Read the Docs build information Build id: 315120 Project: cyverse-sciapps-guide Version: latest Commit: b46efdaa7aea973660d5d84be815d40d306124cc Date: 2020-04-10T20:13:07.060433Z State: finished Success: True [rtd-command-info] start-time: 2020-04-10T20:13:09.231244Z, end-time: 2020-04-10T20:13:10.925404Z, duration: 1, exit-code: 0 git clone --no-single-branch --depth 50 https://github.com/CyVerse-learning-materials/SciApps_guide.git . Cloning into '.'... [rtd-command-info] start-time: 2020-04-10T20:13:11.423380Z, end-time: 2020-04-10T20:13:11.685334Z, 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 b46efda Added direct query support for EMS mutations [rtd-command-info] start-time: 2020-04-10T20:13:11.849271Z, end-time: 2020-04-10T20:13:12.048797Z, duration: 0, exit-code: 0 git clean -d -f -f [rtd-command-info] start-time: 2020-04-10T20:13:13.535306Z, end-time: 2020-04-10T20:13:17.230599Z, duration: 3, exit-code: 0 python3.7 -mvirtualenv Using base prefix '/home/docs/.pyenv/versions/3.7.3' New python executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/envs/latest/bin/python3.7 Also creating executable in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/envs/latest/bin/python Installing setuptools, pip, wheel... done. [rtd-command-info] start-time: 2020-04-10T20:13:17.353197Z, end-time: 2020-04-10T20:13:18.128799Z, duration: 0, exit-code: 0 python -m pip install --upgrade --no-cache-dir pip Requirement already up-to-date: pip in /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/envs/latest/lib/python3.7/site-packages (20.0.2) [rtd-command-info] start-time: 2020-04-10T20:13:18.304792Z, end-time: 2020-04-10T20:13:27.485751Z, duration: 9, exit-code: 0 python -m pip install --upgrade --no-cache-dir Pygments==2.3.1 setuptools==41.0.1 docutils==0.14 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<1.1 Collecting Pygments==2.3.1 Downloading Pygments-2.3.1-py2.py3-none-any.whl (849 kB) Collecting setuptools==41.0.1 Downloading setuptools-41.0.1-py2.py3-none-any.whl (575 kB) Collecting docutils==0.14 Downloading docutils-0.14-py3-none-any.whl (543 kB) Collecting mock==1.0.1 Downloading mock-1.0.1.tar.gz (818 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<1.1 Downloading readthedocs_sphinx_ext-1.0.1-py2.py3-none-any.whl (14 kB) Collecting future Downloading future-0.18.2.tar.gz (829 kB) Collecting sphinxcontrib-websupport Downloading sphinxcontrib_websupport-1.2.1-py2.py3-none-any.whl (39 kB) Collecting babel!=2.0,>=1.3 Downloading Babel-2.8.0-py2.py3-none-any.whl (8.6 MB) Collecting packaging Downloading packaging-20.3-py2.py3-none-any.whl (37 kB) Collecting imagesize Downloading imagesize-1.2.0-py2.py3-none-any.whl (4.8 kB) Collecting six>=1.5 Downloading six-1.14.0-py2.py3-none-any.whl (10 kB) Collecting Jinja2>=2.3 Downloading Jinja2-2.11.1-py2.py3-none-any.whl (126 kB) Collecting requests>=2.0.0 Downloading requests-2.23.0-py2.py3-none-any.whl (58 kB) Collecting snowballstemmer>=1.1 Downloading snowballstemmer-2.0.0-py2.py3-none-any.whl (97 kB) Collecting pytz>=2015.7 Downloading pytz-2019.3-py2.py3-none-any.whl (509 kB) Collecting pyparsing>=2.0.2 Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB) Collecting MarkupSafe>=0.23 Downloading MarkupSafe-1.1.1-cp37-cp37m-manylinux1_x86_64.whl (27 kB) Collecting urllib3!=1.25.0,!=1.25.1,<1.26,>=1.21.1 Downloading urllib3-1.25.8-py2.py3-none-any.whl (125 kB) Collecting chardet<4,>=3.0.2 Downloading chardet-3.0.4-py2.py3-none-any.whl (133 kB) Collecting certifi>=2017.4.17 Downloading certifi-2020.4.5.1-py2.py3-none-any.whl (157 kB) Collecting idna<3,>=2.5 Downloading idna-2.9-py2.py3-none-any.whl (58 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=23754 sha256=eae87d7dd6ff8e7435fdb91902f6ea713f3fe42ab419ca7a80754589c70b69df Stored in directory: /tmp/pip-ephem-wheel-cache-13fw_868/wheels/16/03/37/f0a64ab894c9102906f192db1a4071b7592292ad661563c69b 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=491058 sha256=04bcc0ff89300cc270c9ffa22073d9d6e2f7d5e74d5e7b63af34e56c2e6b2b25 Stored in directory: /tmp/pip-ephem-wheel-cache-13fw_868/wheels/56/b0/fe/4410d17b32f1f0c3cf54cdfb2bc04d7b4b8f4ae377e2229ba0 Successfully built mock future Installing collected packages: Pygments, setuptools, docutils, mock, pillow, alabaster, future, commonmark, sphinxcontrib-websupport, pytz, babel, six, pyparsing, packaging, imagesize, MarkupSafe, Jinja2, urllib3, chardet, certifi, idna, requests, snowballstemmer, sphinx, recommonmark, sphinx-rtd-theme, readthedocs-sphinx-ext Attempting uninstall: setuptools Found existing installation: setuptools 46.1.3 Uninstalling setuptools-46.1.3: Successfully uninstalled setuptools-46.1.3 Successfully installed Jinja2-2.11.1 MarkupSafe-1.1.1 Pygments-2.3.1 alabaster-0.7.12 babel-2.8.0 certifi-2020.4.5.1 chardet-3.0.4 commonmark-0.8.1 docutils-0.14 future-0.18.2 idna-2.9 imagesize-1.2.0 mock-1.0.1 packaging-20.3 pillow-5.4.1 pyparsing-2.4.7 pytz-2019.3 readthedocs-sphinx-ext-1.0.1 recommonmark-0.5.0 requests-2.23.0 setuptools-41.0.1 six-1.14.0 snowballstemmer-2.0.0 sphinx-1.8.5 sphinx-rtd-theme-0.4.3 sphinxcontrib-websupport-1.2.1 urllib3-1.25.8 [rtd-command-info] start-time: 2020-04-10T20:13:28.617935Z, end-time: 2020-04-10T20:13:28.834134Z, duration: 0, exit-code: 0 cat conf.py #!/usr/bin/env python3 # -*- coding: utf-8 -*- # # General information about the project. import sys import os sys.path.insert(0, os.path.dirname(__file__)) from misc.cyverse_sphinx_conf import * # noqa project = 'SciApps Guide' copyright = '2017, CyVerse' author = 'CyVerse' version = '1.0' release = '1.0' html_static_path = [] epub_title = project epub_author = author epub_publisher = author epub_copyright = copyright exclude_patterns = ['README.md', 'License.md', 'Contributors_maintainers.md'] ########################################################################### # 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 # import importlib import sys import os.path from six import string_types 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': [ ], 'downloads': [ ("pdf", "//cyverse-sciapps-guide.readthedocs-hosted.com/_/downloads/en/latest/pdf/"), ("html", "//cyverse-sciapps-guide.readthedocs-hosted.com/_/downloads/en/latest/htmlzip/"), ("epub", "//cyverse-sciapps-guide.readthedocs-hosted.com/_/downloads/en/latest/epub/"), ], 'subprojects': [ ], 'slug': 'cyverse-sciapps-guide', 'name': u'SciApps_guide', 'rtd_language': u'en', 'programming_language': u'words', 'canonical_url': 'https://cyverse-sciapps-guide.readthedocs-hosted.com/en/latest/', 'analytics_code': 'None', 'single_version': False, 'conf_py_path': '/', 'api_host': 'https://readthedocs.com', 'proxied_api_host': '/_', 'github_user': 'CyVerse-learning-materials', 'github_repo': 'SciApps_guide', '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, 'user_analytics_code': '', 'global_analytics_code': 'UA-17997319-2', 'commit': 'b46efdaa', } 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") 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' [rtd-command-info] start-time: 2020-04-10T20:13:28.955788Z, end-time: 2020-04-10T20:13:30.672975Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocs -d _build/doctrees-readthedocs -D language=en . _build/html Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocs]: targets for 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] annotation reading sources... [ 22%] association reading sources... [ 33%] bsa reading sources... [ 44%] index reading sources... [ 55%] maizecode reading sources... [ 66%] step1 reading sources... [ 77%] step2 reading sources... [ 88%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/bsa.rst:8: WARNING: Title underline too short. The Bulked Segregant Analysis Tutorial --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/bsa.rst:21: WARNING: Insufficient data supplied (1 row(s)); no data remaining for table body, required by "list-table" directive. .. list-table:: :header-rows: 1 * - Input - Description - Example - Variants called with bcftools - `snp_bw2_ms9_1.vcf.gz `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/maizecode.rst:8: WARNING: Duplicate explicit target name: "mcrna-0.0.1". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 11%] annotation writing output... [ 22%] association writing output... [ 33%] bsa writing output... [ 44%] index writing output... [ 55%] maizecode writing output... [ 66%] step1 writing output... [ 77%] step2 writing output... [ 88%] step3 writing output... 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[ 98%] ./img/sci_apps/myjobs_window.gif copying images... [100%] ./img/sci_apps/running_workflow2.gif copying static files... done copying readthedocs static files... done copying searchtools... done copying extra files... done dumping search index in English (code: en) ... done dumping object inventory... done build succeeded, 3 warnings. The HTML pages are in _build/html. [rtd-command-info] start-time: 2020-04-10T20:13:30.850768Z, end-time: 2020-04-10T20:13:32.446821Z, duration: 1, exit-code: 0 python sphinx-build -T -b readthedocssinglehtmllocalmedia -d _build/doctrees-readthedocssinglehtmllocalmedia -D language=en . _build/localmedia Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [readthedocssinglehtmllocalmedia]: all documents updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] annotation reading sources... [ 22%] association reading sources... 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[100%] ./img/sci_apps/ballgown_out.gif copying TeX support files... done build succeeded, 3 warnings. The LaTeX files are in _build/latex. Run 'make' in that directory to run these through (pdf)latex (use `make latexpdf' here to do that automatically). [rtd-command-info] start-time: 2020-04-10T20:13:47.977150Z, end-time: 2020-04-10T20:13:48.190549Z, duration: 0, exit-code: 0 cat latexmkrc $latex = 'latex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $pdflatex = 'pdflatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $lualatex = 'lualatex ' . $ENV{'LATEXOPTS'} . ' %O %S'; $xelatex = 'xelatex --no-pdf ' . $ENV{'LATEXOPTS'} . ' %O %S'; $makeindex = 'makeindex -s python.ist %O -o %D %S'; add_cus_dep( "glo", "gls", 0, "makeglo" ); sub makeglo { return system( "makeindex -s gglo.ist -o '$_[0].gls' '$_[0].glo'" ); } [rtd-command-info] start-time: 2020-04-10T20:13:48.295108Z, end-time: 2020-04-10T20:13:50.503421Z, duration: 2, exit-code: 0 latexmk -r latexmkrc -pdf -f -dvi- -ps- -jobname=cyverse-sciapps-guide -interaction=nonstopmode Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 10) line 4, chunk 1. Subroutine makeglo redefined at (eval 11) line 7, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 1, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 2, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 3, chunk 1. Use of uninitialized value $ENV{"LATEXOPTS"} in concatenation (.) or string at (eval 11) line 4, chunk 1. Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41. File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482. Rule 'pdflatex': Rules & subrules not known to be previously run: pdflatex Rule 'pdflatex': The following rules & subrules became out-of-date: 'pdflatex' ------------ Run number 1 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-sciapps-guide" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... 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LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1393 ...226\sphinxpxdimen]{{build_workflow}.gif} [16] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1405 ...292\sphinxpxdimen]{{emmax_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1449 ...inxpxdimen]{{association_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1454 ...inxpxdimen]{{association_workflow3}.gif} [17] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1520 ...ht=170\sphinxpxdimen]{{sorghum_ms9}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 Notes/other Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2 doc-u- Overfull \hbox (12.84023pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_call| Overfull \hbox (5.70792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_call- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Overfull \hbox (17.29018pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_filter| Overfull \hbox (9.95792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_filter- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G doc-u- Overfull \hbox (6.47052pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bsa_viewer| Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bsa_viewer- [18] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1622 ...t=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1630 ...height=343\sphinxpxdimen]{{de_data}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1652 ...ght=356\sphinxpxdimen]{{url_window}.gif} [19] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1688 ...57\sphinxpxdimen]{{bcftools_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1718 ...t=100\sphinxpxdimen]{{bcftools_res}.gif} [20] Underfull \hbox (badness 5578) in paragraph at lines 1738--1740 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 1: bcftools_filter-1.8 \T1/ptm/m/n/10 in the His-tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1741 ...,height=276\sphinxpxdimen]{{snpeff}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1782--1783 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 2: SnpEff-4.3.1 \T1/ptm/m/n/10 in the His -tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1784 ...en,height=276\sphinxpxdimen]{{sift}.gif} [21] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1830 ...eight=363\sphinxpxdimen]{{ems_view}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1835 ...=123\sphinxpxdimen]{{ems_view_diag}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1844 ...ht=268\sphinxpxdimen]{{ems_viewer2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1857 ...ght=362\sphinxpxdimen]{{ems_viewer}.gif} [22] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1908 ...men,height=796\sphinxpxdimen]{{bsa}.gif} [23] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1962 ...n,height=260\sphinxpxdimen]{{mcrna}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1985 ...ight=449\sphinxpxdimen]{{maizecode}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2004 ...t=182\sphinxpxdimen]{{workflow_URL}.gif} [24] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2035 ...eight=304\sphinxpxdimen]{{mcrnares}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2058 ...ight=338\sphinxpxdimen]{{MCrna_URL}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2067 ...ht=254\sphinxpxdimen]{{jbrowse_add}.gif} [25] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2097 ...ht=428\sphinxpxdimen]{{de_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2109 ...ight=242\sphinxpxdimen]{{de_result}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2132 ...t=421\sphinxpxdimen]{{iso_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2141 ...ight=439\sphinxpxdimen]{{iso_build}.gif} [26] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2160 ...t=588\sphinxpxdimen]{{iso_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2165 ...=230\sphinxpxdimen]{{iso_analysis2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2175 ...height=596\sphinxpxdimen]{{iso_run}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2184 ...t=228\sphinxpxdimen]{{ballgown_out}.gif} [27] [28] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Pre- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/phv/m/n/10 req-ui- Overfull \hbox (27.43803pt too wide) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Sci- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Apps Underfull \hbox (badness 10000) in paragraph at lines 2--2261 [][][]\T1/ptm/m/n/10 Cy-Verse Underfull \hbox (badness 10000) in paragraph at lines 2--2261 \T1/ptm/m/n/10 User No file cyverse-sciapps-guide.ind. [29] (./cyverse-sciapps-guide.aux) Package rerunfilecheck Warning: File `cyverse-sciapps-guide.out' has changed. (rerunfilecheck) Rerun to get outlines right (rerunfilecheck) or use package `bookmark'. 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 cyverse-sciapps-guide.pdf (33 pages, 204026 bytes). Transcript written on cyverse-sciapps-guide.log. Latexmk: Index file 'cyverse-sciapps-guide.idx' was written Latexmk: Missing input file: 'cyverse-sciapps-guide.ind' from line 'No file cyverse-sciapps-guide.ind.' Latexmk: References changed. Latexmk: References changed. Latexmk: Log file says output to 'cyverse-sciapps-guide.pdf' Rule 'makeindex cyverse-sciapps-guide.idx': File changes, etc: Non-existent destination files: 'cyverse-sciapps-guide.ind' ------------ Run number 1 of rule 'makeindex cyverse-sciapps-guide.idx' ------------ ------------ Running 'makeindex -s python.ist -o "cyverse-sciapps-guide.ind" "cyverse-sciapps-guide.idx"' ------------ Latexmk: applying rule 'makeindex cyverse-sciapps-guide.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 cyverse-sciapps-guide.idx...done (0 entries accepted, 0 rejected). Nothing written in cyverse-sciapps-guide.ind. Transcript written in cyverse-sciapps-guide.ilg. Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-sciapps-guide.aux' 'cyverse-sciapps-guide.ind' ------------ Run number 2 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-sciapps-guide" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. 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(./cyverse-sciapps-guide.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-sciapps-guide.toc) [1] [2] [1 <./cyverse_rgb.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.231 ...ht=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.240 ...=172\sphinxpxdimen]{{sciapps_launch}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.248 ...ght=264\sphinxpxdimen]{{data_window}.gif} [5] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.417 ...men,height=325\sphinxpxdimen]{{snap}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.430 ...en,height=62\sphinxpxdimen]{{status}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.439 ...ht=294\sphinxpxdimen]{{agave_status}.gif} [6] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.468 ...t=114\sphinxpxdimen]{{visual_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.472 ...=182\sphinxpxdimen]{{visual_window2}.gif} [7] Overfull \hbox (12.68977pt too wide) in paragraph at lines 2--554 [][][]\T1/ptm/m/n/10 test_genome.fasta[][]| Underfull \hbox (badness 10000) in paragraph at lines 554--554 []\T1/ptm/m/n/10 An-no-tated gene Overfull \hbox (9.38023pt too wide) in paragraph at lines 2--554 [][][]\T1/ptm/m/n/10 maker_out.gff.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 599--599 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 599--599 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 2--599 [][][]\T1/ptm/m/n/10 MAKER- Underfull \hbox (badness 10000) in paragraph at lines 2--599 [][][]\T1/ptm/m/n/10 SNAP doc-u-men-ta- ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.620 ...t=197\sphinxpxdimen]{{myjobs_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.629 ...310\sphinxpxdimen]{{build_workflow2}.gif} [8] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.643 ...ght=325\sphinxpxdimen]{{jbrowse_out}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.666 ...198\sphinxpxdimen]{{build_workflow3}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.675 ...phinxpxdimen]{{annotation_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.705 ...ght=168\sphinxpxdimen]{{my_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.721 ...ht=182\sphinxpxdimen]{{workflow_URL}.gif} [9] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.740 ...6\sphinxpxdimen]{{running_workflow2}.gif} [10] Underfull \hbox (badness 10000) in paragraph at lines 852--852 []\T1/ptm/m/n/10 As-sem-bled Overfull \hbox (16.02496pt too wide) in paragraph at lines 2--852 [][][]\T1/ptm/m/n/10 test_genome.fasta.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 852--852 []\T1/ptm/m/n/10 An-no-tated gene Overfull \hbox (0.77548pt too wide) in paragraph at lines 2--852 [][][]\T1/ptm/m/n/10 maker_out.gff.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 897--897 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 897--897 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 MAKER- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 SNAP- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 SNAP doc-u-men-ta- ! LaTeX Error: Unknown graphics extension: .gif. 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Type H for immediate help. ... l.1066 ...ht=170\sphinxpxdimen]{{my_workflow}.gif} [13] [14] Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 Nu-mer-i-cal- Overfull \hbox (18.41133pt too wide) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 NumericalTransform- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 TAS-SEL doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 EM-MAX doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 PCA doc-u-men-ta- Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 STRUC- Overfull \hbox (6.23843pt too wide) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 2.3.4.1| Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 STRUCTURE- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 STRUC-TURE ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1313 ...2\sphinxpxdimen]{{public_workflows}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1325 ...inxpxdimen]{{association_workflow0}.gif} [15] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1351 ...355\sphinxpxdimen]{{manhattan_plot}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1378 ...ht=297\sphinxpxdimen]{{pca_output1}.gif} \sphinxincludegraphics[wi... ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1378 ...ht=284\sphinxpxdimen]{{pca_output2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1393 ...226\sphinxpxdimen]{{build_workflow}.gif} [16] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1405 ...292\sphinxpxdimen]{{emmax_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1449 ...inxpxdimen]{{association_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1454 ...inxpxdimen]{{association_workflow3}.gif} [17] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1520 ...ht=170\sphinxpxdimen]{{sorghum_ms9}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 Notes/other Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2 doc-u- Overfull \hbox (12.84023pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_call| Overfull \hbox (5.70792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_call- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Overfull \hbox (17.29018pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_filter| Overfull \hbox (9.95792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_filter- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G doc-u- Overfull \hbox (6.47052pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bsa_viewer| Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bsa_viewer- [18] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1622 ...t=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1630 ...height=343\sphinxpxdimen]{{de_data}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1652 ...ght=356\sphinxpxdimen]{{url_window}.gif} [19] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1688 ...57\sphinxpxdimen]{{bcftools_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1718 ...t=100\sphinxpxdimen]{{bcftools_res}.gif} [20] Underfull \hbox (badness 5578) in paragraph at lines 1738--1740 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 1: bcftools_filter-1.8 \T1/ptm/m/n/10 in the His-tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1741 ...,height=276\sphinxpxdimen]{{snpeff}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1782--1783 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 2: SnpEff-4.3.1 \T1/ptm/m/n/10 in the His -tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1784 ...en,height=276\sphinxpxdimen]{{sift}.gif} [21] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1830 ...eight=363\sphinxpxdimen]{{ems_view}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1835 ...=123\sphinxpxdimen]{{ems_view_diag}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1844 ...ht=268\sphinxpxdimen]{{ems_viewer2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1857 ...ght=362\sphinxpxdimen]{{ems_viewer}.gif} [22] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1908 ...men,height=796\sphinxpxdimen]{{bsa}.gif} [23] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1962 ...n,height=260\sphinxpxdimen]{{mcrna}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1985 ...ight=449\sphinxpxdimen]{{maizecode}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2004 ...t=182\sphinxpxdimen]{{workflow_URL}.gif} [24] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2035 ...eight=304\sphinxpxdimen]{{mcrnares}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2058 ...ight=338\sphinxpxdimen]{{MCrna_URL}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2067 ...ht=254\sphinxpxdimen]{{jbrowse_add}.gif} [25] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2097 ...ht=428\sphinxpxdimen]{{de_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2109 ...ight=242\sphinxpxdimen]{{de_result}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2132 ...t=421\sphinxpxdimen]{{iso_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2141 ...ight=439\sphinxpxdimen]{{iso_build}.gif} [26] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2160 ...t=588\sphinxpxdimen]{{iso_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2165 ...=230\sphinxpxdimen]{{iso_analysis2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2175 ...height=596\sphinxpxdimen]{{iso_run}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2184 ...t=228\sphinxpxdimen]{{ballgown_out}.gif} [27] [28] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Pre- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/phv/m/n/10 req-ui- Overfull \hbox (27.43803pt too wide) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Sci- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Apps Underfull \hbox (badness 10000) in paragraph at lines 2--2261 [][][]\T1/ptm/m/n/10 Cy-Verse Underfull \hbox (badness 10000) in paragraph at lines 2--2261 \T1/ptm/m/n/10 User (./cyverse-sciapps-guide.ind) [29] (./cyverse-sciapps-guide.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-sciapps-guide.pdf (33 pages, 205880 bytes). Transcript written on cyverse-sciapps-guide.log. Latexmk: Index file 'cyverse-sciapps-guide.idx' was written Latexmk: Log file says output to 'cyverse-sciapps-guide.pdf' Rule 'pdflatex': File changes, etc: Changed files, or newly in use since previous run(s): 'cyverse-sciapps-guide.out' 'cyverse-sciapps-guide.toc' ------------ Run number 3 of rule 'pdflatex' ------------ ------------ Running 'pdflatex -interaction=nonstopmode -recorder --jobname="cyverse-sciapps-guide" "CyVerseDocumentation.tex"' ------------ Latexmk: applying rule 'pdflatex'... This is pdfTeX, Version 3.14159265-2.6-1.40.18 (TeX Live 2017/Debian) (preloaded format=pdflatex) restricted \write18 enabled. entering extended mode (./CyVerseDocumentation.tex LaTeX2e <2017-04-15> Babel <3.18> and hyphenation patterns for 84 language(s) loaded. (./sphinxmanual.cls Document Class: sphinxmanual 2018/12/22 v1.8.3 Document class (Sphinx manual) (/usr/share/texlive/texmf-dist/tex/latex/base/report.cls Document Class: report 2014/09/29 v1.4h Standard LaTeX document class (/usr/share/texlive/texmf-dist/tex/latex/base/size10.clo))) (/usr/share/texlive/texmf-dist/tex/latex/base/inputenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/utf8.def (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/ot1enc.dfu) (/usr/share/texlive/texmf-dist/tex/latex/base/omsenc.dfu))) (/usr/share/texlive/texmf-dist/tex/latex/cmap/cmap.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/fontenc.sty (/usr/share/texlive/texmf-dist/tex/latex/base/t1enc.def)<>) (/usr/share/texlive/texmf-dist/tex/latex/amsmath/amsmath.sty For additional information on amsmath, use the `?' option. 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(/usr/share/texlive/texmf-dist/tex/latex/framed/framed.sty) (/usr/share/texlive/texmf-dist/tex/latex/xcolor/xcolor.sty (/usr/share/texlive/texmf-dist/tex/latex/graphics-cfg/color.cfg)) (/usr/share/texlive/texmf-dist/tex/latex/fancyvrb/fancyvrb.sty Style option: `fancyvrb' v2.7a, with DG/SPQR fixes, and firstline=lastline fix <2008/02/07> (tvz)) (./footnotehyper-sphinx.sty) (/usr/share/texlive/texmf-dist/tex/latex/float/float.sty) (/usr/share/texlive/texmf-dist/tex/latex/wrapfig/wrapfig.sty) (/usr/share/texlive/texmf-dist/tex/latex/parskip/parskip.sty) (/usr/share/texlive/texmf-dist/tex/latex/base/alltt.sty) (/usr/share/texlive/texmf-dist/tex/latex/upquote/upquote.sty) (/usr/share/texlive/texmf-dist/tex/latex/capt-of/capt-of.sty) (/usr/share/texlive/texmf-dist/tex/latex/needspace/needspace.sty) (/usr/share/texlive/texmf-dist/tex/latex/carlisle/remreset.sty) (./sphinxhighlight.sty) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/kvoptions.sty 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(/usr/share/texlive/texmf-dist/tex/latex/url/url.sty)) (/usr/share/texlive/texmf-dist/tex/latex/hyperref/hpdftex.def (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/rerunfilecheck.sty)) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/hypcap.sty) Writing index file cyverse-sciapps-guide.idx (./cyverse-sciapps-guide.aux) (/usr/share/texlive/texmf-dist/tex/latex/base/ts1cmr.fd) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1ptm.fd) (/usr/share/texlive/texmf-dist/tex/context/base/mkii/supp-pdf.mkii [Loading MPS to PDF converter (version 2006.09.02).] ) (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/epstopdf-base.sty (/usr/share/texlive/texmf-dist/tex/latex/oberdiek/grfext.sty) (/usr/share/texlive/texmf-dist/tex/latex/latexconfig/epstopdf-sys.cfg)) *geometry* driver: auto-detecting *geometry* detected driver: pdftex (/usr/share/texlive/texmf-dist/tex/latex/hyperref/nameref.sty (/usr/share/texlive/texmf-dist/tex/generic/oberdiek/gettitlestring.sty)) (./cyverse-sciapps-guide.out) (./cyverse-sciapps-guide.out) (/usr/share/texlive/texmf-dist/tex/latex/psnfss/t1phv.fd)<><><><> (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsa.fd) (/usr/share/texlive/texmf-dist/tex/latex/amsfonts/umsb.fd) [1{/var/lib/texmf/fo nts/map/pdftex/updmap/pdftex.map}] [2] (./cyverse-sciapps-guide.toc) [1] [2] [1 <./cyverse_rgb.png> <./homeicon.png>] [2] Chapter 1. (/usr/share/texlive/texmf-dist/tex/latex/psnfss/ts1ptm.fd) [3] [4] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.231 ...ht=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.240 ...=172\sphinxpxdimen]{{sciapps_launch}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.248 ...ght=264\sphinxpxdimen]{{data_window}.gif} [5] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.417 ...men,height=325\sphinxpxdimen]{{snap}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.430 ...en,height=62\sphinxpxdimen]{{status}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.439 ...ht=294\sphinxpxdimen]{{agave_status}.gif} [6] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.468 ...t=114\sphinxpxdimen]{{visual_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.472 ...=182\sphinxpxdimen]{{visual_window2}.gif} [7] Overfull \hbox (12.68977pt too wide) in paragraph at lines 2--554 [][][]\T1/ptm/m/n/10 test_genome.fasta[][]| Underfull \hbox (badness 10000) in paragraph at lines 554--554 []\T1/ptm/m/n/10 An-no-tated gene Overfull \hbox (9.38023pt too wide) in paragraph at lines 2--554 [][][]\T1/ptm/m/n/10 maker_out.gff.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 599--599 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 599--599 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 2--599 [][][]\T1/ptm/m/n/10 MAKER- Underfull \hbox (badness 10000) in paragraph at lines 2--599 [][][]\T1/ptm/m/n/10 SNAP doc-u-men-ta- ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.620 ...t=197\sphinxpxdimen]{{myjobs_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.629 ...310\sphinxpxdimen]{{build_workflow2}.gif} [8] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.643 ...ght=325\sphinxpxdimen]{{jbrowse_out}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.666 ...198\sphinxpxdimen]{{build_workflow3}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.675 ...phinxpxdimen]{{annotation_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.705 ...ght=168\sphinxpxdimen]{{my_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.721 ...ht=182\sphinxpxdimen]{{workflow_URL}.gif} [9] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.740 ...6\sphinxpxdimen]{{running_workflow2}.gif} [10] Underfull \hbox (badness 10000) in paragraph at lines 852--852 []\T1/ptm/m/n/10 As-sem-bled Overfull \hbox (16.02496pt too wide) in paragraph at lines 2--852 [][][]\T1/ptm/m/n/10 test_genome.fasta.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 852--852 []\T1/ptm/m/n/10 An-no-tated gene Overfull \hbox (0.77548pt too wide) in paragraph at lines 2--852 [][][]\T1/ptm/m/n/10 maker_out.gff.gz[][]| Underfull \hbox (badness 10000) in paragraph at lines 897--897 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 897--897 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 MAKER- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 SNAP- Underfull \hbox (badness 10000) in paragraph at lines 2--897 [][][]\T1/ptm/m/n/10 SNAP doc-u-men-ta- ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.915 ...ht=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.923 ...,height=343\sphinxpxdimen]{{de_data}.gif} [11] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.945 ...ight=356\sphinxpxdimen]{{url_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.971 ...ht=329\sphinxpxdimen]{{data_window2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1000 ...10\sphinxpxdimen]{{build_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1011 ...ht=325\sphinxpxdimen]{{jbrowse_out}.gif} [12] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1026 ...98\sphinxpxdimen]{{build_workflow3}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1035 ...hinxpxdimen]{{annotation_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1046 ...t=182\sphinxpxdimen]{{workflow_URL}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1066 ...ht=170\sphinxpxdimen]{{my_workflow}.gif} [13] [14] Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/phv/m/n/10 Ver- Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 Nu-mer-i-cal- Overfull \hbox (18.41133pt too wide) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 NumericalTransform- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 TAS-SEL doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 EM-MAX doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 PCA doc-u-men-ta- Underfull \hbox (badness 10000) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 STRUC- Overfull \hbox (6.23843pt too wide) in paragraph at lines 1295--1295 []\T1/ptm/m/n/10 2.3.4.1| Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 STRUCTURE- Underfull \hbox (badness 10000) in paragraph at lines 2--1295 [][][]\T1/ptm/m/n/10 STRUC-TURE ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1313 ...2\sphinxpxdimen]{{public_workflows}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1325 ...inxpxdimen]{{association_workflow0}.gif} [15] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1351 ...355\sphinxpxdimen]{{manhattan_plot}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1378 ...ht=297\sphinxpxdimen]{{pca_output1}.gif} \sphinxincludegraphics[wi... ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1378 ...ht=284\sphinxpxdimen]{{pca_output2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1393 ...226\sphinxpxdimen]{{build_workflow}.gif} [16] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1405 ...292\sphinxpxdimen]{{emmax_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1449 ...inxpxdimen]{{association_workflow2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1454 ...inxpxdimen]{{association_workflow3}.gif} [17] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1520 ...ht=170\sphinxpxdimen]{{sorghum_ms9}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 App Underfull \hbox (badness 10000) in paragraph at lines 1604--1604 []\T1/phv/m/n/10 Notes/other Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 Bowtie2 doc-u- Overfull \hbox (12.84023pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_call| Overfull \hbox (5.70792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_call- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Overfull \hbox (17.29018pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bcftools_filter| Overfull \hbox (9.95792pt too wide) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools_filter- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bcftools doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SnpEff doc-u- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G- Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 SIFT4G doc-u- Overfull \hbox (6.47052pt too wide) in paragraph at lines 1604--1604 []\T1/ptm/m/n/10 bsa_viewer| Underfull \hbox (badness 10000) in paragraph at lines 2--1604 [][][]\T1/ptm/m/n/10 bsa_viewer- [18] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1622 ...t=327\sphinxpxdimen]{{cyverse_user}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1630 ...height=343\sphinxpxdimen]{{de_data}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1652 ...ght=356\sphinxpxdimen]{{url_window}.gif} [19] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1688 ...57\sphinxpxdimen]{{bcftools_window}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1718 ...t=100\sphinxpxdimen]{{bcftools_res}.gif} [20] Underfull \hbox (badness 5578) in paragraph at lines 1738--1740 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 1: bcftools_filter-1.8 \T1/ptm/m/n/10 in the His-tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1741 ...,height=276\sphinxpxdimen]{{snpeff}.gif} Underfull \hbox (badness 10000) in paragraph at lines 1782--1783 []\T1/ptm/m/n/10 Click \T1/ptm/b/n/10 2: SnpEff-4.3.1 \T1/ptm/m/n/10 in the His -tory panel to ex-pand its out-puts, then drag and drop ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1784 ...en,height=276\sphinxpxdimen]{{sift}.gif} [21] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1830 ...eight=363\sphinxpxdimen]{{ems_view}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1835 ...=123\sphinxpxdimen]{{ems_view_diag}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1844 ...ht=268\sphinxpxdimen]{{ems_viewer2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1857 ...ght=362\sphinxpxdimen]{{ems_viewer}.gif} [22] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1908 ...men,height=796\sphinxpxdimen]{{bsa}.gif} [23] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1962 ...n,height=260\sphinxpxdimen]{{mcrna}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.1985 ...ight=449\sphinxpxdimen]{{maizecode}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2004 ...t=182\sphinxpxdimen]{{workflow_URL}.gif} [24] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2035 ...eight=304\sphinxpxdimen]{{mcrnares}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2058 ...ight=338\sphinxpxdimen]{{MCrna_URL}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2067 ...ht=254\sphinxpxdimen]{{jbrowse_add}.gif} [25] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2097 ...ht=428\sphinxpxdimen]{{de_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2109 ...ight=242\sphinxpxdimen]{{de_result}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2132 ...t=421\sphinxpxdimen]{{iso_workflow}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2141 ...ight=439\sphinxpxdimen]{{iso_build}.gif} [26] ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2160 ...t=588\sphinxpxdimen]{{iso_analysis}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2165 ...=230\sphinxpxdimen]{{iso_analysis2}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2175 ...height=596\sphinxpxdimen]{{iso_run}.gif} ! LaTeX Error: Unknown graphics extension: .gif. See the LaTeX manual or LaTeX Companion for explanation. Type H for immediate help. ... l.2184 ...t=228\sphinxpxdimen]{{ballgown_out}.gif} [27] [28] Chapter 2. Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Pre- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/phv/m/n/10 req-ui- Overfull \hbox (27.43803pt too wide) in paragraph at lines 2261--2261 []\T1/phv/m/n/10 Link/Download| Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Cy- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Verse Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 []\T1/ptm/m/n/10 Sci- Underfull \hbox (badness 10000) in paragraph at lines 2261--2261 \T1/ptm/m/n/10 Apps Underfull \hbox (badness 10000) in paragraph at lines 2--2261 [][][]\T1/ptm/m/n/10 Cy-Verse Underfull \hbox (badness 10000) in paragraph at lines 2--2261 \T1/ptm/m/n/10 User (./cyverse-sciapps-guide.ind) [29] (./cyverse-sciapps-guide.aux) ) (see the transcript file for additional information){/usr/share/texlive/texmf-d ist/fonts/enc/dvips/base/8r.enc} Output written on cyverse-sciapps-guide.pdf (33 pages, 205880 bytes). Transcript written on cyverse-sciapps-guide.log. Latexmk: Index file 'cyverse-sciapps-guide.idx' was written Latexmk: Log file says output to 'cyverse-sciapps-guide.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: 2020-04-10T20:13:51.707997Z, end-time: 2020-04-10T20:13:51.926769Z, duration: 0, exit-code: 0 mv -f /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/./_build/latex/cyverse-sciapps-guide.pdf /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/artifacts/latest/sphinx_pdf/cyverse-sciapps-guide.pdf [rtd-command-info] start-time: 2020-04-10T20:13:52.184341Z, end-time: 2020-04-10T20:13:53.933304Z, duration: 1, exit-code: 0 python sphinx-build -T -b epub -d _build/doctrees-epub -D language=en . _build/epub Running Sphinx v1.8.5 loading translations [en]... done making output directory... building [mo]: targets for 0 po files that are out of date building [epub]: targets for 9 source files that are out of date updating environment: 9 added, 0 changed, 0 removed reading sources... [ 11%] annotation reading sources... [ 22%] association reading sources... [ 33%] bsa reading sources... [ 44%] index reading sources... [ 55%] maizecode reading sources... [ 66%] step1 reading sources... [ 77%] step2 reading sources... [ 88%] step3 reading sources... [100%] step4 /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/bsa.rst:8: WARNING: Title underline too short. The Bulked Segregant Analysis Tutorial --------------------------- /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/bsa.rst:21: WARNING: Insufficient data supplied (1 row(s)); no data remaining for table body, required by "list-table" directive. .. list-table:: :header-rows: 1 * - Input - Description - Example - Variants called with bcftools - `snp_bw2_ms9_1.vcf.gz `_ /home/docs/checkouts/readthedocs.org/user_builds/cyverse-sciapps-guide/checkouts/latest/maizecode.rst:8: WARNING: Duplicate explicit target name: "mcrna-0.0.1". looking for now-outdated files... none found pickling environment... done checking consistency... done preparing documents... done writing output... [ 11%] annotation writing output... [ 22%] association writing output... [ 33%] bsa writing output... [ 44%] index writing output... [ 55%] maizecode writing output... [ 66%] step1 writing output... [ 77%] step2 writing output... [ 88%] step3 writing output... 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