bin:$PATH\"',\n",
+       " \"bsub -R 'select[mem>100GB] rusage[mem=100GB] span[hosts=1]' -M 101GB -n 1 -q general -G compute-dinglab -a 'docker(estorrs/ancestry-pipeline:0.0.1)' -oo /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/logs/c.txt 'python  /ancestry-pipeline/ancestry/readcount_caller.py --readcount-dir /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/1.slate/results --genomes-vcf /storage1/fs1/dinglab/Active/Projects/Ancestry_Data/hg38/all.coding.sorted.02maf.snps.chr.vcf --output /scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/results/output.vcf'\"]"
+      ]
+     },
+     "execution_count": 81,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "args['username'] = 'estorrs' # change username if you arent me :) \n",
+    "args['docker'] = 'estorrs/ancestry-pipeline:0.0.1'\n",
+    "args['queue'] = 'general'\n",
+    "args['mem'] = 100\n",
+    "\n",
+    "command = get_genotype_calling_command(\n",
+    "    '/ancestry-pipeline/ancestry/readcount_caller.py',\n",
+    "    os.path.join(run_dir, '1.slate', 'results'),\n",
+    "    os.path.join(result_dir, 'output.vcf'))\n",
+    "\n",
+    "                     \n",
+    "bsub_commands = batch_bsub_commands([command], 'call readcounts', log_dir, args, volumes=volumes, exports=exports)\n",
+    "bsub_commands"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "444bfb55",
+   "metadata": {},
+   "source": [
+    "run the below script"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 82,
+   "id": "b8cd5ca8",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/scratch1/fs1/dinglab/estorrs/ancestry/executions/gbm_test/2.genotype_caller/run_readcount_caller.sh'"
+      ]
+     },
+     "execution_count": 82,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "fp = os.path.join(execution_dir, 'run_readcount_caller.sh')\n",
+    "write_command_file(bsub_commands, fp)\n",
+    "fp"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "38fee9f5",
+   "metadata": {},
+   "source": [
+    "## step 3: predict ancestry"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c0b591bf",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "execution_dir = os.path.join(run_dir, '3.predict_ancestry')\n",
+    "log_dir = os.path.join(execution_dir, 'logs')\n",
+    "result_dir = os.path.join(execution_dir, 'results')\n",
+    "Path(log_dir).mkdir(parents=True, exist_ok=True)\n",
+    "Path(result_dir).mkdir(parents=True, exist_ok=True)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "472e79e0",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "def get_ancestry_prediction_command(script, output_dir, sample_vcf_fp):\n",
+    "    return f'python  {script} \\\n",
+    "--output-dir {output_dir} {thousand_genomes_vcf} {thousand_genomes_panel} {sample_vcf_fp}'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "df4357c6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "volumes = ['/storage1/fs1/dinglab', '/scratch1/fs1/dinglab', '/home/estorrs'] # compute1 needs to know which directories to map, replace /home/<username> if you are not me\n",
+    "exports = ['/miniconda/envs/ancestry/bin'] # need to override compute1 PATH defaults\n",
+    "args = DEFAULT_ARGS.copy()\n",
+    "args"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "211f3336",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "args['username'] = 'estorrs' # change username if you arent me :) \n",
+    "args['docker'] = 'estorrs/ancestry-pipeline:0.0.1'\n",
+    "args['queue'] = 'general'\n",
+    "args['mem'] = 100\n",
+    "\n",
+    "command = get_ancestry_prediction_command(\n",
+    "    '/ancestry-pipeline/ancestry/ancestry_cli.py',\n",
+    "    result_dir,\n",
+    "    os.path.join(run_dir, '2.genotype_caller', 'results', 'output.vcf'))\n",
+    "   \n",
+    "bsub_commands = batch_bsub_commands([command], 'predict ancestry', log_dir, args, volumes=volumes)\n",
+    "bsub_commands"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "5ee88ca2",
+   "metadata": {},
+   "source": [
+    "run the below script"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0a179f13",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "fp = os.path.join(execution_dir, 'predict_ancestry.sh')\n",
+    "write_command_file(bsub_commands, fp)\n",
+    "fp"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "ba4be768",
+   "metadata": {},
+   "source": [
+    "## inspect results"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "ba3671af",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}