Read the Docs build information Build id: 725666 Project: life-epigenetics-methylprep Version: latest Commit: 2f7095dee4b439fac0dc3cd1e245fa5475cd4596 Date: 2021-09-20T18:52:24.325653Z State: finished Success: True [rtd-command-info] start-time: 2021-09-20T18:52:25.759165Z, end-time: 2021-09-20T18:52:43.369298Z, duration: 17, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/FOXOBioScience/methylprep.git . Cloning into '.'... 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[rtd-command-info] start-time: 2021-09-20T18:52:43.502611Z, end-time: 2021-09-20T18:52:44.033217Z, duration: 0, exit-code: 0 git checkout --force origin/master Note: checking out 'origin/master'. You are in 'detached HEAD' state. You can look around, make experimental changes and commit them, and you can discard any commits you make in this state without impacting any branches by performing another checkout. If you want to create a new branch to retain commits you create, you may do so (now or later) by using -b with the checkout command again. Example: git checkout -b HEAD is now at 2f7095d feature/v1.5.6 and feature/v1.5.5-docs (#95) [rtd-command-info] start-time: 2021-09-20T18:52:44.145505Z, end-time: 2021-09-20T18:52:44.221938Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2021-09-20T18:52:53.609328Z, end-time: 2021-09-20T18:52:58.132215Z, duration: 4, exit-code: 0 python3.7 -mvirtualenv --system-site-packages Using base prefix '/home/docs/.pyenv/versions/3.7.9' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2021-09-20T18:52:58.285019Z, end-time: 2021-09-20T18:52:59.502949Z, duration: 1, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip setuptools Requirement already satisfied: pip in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (21.2.4) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (58.0.4) [rtd-command-info] start-time: 2021-09-20T18:52:59.606277Z, end-time: 2021-09-20T18:53:08.535619Z, duration: 8, exit-code: 0 python -m pip install --upgrade --no-cache-dir -I mock==1.0.1 pillow==5.4.1 alabaster>=0.7,<0.8,!=0.7.5 commonmark==0.8.1 recommonmark==0.5.0 sphinx<2 sphinx-rtd-theme<0.5 readthedocs-sphinx-ext<2.2 Collecting mock==1.0.1 Downloading mock-1.0.1.zip (861 kB) Collecting pillow==5.4.1 Downloading Pillow-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (2.0 MB) Collecting alabaster!=0.7.5,<0.8,>=0.7 Downloading alabaster-0.7.12-py2.py3-none-any.whl (14 kB) Collecting commonmark==0.8.1 Downloading commonmark-0.8.1-py2.py3-none-any.whl (47 kB) Collecting recommonmark==0.5.0 Downloading recommonmark-0.5.0-py2.py3-none-any.whl (9.8 kB) Collecting sphinx<2 Downloading Sphinx-1.8.5-py2.py3-none-any.whl (3.1 MB) Collecting sphinx-rtd-theme<0.5 Downloading sphinx_rtd_theme-0.4.3-py2.py3-none-any.whl (6.4 MB) Collecting readthedocs-sphinx-ext<2.2 Downloading readthedocs_sphinx_ext-2.1.4-py2.py3-none-any.whl (29 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting docutils>=0.11 Downloading docutils-0.17.1-py2.py3-none-any.whl (575 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.9.1-py2.py3-none-any.whl (8.8 MB) Collecting requests>=2.0.0 Downloading requests-2.26.0-py2.py3-none-any.whl (62 kB) Collecting Pygments>=2.0 Downloading Pygments-2.10.0-py3-none-any.whl (1.0 MB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.4-py2.py3-none-any.whl (39 kB) Collecting Jinja2>=2.3 Downloading Jinja2-3.0.1-py3-none-any.whl (133 kB) Collecting six>=1.5 Downloading six-1.16.0-py2.py3-none-any.whl (11 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.1.0-py2.py3-none-any.whl (93 kB) Collecting packaging Downloading packaging-21.0-py3-none-any.whl (40 kB) Collecting setuptools Downloading setuptools-58.0.4-py3-none-any.whl (816 kB) Collecting pytz>=2015.7 Downloading pytz-2021.1-py2.py3-none-any.whl (510 kB) Collecting MarkupSafe>=2.0 Downloading MarkupSafe-2.0.1-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.manylinux_2_12_x86_64.manylinux2010_x86_64.whl (31 kB) Collecting idna<4,>=2.5 Downloading idna-3.2-py3-none-any.whl (59 kB) Collecting charset-normalizer~=2.0.0 Downloading charset_normalizer-2.0.6-py3-none-any.whl (37 kB) Collecting certifi>=2017.4.17 Downloading certifi-2021.5.30-py2.py3-none-any.whl (145 kB) Collecting urllib3<1.27,>=1.21.1 Downloading urllib3-1.26.6-py2.py3-none-any.whl (138 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting sphinxcontrib-serializinghtml Downloading sphinxcontrib_serializinghtml-1.1.5-py2.py3-none-any.whl (94 kB) Building wheels for collected packages: mock, future Building wheel for mock (setup.py): started Building wheel for mock (setup.py): finished with status 'done' Created wheel for mock: filename=mock-1.0.1-py3-none-any.whl size=23772 sha256=cf0def386b20e6d64fa9a822cce54e9ebb0dfe1cbf85ec592f20e55fbae3e4eb Stored in directory: /tmp/pip-ephem-wheel-cache-h4wob17o/wheels/7a/94/b1/0fdc5339a5bd487a5cc15421ec200d9ba3e2aa7190e4a727f1 Building wheel for future (setup.py): started Building wheel for future (setup.py): finished with status 'done' Created wheel for future: filename=future-0.18.2-py3-none-any.whl size=491070 sha256=6df9f3717fd45671fd8474b89f67e0877135087569a8befa83f4c6089610e136 Stored in directory: /tmp/pip-ephem-wheel-cache-h4wob17o/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: urllib3, sphinxcontrib-serializinghtml, pytz, pyparsing, MarkupSafe, idna, charset-normalizer, certifi, sphinxcontrib-websupport, snowballstemmer, six, setuptools, requests, Pygments, packaging, Jinja2, imagesize, future, docutils, babel, alabaster, sphinx, commonmark, sphinx-rtd-theme, recommonmark, readthedocs-sphinx-ext, pillow, mock ERROR: pip's dependency resolver does not currently take into account all the packages that are installed. This behaviour is the source of the following dependency conflicts. matplotlib 3.3.2 requires pillow>=6.2.0, but you have pillow 5.4.1 which is incompatible. Successfully installed Jinja2-3.0.1 MarkupSafe-2.0.1 Pygments-2.10.0 alabaster-0.7.12 babel-2.9.1 certifi-2021.5.30 charset-normalizer-2.0.6 commonmark-0.8.1 docutils-0.17.1 future-0.18.2 idna-3.2 imagesize-1.2.0 mock-1.0.1 packaging-21.0 pillow-5.4.1 pyparsing-2.4.7 pytz-2021.1 readthedocs-sphinx-ext-2.1.4 recommonmark-0.5.0 requests-2.26.0 setuptools-58.0.4 six-1.16.0 snowballstemmer-2.1.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-serializinghtml-1.1.5 sphinxcontrib-websupport-1.2.4 urllib3-1.26.6 [rtd-command-info] start-time: 2021-09-20T18:53:08.649525Z, end-time: 2021-09-20T18:53:23.452062Z, duration: 14, exit-code: 0 python -m pip install --exists-action=w --no-cache-dir -r requirements.txt Requirement already satisfied: numpy>=1.18.5 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 1)) (1.19.2) Collecting pandas<1.3,>=1.2 Downloading pandas-1.2.5-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (9.9 MB) Requirement already satisfied: scipy>=1.2.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from -r requirements.txt (line 3)) (1.5.3) Collecting statsmodels Downloading statsmodels-0.12.2-cp37-cp37m-manylinux1_x86_64.whl (9.5 MB) Collecting pytest Downloading pytest-6.2.5-py3-none-any.whl (280 kB) Collecting coverage Downloading coverage-5.5-cp37-cp37m-manylinux2010_x86_64.whl (242 kB) Collecting python-coveralls Downloading python_coveralls-2.9.3-py2.py3-none-any.whl (9.9 kB) Collecting sphinxcontrib-apidoc Downloading sphinxcontrib_apidoc-0.3.0-py2.py3-none-any.whl (8.5 kB) Collecting m2r Downloading m2r-0.2.1.tar.gz (16 kB) Collecting nbsphinx Downloading nbsphinx-0.8.7-py3-none-any.whl (25 kB) Collecting tqdm Downloading tqdm-4.62.3-py2.py3-none-any.whl (76 kB) Collecting bs4 Downloading bs4-0.0.1.tar.gz (1.1 kB) Collecting lxml Downloading lxml-4.6.3-cp37-cp37m-manylinux2014_x86_64.whl (6.3 MB) Requirement already satisfied: requests in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from -r requirements.txt (line 14)) (2.26.0) Requirement already satisfied: python-dateutil>=2.7.3 in /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages (from pandas<1.3,>=1.2->-r requirements.txt (line 2)) (2.8.1) Requirement already satisfied: pytz>=2017.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pandas<1.3,>=1.2->-r requirements.txt (line 2)) (2021.1) Collecting patsy>=0.5 Downloading patsy-0.5.1-py2.py3-none-any.whl (231 kB) Collecting attrs>=19.2.0 Downloading attrs-21.2.0-py2.py3-none-any.whl (53 kB) Collecting py>=1.8.2 Downloading py-1.10.0-py2.py3-none-any.whl (97 kB) Collecting pluggy<2.0,>=0.12 Downloading pluggy-1.0.0-py2.py3-none-any.whl (13 kB) Collecting toml Downloading toml-0.10.2-py2.py3-none-any.whl (16 kB) Collecting importlib-metadata>=0.12 Downloading importlib_metadata-4.8.1-py3-none-any.whl (17 kB) Requirement already satisfied: packaging in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from pytest->-r requirements.txt (line 5)) (21.0) Collecting iniconfig Downloading iniconfig-1.1.1-py2.py3-none-any.whl (5.0 kB) Requirement already satisfied: six in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from python-coveralls->-r requirements.txt (line 7)) (1.16.0) Collecting PyYAML Downloading PyYAML-5.4.1-cp37-cp37m-manylinux1_x86_64.whl (636 kB) Collecting pbr Downloading pbr-5.6.0-py2.py3-none-any.whl (111 kB) Requirement already satisfied: Sphinx>=1.6.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.8.5) Collecting mistune Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB) Requirement already satisfied: docutils in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from m2r->-r requirements.txt (line 9)) (0.17.1) Collecting nbformat Downloading nbformat-5.1.3-py3-none-any.whl (178 kB) Collecting nbconvert!=5.4 Downloading nbconvert-6.1.0-py3-none-any.whl (551 kB) Collecting traitlets Downloading traitlets-5.1.0-py3-none-any.whl (101 kB) Requirement already satisfied: jinja2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from nbsphinx->-r requirements.txt (line 10)) (3.0.1) Collecting beautifulsoup4 Downloading beautifulsoup4-4.10.0-py3-none-any.whl (97 kB) Requirement already satisfied: idna<4,>=2.5 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (3.2) Requirement already satisfied: charset-normalizer~=2.0.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (2.0.6) Requirement already satisfied: urllib3<1.27,>=1.21.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (1.26.6) Requirement already satisfied: certifi>=2017.4.17 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from requests->-r requirements.txt (line 14)) (2021.5.30) Collecting zipp>=0.5 Downloading zipp-3.5.0-py3-none-any.whl (5.7 kB) Collecting typing-extensions>=3.6.4 Downloading typing_extensions-3.10.0.2-py3-none-any.whl (26 kB) Collecting defusedxml Downloading defusedxml-0.7.1-py2.py3-none-any.whl (25 kB) Collecting jupyterlab-pygments Downloading jupyterlab_pygments-0.1.2-py2.py3-none-any.whl (4.6 kB) Collecting entrypoints>=0.2.2 Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB) Collecting nbclient<0.6.0,>=0.5.0 Downloading nbclient-0.5.4-py3-none-any.whl (66 kB) Collecting jupyter-core Downloading jupyter_core-4.8.1-py3-none-any.whl (86 kB) Requirement already satisfied: pygments>=2.4.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from nbconvert!=5.4->nbsphinx->-r requirements.txt (line 10)) (2.10.0) Collecting bleach Downloading bleach-4.1.0-py2.py3-none-any.whl (157 kB) Collecting testpath Downloading testpath-0.5.0-py3-none-any.whl (84 kB) Collecting pandocfilters>=1.4.1 Downloading pandocfilters-1.5.0-py2.py3-none-any.whl (8.7 kB) Requirement already satisfied: MarkupSafe>=2.0 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from jinja2->nbsphinx->-r requirements.txt (line 10)) (2.0.1) Collecting jupyter-client>=6.1.5 Downloading jupyter_client-7.0.3-py3-none-any.whl (122 kB) Collecting nest-asyncio Downloading nest_asyncio-1.5.1-py3-none-any.whl (5.0 kB) Collecting tornado>=4.1 Downloading tornado-6.1-cp37-cp37m-manylinux2010_x86_64.whl (428 kB) Collecting pyzmq>=13 Downloading pyzmq-22.3.0-cp37-cp37m-manylinux_2_5_x86_64.manylinux1_x86_64.whl (1.1 MB) Collecting jsonschema!=2.5.0,>=2.4 Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB) Collecting ipython-genutils Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB) Requirement already satisfied: setuptools in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat->nbsphinx->-r requirements.txt (line 10)) (58.0.4) Collecting pyrsistent>=0.14.0 Downloading pyrsistent-0.18.0-cp37-cp37m-manylinux1_x86_64.whl (119 kB) Requirement already satisfied: snowballstemmer>=1.1 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.1.0) Requirement already satisfied: sphinxcontrib-websupport in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.2.4) Requirement already satisfied: imagesize in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.2.0) Requirement already satisfied: babel!=2.0,>=1.3 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (2.9.1) Requirement already satisfied: alabaster<0.8,>=0.7 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (0.7.12) Collecting soupsieve>1.2 Downloading soupsieve-2.2.1-py3-none-any.whl (33 kB) Collecting webencodings Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB) Requirement already satisfied: pyparsing>=2.0.2 in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from packaging->pytest->-r requirements.txt (line 5)) (2.4.7) Requirement already satisfied: sphinxcontrib-serializinghtml in /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest/lib/python3.7/site-packages (from sphinxcontrib-websupport->Sphinx>=1.6.0->sphinxcontrib-apidoc->-r requirements.txt (line 8)) (1.1.5) Building wheels for collected packages: m2r, bs4 Building wheel for m2r (setup.py): started Building wheel for m2r (setup.py): finished with status 'done' Created wheel for m2r: filename=m2r-0.2.1-py3-none-any.whl size=10475 sha256=8620b4ae3bc2a4bf5e838e7629dd3ff5fdd2dac621a636d41a6d68272000dbab Stored in directory: /tmp/pip-ephem-wheel-cache-qacld184/wheels/02/47/3a/e1c46c2cca442c8781612542397c9559a579f10e2dd87e7c9f Building wheel for bs4 (setup.py): started Building wheel for bs4 (setup.py): finished with status 'done' Created wheel for bs4: filename=bs4-0.0.1-py3-none-any.whl size=1271 sha256=a951b5b7c1df1e8f1f83c48ab3424b24775a15b8e9adc0496d4e03bdc696ac0f Stored in directory: /tmp/pip-ephem-wheel-cache-qacld184/wheels/0a/9e/ba/20e5bbc1afef3a491f0b3bb74d508f99403aabe76eda2167ca Successfully built m2r bs4 Installing collected packages: zipp, typing-extensions, traitlets, pyrsistent, importlib-metadata, attrs, tornado, pyzmq, nest-asyncio, jupyter-core, jsonschema, ipython-genutils, entrypoints, webencodings, nbformat, jupyter-client, testpath, soupsieve, pandocfilters, nbclient, mistune, jupyterlab-pygments, defusedxml, bleach, toml, PyYAML, py, pluggy, pbr, patsy, pandas, nbconvert, iniconfig, coverage, beautifulsoup4, tqdm, statsmodels, sphinxcontrib-apidoc, python-coveralls, pytest, nbsphinx, m2r, lxml, bs4 Attempting uninstall: pandas Found existing installation: pandas 1.1.3 Not uninstalling pandas at /home/docs/.pyenv/versions/3.7.9/lib/python3.7/site-packages, outside environment /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/envs/latest Can't uninstall 'pandas'. No files were found to uninstall. Successfully installed PyYAML-5.4.1 attrs-21.2.0 beautifulsoup4-4.10.0 bleach-4.1.0 bs4-0.0.1 coverage-5.5 defusedxml-0.7.1 entrypoints-0.3 importlib-metadata-4.8.1 iniconfig-1.1.1 ipython-genutils-0.2.0 jsonschema-3.2.0 jupyter-client-7.0.3 jupyter-core-4.8.1 jupyterlab-pygments-0.1.2 lxml-4.6.3 m2r-0.2.1 mistune-0.8.4 nbclient-0.5.4 nbconvert-6.1.0 nbformat-5.1.3 nbsphinx-0.8.7 nest-asyncio-1.5.1 pandas-1.2.5 pandocfilters-1.5.0 patsy-0.5.1 pbr-5.6.0 pluggy-1.0.0 py-1.10.0 pyrsistent-0.18.0 pytest-6.2.5 python-coveralls-2.9.3 pyzmq-22.3.0 soupsieve-2.2.1 sphinxcontrib-apidoc-0.3.0 statsmodels-0.12.2 testpath-0.5.0 toml-0.10.2 tornado-6.1 tqdm-4.62.3 traitlets-5.1.0 typing-extensions-3.10.0.2 webencodings-0.5.1 zipp-3.5.0 [rtd-command-info] start-time: 2021-09-20T18:53:24.476490Z, end-time: 2021-09-20T18:53:24.554719Z, duration: 0, exit-code: 0 cat conf.py # -*- coding: utf-8 -*- # # Configuration file for the Sphinx documentation builder. # # This file does only contain a selection of the most common options. For a # full list see the documentation: # http://www.sphinx-doc.org/en/master/config # -- Path setup -------------------------------------------------------------- # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. # import os import sys sys.path.insert(0, os.path.abspath('.')) # -- Project information ----------------------------------------------------- project = 'methylprep' copyright = '2021, FOXO Technologies, inc.' author = 'FOXO Technologies, inc.' # The short X.Y version version = '1.5' # The full version, including alpha/beta/rc tags release = '1.5' # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ 'sphinx.ext.autodoc', 'sphinxcontrib.apidoc', 'm2r', 'nbsphinx', 'sphinx.ext.autosummary', 'sphinx.ext.doctest', 'sphinx.ext.intersphinx', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.mathjax', 'sphinx.ext.ifconfig', 'sphinx.ext.viewcode', 'sphinx.ext.githubpages', ] # instead of CLI "sphinx-autodoc . _build/html" you write this apidoc_module_dir = '.' apidoc_output_dir = '_sphinx_build' apidoc_excluded_paths = ['tests'] apidoc_separate_modules = False # Add any paths that contain templates here, relative to this directory. templates_path = ['_sphinx_templates'] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # source_suffix = ['.rst', '.md'] # source_suffix = '.rst' # The master toctree document. master_doc = 'index' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path . exclude_patterns = ['_sphinx_build', 'Thumbs.db', '.DS_Store'] # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' todo_include_todos = True # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # html_theme = 'sphinx_rtd_theme' #'alabaster', 'nature' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['_sphinx_static'] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = 'methylpredoc' # -- Options for LaTeX output ------------------------------------------------ #latex_engine = 'xelatex' #latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', #} # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, 'methylprep.tex', 'methylprep Documentation', 'Life Epigenetics', 'manual'), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [ (master_doc, 'methylprep', 'methylprep Documentation', [author], 1) ] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ (master_doc, 'methylprep', 'methylprep Documentation', author, 'methylprep', 'One line description of project.', 'Miscellaneous'), ] # -- Extension configuration ------------------------------------------------- ########################################################################### # auto-created readthedocs.org specific configuration # ########################################################################### # # The following code was added during an automated build on readthedocs.org # It is auto created and injected for every build. The result is based on the # conf.py.tmpl file found in the readthedocs.org codebase: # https://github.com/rtfd/readthedocs.org/blob/master/readthedocs/doc_builder/templates/doc_builder/conf.py.tmpl # # Note: this file shouldn't rely on extra dependencies. import importlib import sys import os.path # Borrowed from six. PY3 = sys.version_info[0] == 3 string_types = str if PY3 else basestring from sphinx import version_info # Get suffix for proper linking to GitHub # This is deprecated in Sphinx 1.3+, # as each page can have its own suffix if globals().get('source_suffix', False): if isinstance(source_suffix, string_types): SUFFIX = source_suffix elif isinstance(source_suffix, (list, tuple)): # Sphinx >= 1.3 supports list/tuple to define multiple suffixes SUFFIX = source_suffix[0] elif isinstance(source_suffix, dict): # Sphinx >= 1.8 supports a mapping dictionary for multiple suffixes SUFFIX = list(source_suffix.keys())[0] # make a ``list()`` for py2/py3 compatibility else: # default to .rst SUFFIX = '.rst' else: SUFFIX = '.rst' # Add RTD Static Path. Add to the end because it overwrites previous files. if not 'html_static_path' in globals(): html_static_path = [] if os.path.exists('_static'): html_static_path.append('_static') # Add RTD Theme only if they aren't overriding it already using_rtd_theme = ( ( 'html_theme' in globals() and html_theme in ['default'] and # Allow people to bail with a hack of having an html_style 'html_style' not in globals() ) or 'html_theme' not in globals() ) if using_rtd_theme: theme = importlib.import_module('sphinx_rtd_theme') html_theme = 'sphinx_rtd_theme' html_style = None html_theme_options = {} if 'html_theme_path' in globals(): html_theme_path.append(theme.get_html_theme_path()) else: html_theme_path = [theme.get_html_theme_path()] if globals().get('websupport2_base_url', False): websupport2_base_url = 'https://readthedocs.com/websupport' websupport2_static_url = 'https://assets.readthedocs.com/' #Add project information to the template context. context = { 'using_theme': using_rtd_theme, 'html_theme': html_theme, 'current_version': "latest", 'version_slug': "latest", 'MEDIA_URL': "https://media.readthedocs.com/media/", 'STATIC_URL': "https://assets.readthedocs.com/", 'PRODUCTION_DOMAIN': "readthedocs.com", 'versions': [ ("latest", "/en/latest/"), ], 'downloads': [ ("html", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//life-epigenetics-methylprep.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'life-epigenetics-methylprep', 'name': u'methylprep', 'rtd_language': u'en', 'programming_language': u'py', 'canonical_url': 'https://life-epigenetics-methylprep.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'github_user': 'FOXOBioScience', 'proxied_api_host': '/_', 'github_repo': 'methylprep', 'github_version': 'master', 'display_github': True, 'bitbucket_user': 'None', 'bitbucket_repo': 'None', 'bitbucket_version': 'master', 'display_bitbucket': False, 'gitlab_user': 'None', 'gitlab_repo': 'None', 'gitlab_version': 'master', 'display_gitlab': False, 'READTHEDOCS': True, 'using_theme': (html_theme == "default"), 'new_theme': (html_theme == "sphinx_rtd_theme"), 'source_suffix': SUFFIX, 'ad_free': False, 'docsearch_disabled': False, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': '2f7095de', } # For sphinx >=1.8 we can use html_baseurl to set the canonical URL. # https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_baseurl if version_info >= (1, 8): if not globals().get('html_baseurl'): html_baseurl = context['canonical_url'] context['canonical_url'] = None if 'html_context' in globals(): html_context.update(context) else: html_context = context # Add custom RTD extension if 'extensions' in globals(): # Insert at the beginning because it can interfere # with other extensions. # See https://github.com/rtfd/readthedocs.org/pull/4054 extensions.insert(0, "readthedocs_ext.readthedocs") else: extensions = ["readthedocs_ext.readthedocs"] # Add External version warning banner to the external version documentation if 'branch' == 'external': extensions.insert(1, "readthedocs_ext.external_version_warning") readthedocs_vcs_url = 'None' readthedocs_build_url = 'https://readthedocs.com/projects/life-epigenetics-methylprep/builds/725666/' project_language = 'en' # User's Sphinx configurations language_user = globals().get('language', None) latex_engine_user = globals().get('latex_engine', None) latex_elements_user = globals().get('latex_elements', None) # Remove this once xindy gets installed in Docker image and XINDYOPS # env variable is supported # https://github.com/rtfd/readthedocs-docker-images/pull/98 latex_use_xindy = False chinese = any([ language_user in ('zh_CN', 'zh_TW'), project_language in ('zh_CN', 'zh_TW'), ]) japanese = any([ language_user == 'ja', project_language == 'ja', ]) if chinese: latex_engine = latex_engine_user or 'xelatex' latex_elements_rtd = { 'preamble': '\\usepackage[UTF8]{ctex}\n', } latex_elements = latex_elements_user or latex_elements_rtd elif japanese: latex_engine = latex_engine_user or 'platex' # Make sure our build directory is always excluded exclude_patterns = globals().get('exclude_patterns', []) exclude_patterns.extend(['_build']) [rtd-command-info] start-time: 2021-09-20T18:53:24.665111Z, end-time: 2021-09-20T18:53:34.211340Z, duration: 9, exit-code: 0 python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/setup.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.download.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.files.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.models.rst. Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/methylprep.processing.rst. 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1264--1264 []\T1/pcr/m/n/10 bool| Overfull \hbox (8.05069pt too wide) in paragraph at lines 1264--1264 []\T1/pcr/m/n/10 True| [20] Overfull \hbox (6.03357pt too wide) in paragraph at lines 1346--1346 []\T1/phv/m/n/10 Type| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1346--1346 []\T1/pcr/m/n/10 str| Overfull \hbox (9.00366pt too wide) in paragraph at lines 1346--1346 []\T1/pcr/m/n/10 bool| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1346--1346 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1419--1420 []|\T1/ptm/m/n/10 -b BATCH_SIZE, Underfull \hbox (badness 10000) in paragraph at lines 1419--1420 \T1/ptm/m/n/10 ^^Ubatch_size [21] Overfull \hbox (6.03357pt too wide) in paragraph at lines 1513--1513 []\T1/phv/m/n/10 Type| Overfull \hbox (1.11353pt too wide) in paragraph at lines 1513--1513 []\T1/phv/m/n/10 De- Overfull \hbox (3.60335pt too wide) in paragraph at lines 1513--1513 \T1/phv/m/n/10 fault| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1513--1513 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1513--1513 []\T1/ptm/m/n/10 -d DATA_DIR, ^^Udata_dir Overfull \hbox (3.00366pt too wide) in paragraph at lines 1513--1513 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 10000) in paragraph at lines 1513--1513 []\T1/ptm/m/n/10 -b BUCKET, ^^Ubucket Overfull \hbox (3.00366pt too wide) in paragraph at lines 1513--1513 []\T1/pcr/m/n/10 str| Overfull \hbox (3.00366pt too wide) in paragraph at lines 1513--1513 []\T1/pcr/m/n/10 str| Underfull \hbox (badness 7012) in paragraph at lines 1513--1513 []\T1/ptm/m/n/10 -p PRO-CESSED_BUCKET, Underfull \hbox (badness 10000) in paragraph at lines 1513--1513 \T1/ptm/m/n/10 ^^Upro-cessed_bucket PRO- Overfull \hbox (3.00366pt too wide) in paragraph at lines 1513--1513 []\T1/pcr/m/n/10 str| [22] Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/pcr/m/n/10 str\T1/ptm/m/n/10 , Overfull \hbox (3.16339pt too wide) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/ptm/m/n/10 -d DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/pcr/m/n/10 str\T1/ptm/m/n/10 , Overfull \hbox (3.16339pt too wide) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/ptm/m/n/10 -k KEY-WORD Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 ^^Ukey-word KEY- [23] Overfull \hbox (2.91867pt too wide) in paragraph at lines 1705--1705 []\T1/phv/m/n/10 Type| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -d Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 str Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 or Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 \T1/pcr/m/n/10 path| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -k KEY- Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 WORD, Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Ukey-word Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -s, Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 bool| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -o, Overfull \hbox (14.47574pt too wide) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Udont_download| Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 bool| [24] Underfull \hbox (badness 10000) in paragraph at lines 1758--1760 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1758--1760 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 1758--1760 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 1779--1780 []|\T1/pcr/m/n/10 sample_sheet_filepath| [25] Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 []|\T1/ptm/m/n/10 List of pro-cess-ing Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 \T1/ptm/m/n/10 steps: [`all', `in- Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 \T1/ptm/m/n/10 fer_channel_switch', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 Any-thing not spec-i-fied Underfull \hbox (badness 6380) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 is not saved. [`all', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 `un-meth', `noob_meth', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 `noob_unmeth', `sam- Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 ple_sheet_meta_data', Underfull \hbox (badness 10000) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 re-turn [beta, m_value, Underfull \hbox (badness 10000) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 copy_number, None] Underfull \hbox (badness 5022) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 (re-turns data con-tain-ers [26] Overfull \hbox (978.80003pt too wide) in paragraph at lines 2--1865 [][][][][][] [27] Overfull \vbox (164.14424pt too high) has occurred while \output is active [28 <./processing_pipeline.png>] Overfull \hbox (21.06123pt too wide) in paragraph at lines 1904--1905 []|\T1/pcr/m/n/10 sample_sheet_filepath| [29] Underfull \hbox (badness 10000) in paragraph at lines 1987--1989 []\T1/ptm/m/n/10 methylprep does not rec-og-nize the older 27k ar-ray file-name for-mat: [30] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562837| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in 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[57] [58] LaTeX Warning: Reference `docs/source/modules:module-methylprep' on page 59 und efined on input line 4985. LaTeX Warning: Reference `docs/source/modules:module-methylprep.download' on pa ge 59 undefined on input line 4986. LaTeX Warning: Reference `docs/source/modules:module-methylprep.files' on page 59 undefined on input line 4987. LaTeX Warning: Reference `docs/source/modules:module-methylprep.models' on page 59 undefined on input line 4988. LaTeX Warning: Reference `docs/source/modules:module-methylprep.processing' on page 59 undefined on input line 4989. [59] No file life-epigenetics-methylprep.ind. Package longtable Warning: Table widths have changed. Rerun LaTeX. (./life-epigenetics-methylprep.aux) Package rerunfilecheck Warning: File `life-epigenetics-methylprep.out' has chan ged. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. LaTeX Warning: Label(s) may have changed. Rerun to get cross-references right. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylprep.pdf (63 pages, 941015 bytes). Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: Missing input file: 'life-epigenetics-methylprep.ind' from line 'No file life-epigenetics-methylprep.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylprep.pdf' Latexmk: List of undefined refs and citations: Reference `docs/source/modules:module-methylprep' on page 59 undefined on input line 4985 Reference `docs/source/modules:module-methylprep.download' on page 59 undefined on input line 4986 Reference `docs/source/modules:module-methylprep.files' on page 59 undefined on input line 4987 Reference `docs/source/modules:module-methylprep.models' on page 59 undefined on input line 4988 Reference `docs/source/modules:module-methylprep.processing' on page 59 undefined on input line 4989 Latexmk: Summary of warnings: Latex failed to resolve 5 reference(s) Rule 'makeindex life-epigenetics-methylprep.idx': File changes, etc: Non-existent destination files: 'life-epigenetics-methylprep.ind' ------------ Run number 1 of rule 'makeindex life-epigenetics-methylprep.idx' ------------ ------------ Running 'makeindex -s python.ist -o "life-epigenetics-methylprep.ind" "life-epigenetics-methylprep.idx"' ------------ Latexmk: applying rule 'makeindex life-epigenetics-methylprep.idx'... This is makeindex, version 2.15 [TeX Live 2017] (kpathsea + Thai support). Scanning style file ./python.ist.......done (7 attributes redefined, 0 ignored). Scanning input file life-epigenetics-methylprep.idx....done (93 entries accepted, 0 rejected). Sorting entries....done (643 comparisons). Generating output file life-epigenetics-methylprep.ind....done (158 lines written, 0 warnings). Output written in life-epigenetics-methylprep.ind. Transcript written in life-epigenetics-methylprep.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.aux' 'life-epigenetics-methylprep.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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lines 2250--2250 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562837| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562839| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R03C02| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.06946| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.12989| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.04703| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09808| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.14105| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.54662| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562842| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R05C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.10986| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.13565| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.07657| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09125| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.12521| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.49317| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562846| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840037| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.11508| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.14116| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.0679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09415| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.15311| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.47829| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull 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Underfull \hbox (badness 6380) in paragraph at lines 2756--2757 []|[][]\T1/pcr/m/sl/10 methylprep.run_series[][]\T1/ptm/m/n/10 (id, path[, dict _only, Overfull \hbox (2.88234pt too wide) in paragraph at lines 2766--2767 []|[][]\T1/pcr/m/sl/10 methylprep.build_composite_dataset[][]\T1/ptm/m/n/10 (.. .[, [34] Underfull \hbox (badness 10000) in paragraph at lines 2857--2857 []\T1/ptm/m/it/10 array_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 filepath_or_buffer =None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 on_lambda=False\T1/ptm/m/n/10 , \T1/ptm/m /it/10 ver- [35] Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 \T1/ptm/m/it/10 poobah=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_sig=0.05\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex- [36] Underfull \hbox (badness 10000) in paragraph at lines 3071--3071 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , [37] Underfull \hbox (badness 10000) in paragraph at lines 3130--3130 []\T1/ptm/m/it/10 geo_id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data_dir='.'\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 merge=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 down-load_it= True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3130--3130 \T1/ptm/m/it/10 tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quire_k eyword=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sync_idats=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 sync_idats=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [38] Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i-fest_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 sam-ple_sheet_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam -ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 make_sample_sheet =False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3411--3418 []\T1/ptm/m/n/10 export=False, make_sample_sheet=False, ex-port_poobah=False, s ave_uncorrected=False, Underfull \hbox (badness 10000) in paragraph at lines 3419--3424 []\T1/ptm/m/n/10 betas=False, m_value=False, - Underfull \hbox (badness 10000) in paragraph at lines 3435--3441 []\T1/ptm/m/n/10 data_dir, ar-ray_type=None, Underfull \hbox (badness 10000) in paragraph at lines 3449--3452 [] Overfull \hbox (15.91293pt too wide) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 tain_uncorrected_probe_intensities=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pval=False\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 poobah_decimals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 do_noob=True\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 qual-ity_mask=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 switch_probes=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 do_nonlinear_dye_bias=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de- [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i- Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 fest_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam-ple_shee t_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 sam-ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\ T1/ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 make_sample_sheet=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_s ize=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float 32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 ex-port_poobah=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_dec imals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_memory=True \T1/ptm/m/n/10 , \T1/ptm/m/it/10 sesame=True\T1/ptm/m/n/10 , [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=True\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3819--3819 []\T1/ptm/m/it/10 sample_sheet\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- Underfull \hbox (badness 10000) in paragraph at lines 3819--3819 \T1/ptm/m/it/10 ple_name=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3819--3819 \T1/ptm/m/it/10 from_s3=None\T1/ptm/m/n/10 , [45] [46] [47] Underfull \hbox (badness 10000) in paragraph at lines 4062--4062 []\T1/ptm/m/it/10 filepath_or_buffer\T1/ptm/m/n/10 , \T1/ptm/m/it/10 chan-nel\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 idat_id='IDAT'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4062--4062 \T1/ptm/m/it/10 idat_version=3\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ver-bose=False\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 std_dev=False\T1/ptm/m/n/10 , [48] Underfull \hbox (badness 10000) in paragraph at lines 4280--4280 []\T1/ptm/m/it/10 dir_path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ma-trix_file=False\T 1/ptm/m/n/10 , \T1/ptm/m/it/10 out- Underfull \hbox (badness 10000) in paragraph at lines 4280--4280 \T1/ptm/m/it/10 put_file='samplesheet.csv'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- ple_type=''\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- [49] Underfull \hbox (badness 10000) in paragraph at lines 4343--4343 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4373--4373 []\T1/ptm/m/it/10 list_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=10 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4402--4402 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 4548--4552 []\T1/ptm/m/n/10 to ini-tial-ize, Overfull \hbox (75.29005pt too wide) in paragraph at lines 4583--4583 [] Underfull \hbox (badness 10000) in paragraph at lines 4583--4583 [52] Overfull \hbox (8.5906pt too wide) in paragraph at lines 4596--4596 [] Underfull \hbox (badness 10000) in paragraph at lines 4596--4596 Overfull \hbox (160.70894pt too wide) in paragraph at lines 4607--4607 [] Underfull \hbox (badness 10000) in paragraph at lines 4607--4607 Underfull \hbox (badness 10000) in paragraph at lines 4636--4641 [] Overfull \hbox (15.5806pt too wide) in paragraph at lines 4677--4680 [] Overfull \hbox (65.49059pt too wide) in paragraph at lines 4684--4686 [] [53] Overfull \hbox (60.42044pt too wide) in paragraph at lines 4690--4692 [] [54] Overfull \hbox (30.86986pt too wide) in paragraph at lines 4811--4814 [] Underfull \hbox (badness 10000) in paragraph at lines 4854--4856 [] [55] Underfull \hbox (badness 10000) in paragraph at lines 4952--4955 []\T1/ptm/m/n/10 batch_size will split Underfull \hbox (badness 10000) in paragraph at lines 4962--4964 [] [56] Chapter 2. [57] [58] [59] (./life-epigenetics-methylprep.ind [60] Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 alternate_base_filename \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl - Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 build_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.fi les.SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 check_for_probe_loss() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 31--32 []\T1/pcr/m/n/10 control_data_frame \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .Manifest at- Underfull \hbox (badness 10000) in paragraph at lines 35--36 []\T1/pcr/m/n/10 convert_miniml() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule me thyl- Underfull \hbox (badness 10000) in paragraph at lines 36--37 []\T1/pcr/m/n/10 create_sample_sheet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/pcr/m/n/10 detect_and_drop_duplicates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 download_default() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .files.Manifest Overfull \hbox (5.70073pt too wide) in paragraph at lines 50--52 []\T1/pcr/m/n/10 export() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.processin g.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 from_probe_count \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.A rrayType at- Underfull \hbox (badness 10000) in paragraph at lines 62--64 []\T1/pcr/m/n/10 get_export_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/pcr/m/n/10 get_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.mod els.Sample Underfull \hbox (badness 10000) in paragraph at lines 66--67 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 68--69 []\T1/pcr/m/n/10 get_sample() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.files .SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 71--72 []\T1/pcr/m/n/10 get_sample_sheet_s3() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- Underfull \hbox (badness 10000) in paragraph at lines 72--73 []\T1/pcr/m/n/10 get_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.file s.SampleSheet [61] Underfull \hbox (badness 10000) in paragraph at lines 80--81 []\T1/pcr/m/n/10 ILLUMINA_EPIC_PLUS \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .ArrayType Overfull \hbox (4.1225pt too wide) in paragraph at lines 105--107 []\T1/pcr/m/n/10 parse_sample_sheet_into_idat_datasets() Overfull \hbox (4.1225pt too wide) in paragraph at lines 107--109 []\T1/pcr/m/n/10 parse_sample_sheet_into_idat_datasets() Underfull \hbox (badness 10000) in paragraph at lines 111--112 []\T1/pcr/m/n/10 preprocess_noob() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 113--115 []\T1/pcr/m/n/10 process_all() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 113--115 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 115--117 []\T1/pcr/m/n/10 process_beta_value() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 115--117 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 117--119 []\T1/pcr/m/n/10 process_copy_number() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 117--119 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 119--121 []\T1/pcr/m/n/10 process_m_value() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 119--121 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 128--129 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-p rep.Manifest Underfull \hbox (badness 10000) in paragraph at lines 129--130 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 130--131 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 132--133 []\T1/pcr/m/n/10 read_snp_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep. files.Manifest Underfull 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(rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylprep.pdf (66 pages, 952055 bytes). Transcript written on life-epigenetics-methylprep.log. Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: References changed. Latexmk: Log file says output to 'life-epigenetics-methylprep.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'life-epigenetics-methylprep.aux' 'life-epigenetics-methylprep.out' 'life-epigenetics-methylprep.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="life-epigenetics-methylprep" "methylprep.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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at lines 1602--1602 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/ptm/m/n/10 -d DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/pcr/m/n/10 str\T1/ptm/m/n/10 , Overfull \hbox (3.16339pt too wide) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 filepath| Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 []\T1/ptm/m/n/10 -k KEY-WORD Underfull \hbox (badness 10000) in paragraph at lines 1602--1602 \T1/ptm/m/n/10 ^^Ukey-word KEY- [23] Overfull \hbox (2.91867pt too wide) in paragraph at lines 1705--1705 []\T1/phv/m/n/10 Type| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -d Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 DATA_DIR, Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Udata_dir Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 str Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 or Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 \T1/pcr/m/n/10 path| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -k KEY- Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 WORD, Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Ukey-word Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -s, Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 bool| Underfull \hbox (badness 10000) in paragraph at lines 1705--1705 []\T1/ptm/m/n/10 -o, Overfull \hbox (14.47574pt too wide) in paragraph at lines 1705--1705 \T1/ptm/m/n/10 ^^Udont_download| Overfull \hbox (5.88876pt too wide) in paragraph at lines 1705--1705 []\T1/pcr/m/n/10 bool| [24] Underfull \hbox (badness 10000) in paragraph at lines 1758--1760 \T1/ptm/m/n/10 val-ues are \T1/pcr/m/n/10 custom\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 1758--1760 \T1/pcr/m/n/10 450k\T1/ptm/m/n/10 , \T1/pcr/m/n/10 epic\T1/ptm/m/n/10 , and Underfull \hbox (badness 5302) in paragraph at lines 1758--1760 \T1/ptm/m/n/10 to de-ter-mine the ar-ray Overfull \hbox (21.06123pt too wide) in paragraph at lines 1779--1780 []|\T1/pcr/m/n/10 sample_sheet_filepath| [25] Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 []|\T1/ptm/m/n/10 List of pro-cess-ing Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 \T1/ptm/m/n/10 steps: [`all', `in- Underfull \hbox (badness 10000) in paragraph at lines 1837--1839 \T1/ptm/m/n/10 fer_channel_switch', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 Any-thing not spec-i-fied Underfull \hbox (badness 6380) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 is not saved. [`all', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 `un-meth', `noob_meth', Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 `noob_unmeth', `sam- Underfull \hbox (badness 10000) in paragraph at lines 1846--1848 \T1/ptm/m/n/10 ple_sheet_meta_data', Underfull \hbox (badness 10000) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 re-turn [beta, m_value, Underfull \hbox (badness 10000) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 copy_number, None] Underfull \hbox (badness 5022) in paragraph at lines 1855--1857 \T1/ptm/m/n/10 (re-turns data con-tain-ers [26] Overfull \hbox (978.80003pt too wide) in paragraph at lines 2--1865 [][][][][][] [27] Overfull \vbox (164.14424pt too high) has occurred while \output is active [28 <./processing_pipeline.png>] Overfull \hbox (21.06123pt too wide) in paragraph at lines 1904--1905 []|\T1/pcr/m/n/10 sample_sheet_filepath| [29] Underfull \hbox (badness 10000) in paragraph at lines 1987--1989 []\T1/ptm/m/n/10 methylprep does not rec-og-nize the older 27k ar-ray file-name for-mat: [30] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2250--2250 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562835| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R01C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05544| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07946| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0159| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.09557| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.05515| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.72663| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562836| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C01| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.08279| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.22216| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03107| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0769| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07915| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.54165| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 GSM3562837| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 R02C02| Overfull \hbox (27.51938pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (2.21338pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 case| Overfull \hbox (9.44347pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.03779| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07368| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.00385| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.07548| Overfull \hbox (11.88266pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.0891| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 0.74809| Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 case Underfull \hbox (badness 10000) in paragraph at lines 2250--2250 \T1/ptm/m/n/10 sam- [31] [32] Overfull \hbox (23.34323pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 GSM_ID| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sam- Overfull \hbox (16.54153pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 ple_Name| Overfull \hbox (6.12341pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (14.04317pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_ID| Overfull \hbox (4.55806pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sen- Overfull \hbox (37.5475pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 trix_Position| Overfull \hbox (10.87962pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 source| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 di- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 ag- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 no- Overfull \hbox (1.68347pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 age| Overfull \hbox (1.93358pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 Sex| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 tis- Overfull \hbox (1.12354pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 sue| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 cd8t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (3.90343pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 cd4t| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (5.56348pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 bcell| Overfull \hbox (27.1722pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (9.39243pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 mono| Overfull \hbox (27.7932pt too wide) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 cellcount- Overfull \hbox (4.81345pt too wide) in paragraph at lines 2646--2646 \T1/phv/m/n/10 gran| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/phv/m/n/10 de- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/phv/m/n/10 scrip- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562834| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.07679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09099| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.06041| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.08542| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09072| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.62266| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562839| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R03C02| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.06946| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.12989| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.04703| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09808| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.14105| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.54662| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562842| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840035| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R05C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.10986| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.13565| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.07657| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09125| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.12521| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.49317| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562846| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840037| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R01C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.11508| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.14116| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.0679| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09415| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.15311| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.47829| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (41.67346pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 GSM3562855| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 ge- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 nomic Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 DNA Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 from Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- Overfull \hbox (35.00366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 3999840037| Overfull \hbox (16.77815pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 R06C01| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (24.1994pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol_whole Overfull \hbox (3.64975pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (2.77356pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 con- Overfull \hbox (9.44347pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Overfull \hbox (7.78355pt too wide) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.01668| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.14318| Overfull \hbox (12.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.1096| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.05545| Overfull \hbox (16.88266pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.09695| Overfull \hbox (17.50366pt too wide) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 0.60283| Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 []\T1/ptm/m/n/10 whole Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 blood Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 con- Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 trol Underfull \hbox (badness 10000) in paragraph at lines 2646--2646 \T1/ptm/m/n/10 sam- [33] Underfull \hbox (badness 10000) in paragraph at lines 2746--2747 []|[][]\T1/pcr/m/sl/10 methylprep.files. Underfull \hbox (badness 6380) in paragraph at lines 2756--2757 []|[][]\T1/pcr/m/sl/10 methylprep.run_series[][]\T1/ptm/m/n/10 (id, path[, dict _only, Overfull \hbox (2.88234pt too wide) in paragraph at lines 2766--2767 []|[][]\T1/pcr/m/sl/10 methylprep.build_composite_dataset[][]\T1/ptm/m/n/10 (.. .[, [34] Underfull \hbox (badness 10000) in paragraph at lines 2857--2857 []\T1/ptm/m/it/10 array_type\T1/ptm/m/n/10 , \T1/ptm/m/it/10 filepath_or_buffer =None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 on_lambda=False\T1/ptm/m/n/10 , \T1/ptm/m /it/10 ver- [35] Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3028--3028 \T1/ptm/m/it/10 poobah=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah_sig=0.05\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex- [36] Underfull \hbox (badness 10000) in paragraph at lines 3071--3071 []\T1/ptm/m/it/10 id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , [37] Underfull \hbox (badness 10000) in paragraph at lines 3130--3130 []\T1/ptm/m/it/10 geo_id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 data_dir='.'\T1/ptm/m/ n/10 , \T1/ptm/m/it/10 merge=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 down-load_it= True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3130--3130 \T1/ptm/m/it/10 tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quire_k eyword=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sync_idats=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3170--3170 \T1/ptm/m/it/10 sync_idats=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1 /ptm/m/n/10 , \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- [38] Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i-fest_filepath=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 sam-ple_sheet_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam -ple_name=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 be-tas=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 m_value=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 make_sample_sheet =False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=None\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3228--3228 \T1/ptm/m/it/10 save_uncorrected=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 save_con trol=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 meta_data_frame=True\T1/ptm/m/n/10 , [39] [40] Underfull \hbox (badness 10000) in paragraph at lines 3411--3418 []\T1/ptm/m/n/10 export=False, make_sample_sheet=False, ex-port_poobah=False, s ave_uncorrected=False, Underfull \hbox (badness 10000) in paragraph at lines 3419--3424 []\T1/ptm/m/n/10 betas=False, m_value=False, - Underfull \hbox (badness 10000) in paragraph at lines 3435--3441 []\T1/ptm/m/n/10 data_dir, ar-ray_type=None, Underfull \hbox (badness 10000) in paragraph at lines 3449--3452 [] Overfull \hbox (15.91293pt too wide) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 tain_uncorrected_probe_intensities=False\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 pval=False\T1/ptm /m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 poobah_decimals=3\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 do_noob=True\T1 /ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 qual-ity_mask=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 switch_probes=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3463--3463 \T1/ptm/m/it/10 do_nonlinear_dye_bias=True\T1/ptm/m/n/10 , \T1/ptm/m/it/10 de- [41] [42] Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 []\T1/ptm/m/it/10 data_dir\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ar-ray_type=None\T1/ ptm/m/n/10 , \T1/ptm/m/it/10 ex-port=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 man- i- Underfull \hbox (badness 10000) in paragraph at lines 3579--3579 \T1/ptm/m/it/10 fest_filepath=None\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam-ple_shee 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paragraph at lines 3579--3579 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 low_memory=True \T1/ptm/m/n/10 , \T1/ptm/m/it/10 sesame=True\T1/ptm/m/n/10 , [43] [44] Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 []\T1/ptm/m/it/10 data_containers\T1/ptm/m/n/10 , \T1/ptm/m/it/10 post-pro- Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 cess_func_colname='beta_value'\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 bit='float32'\T1/ptm/m/n/10 , \T1/ptm/m/it/10 poobah=True\T1/pt m/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 3732--3732 \T1/ptm/m/it/10 poobah_sig=0.05\T1/ptm/m/n/10 , \T1/ptm/m/it/10 ex- Underfull \hbox (badness 10000) in paragraph at lines 3819--3819 []\T1/ptm/m/it/10 sample_sheet\T1/ptm/m/n/10 , \T1/ptm/m/it/10 sam- Underfull \hbox (badness 10000) in paragraph at lines 3819--3819 \T1/ptm/m/it/10 ple_name=None\T1/ptm/m/n/10 , Underfull \hbox 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id\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/p tm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=100\T1/pt m/m/n/10 , \T1/ptm/m/it/10 clean=True\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4373--4373 []\T1/ptm/m/it/10 list_file\T1/ptm/m/n/10 , \T1/ptm/m/it/10 path\T1/ptm/m/n/10 , \T1/ptm/m/it/10 dict_only=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 batch_size=10 0\T1/ptm/m/n/10 , Underfull \hbox (badness 10000) in paragraph at lines 4402--4402 \T1/ptm/m/it/10 ex-tract_controls=False\T1/ptm/m/n/10 , \T1/ptm/m/it/10 re-quir e_keyword=None\T1/ptm/m/n/10 , [50] [51] Underfull \hbox (badness 10000) in paragraph at lines 4548--4552 []\T1/ptm/m/n/10 to ini-tial-ize, Overfull \hbox (75.29005pt too wide) in paragraph at lines 4583--4583 [] Underfull \hbox (badness 10000) in paragraph at lines 4583--4583 [52] Overfull \hbox (8.5906pt too wide) in paragraph at lines 4596--4596 [] Underfull \hbox (badness 10000) in paragraph at lines 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[57] [58] [59] (./life-epigenetics-methylprep.ind [60] Underfull \hbox (badness 10000) in paragraph at lines 9--11 []\T1/pcr/m/n/10 alternate_base_filename \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl - Underfull \hbox (badness 10000) in paragraph at lines 19--20 []\T1/pcr/m/n/10 build_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.fi les.SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 24--26 []\T1/pcr/m/n/10 check_for_probe_loss() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 31--32 []\T1/pcr/m/n/10 control_data_frame \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .Manifest at- Underfull \hbox (badness 10000) in paragraph at lines 35--36 []\T1/pcr/m/n/10 convert_miniml() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule me thyl- Underfull \hbox (badness 10000) in paragraph at lines 36--37 []\T1/pcr/m/n/10 create_sample_sheet() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- Underfull \hbox (badness 10000) in paragraph at lines 42--44 []\T1/pcr/m/n/10 detect_and_drop_duplicates() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 44--46 []\T1/pcr/m/n/10 download_default() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .files.Manifest Overfull \hbox (5.70073pt too wide) in paragraph at lines 50--52 []\T1/pcr/m/n/10 export() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.processin g.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 56--57 []\T1/pcr/m/n/10 from_probe_count \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.A rrayType at- Underfull \hbox (badness 10000) in paragraph at lines 62--64 []\T1/pcr/m/n/10 get_export_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 65--66 []\T1/pcr/m/n/10 get_filepath() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.mod els.Sample Underfull \hbox (badness 10000) in paragraph at lines 66--67 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 67--68 []\T1/pcr/m/n/10 get_probe_details() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 68--69 []\T1/pcr/m/n/10 get_sample() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.files .SampleSheet Underfull \hbox (badness 10000) in paragraph at lines 71--72 []\T1/pcr/m/n/10 get_sample_sheet_s3() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-u le methyl- Underfull \hbox (badness 10000) in paragraph at lines 72--73 []\T1/pcr/m/n/10 get_samples() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.file s.SampleSheet [61] Underfull \hbox (badness 10000) in paragraph at lines 80--81 []\T1/pcr/m/n/10 ILLUMINA_EPIC_PLUS \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep .ArrayType Overfull \hbox (4.1225pt too wide) in paragraph at lines 105--107 []\T1/pcr/m/n/10 parse_sample_sheet_into_idat_datasets() Overfull \hbox (4.1225pt too wide) in paragraph at lines 107--109 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in paragraph at lines 119--121 []\T1/pcr/m/n/10 process_m_value() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 119--121 \T1/ptm/m/it/10 prep.processing.SampleDataContainer Underfull \hbox (badness 10000) in paragraph at lines 126--128 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl- Underfull \hbox (badness 10000) in paragraph at lines 128--129 []\T1/pcr/m/n/10 read_control_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-p rep.Manifest Underfull \hbox (badness 10000) in paragraph at lines 129--130 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 130--131 []\T1/pcr/m/n/10 read_mouse_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-pre p.Manifest Underfull \hbox (badness 10000) in paragraph at lines 132--133 []\T1/pcr/m/n/10 read_snp_probes() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep. files.Manifest Underfull \hbox (badness 10000) in paragraph at lines 139--140 []\T1/pcr/m/n/10 run_series_list() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 in mod-ule m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 144--145 []\T1/pcr/m/n/10 SampleDataContainer \T1/ptm/m/n/10 (\T1/ptm/m/it/10 class in m ethyl- Underfull \hbox (badness 10000) in paragraph at lines 149--150 []\T1/pcr/m/n/10 seek_to_start() \T1/ptm/m/n/10 (\T1/ptm/m/it/10 methyl-prep.Ma nifest static [62]) (./life-epigenetics-methylprep.aux) LaTeX Warning: There were undefined references. ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on life-epigenetics-methylprep.pdf (66 pages, 952298 bytes). 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Latexmk: Index file 'life-epigenetics-methylprep.idx' was written Latexmk: Log file says output to 'life-epigenetics-methylprep.pdf' Collected error summary (may duplicate other messages): pdflatex: Command for 'pdflatex' gave return code 256 Latexmk: Errors, in force_mode: so I tried finishing targets [rtd-command-info] start-time: 2021-09-20T18:53:45.293353Z, end-time: 2021-09-20T18:53:45.369677Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_build/latex/life-epigenetics-methylprep.pdf /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/artifacts/latest/sphinx_pdf/life-epigenetics-methylprep.pdf [rtd-command-info] start-time: 2021-09-20T18:53:45.474930Z, end-time: 2021-09-20T18:53:56.707075Z, duration: 11, exit-code: 0 python -m sphinx -T -b epub -d _build/doctrees -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... loading pickled environment... done Creating file /home/docs/checkouts/readthedocs.org/user_builds/life-epigenetics-methylprep/checkouts/latest/_sphinx_build/conf.rst. 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