Logging at level: debug Configuration file: /github/workspace/./docs/_config.yml GitHub Pages: github-pages v228 GitHub Pages: jekyll v3.9.3 Theme: jekyll-theme-primer Theme source: /usr/local/bundle/gems/jekyll-theme-primer-0.6.0 Requiring: jekyll-github-metadata Requiring: jekyll-seo-tag Requiring: jekyll-feed Requiring: jekyll-redirect-from Requiring: jekyll-seo-tag Requiring: jekyll-sitemap Requiring: jekyll-coffeescript Requiring: jekyll-commonmark-ghpages Requiring: jekyll-gist Requiring: jekyll-github-metadata Requiring: jekyll-paginate Requiring: jekyll-relative-links Requiring: jekyll-optional-front-matter Requiring: jekyll-readme-index Requiring: jekyll-default-layout Requiring: jekyll-titles-from-headings GitHub Metadata: Initializing... Source: /github/workspace/./docs Destination: /github/workspace/./docs/_site Incremental build: disabled. Enable with --incremental Generating... EntryFilter: excluded /Gemfile.lock EntryFilter: excluded /README.md EntryFilter: excluded /Gemfile Reading: _posts/2017-05-03-jekyll-doc-theme.md Reading: _posts/2017-02-01-welcome-to-jekyll.md Reading: _docs/data_publication_and_citation/Data-publication-and-citation-obsolete.md Reading: _docs/data_publication_and_citation/Shortcut-URLs-for-citation-and-sharing.md Reading: _docs/data_submission_process/Curation-Workflow.md Reading: _docs/data_submission_process/Reviewing-Data.md Reading: _docs/using_atlas/Query-by-Anatomy.md Reading: _docs/using_atlas/Query-by-Gene.md Reading: _docs/using_atlas/Search-Results.md Reading: _docs/using_atlas/Using-the-ATLAS-D2K-Data-Browser.md Reading: _docs/using_atlas/Boolean-Anatomy-Search.md Reading: _docs/using_atlas/Collections.md Reading: _docs/using_atlas/Exporting-Data.md Reading: _docs/using_atlas/Filtering-Sidebar.md Reading: _docs/using_atlas/Batch-Query.md Reading: _docs/images_and_videos/Video-Players.md Reading: _docs/images_and_videos/Thumbnail-creation-guideline.md Reading: _docs/data_model/Data-submission---curation-state-diagram.md Reading: _docs/data_model/Data-Submission-Workshop-2017_06_12.md Reading: _docs/submitting_data/Submitting-Data-Collections.md Reading: _docs/submitting_data/Uploading-files-via-Deriva-client-tools.md Reading: _docs/submitting_data/Submitting-Cell-Lines.md Reading: _docs/submitting_data/Color-palette-for-annotating-histological-images.md Reading: _docs/submitting_data/Submitting-Histology-Data.md Reading: _docs/submitting_data/Submitting-Cell-Lines-orig.md Reading: _docs/submitting_data/Bulk-uploading-image-files.md Reading: _docs/submitting_data/Submitting-Specimen-Data-v2.md Reading: _docs/submitting_data/Submitting-Sequencing-Data-v3-1.md Reading: _docs/submitting_data/Submitting-Single-Cell-Visualization-Files.md Reading: _docs/submitting_data/Submitting-Protocols.md Reading: _docs/submitting_data/submitting-schematics.md Reading: _docs/submitting_data/Standard-file-formats-for-data-submission.md Reading: _docs/submitting_data/Submitting-Antibodies.md Reading: _docs/submitting_data/Using-the-Annotation-Tool.md Reading: _docs/submitting_data/Submitting-Immunofluorescence-Images.md Reading: _docs/submitting_data/Submitting-Entries-for-the-Functional-Assay-Handbook.md Reading: _docs/submitting_data/Adding-specimen-records-from-a-file.md Reading: _docs/submitting_data/Submitting-Specimen-Data.md Reading: _docs/submitting_data/Submitting-Sequencing-Data-v3.md Reading: _docs/submitting_data/Submitting-Sequencing,-Metabolomics,-IMC-Data.md Reading: _docs/index.md Reading: _docs/access/_bibliography/gudmap_references.bib Reading: _docs/access/_bibliography/rbk_references.bib Reading: _docs/access/Accessing-ATLAS-Resources.md Reading: _docs/misc/GUDMAP-Requirements-Sessions.md Reading: _docs/misc/Accessing-human-sequencing-data.md Reading: _docs/misc/Export-Data.md Reading: _docs/misc/Formatting-with-Markdown.md Reading: _docs/misc/Release-Notes-(Data-Browser).md Reading: _docs/misc/Create-citable-datasets.md Reading: _docs/misc/Uploading-sequencing-workflow-files.md Reading: _docs/misc/Advanced-Editing-Features.md Reading: _docs/misc/Tips-for-Submitting-Larg