Website file tree contains broken links (Feb. 19, 2026)

[github-actions]

Summary

Status	Count
🔍 Total	3977
✅ Successful	3265
⏳ Timeouts	0
🔀 Redirected	80
👻 Excluded	117
❓ Unknown	0
🚫 Errors	24
⛔ Unsupported	491

Errors per input

Errors in _build/html/howto_guides/data_plan/index.html

• [302] https://dmptool.org/plans?plan%5Bfunder%5D%5Bid%5D=%7B+%22id%22%3A+4265%2C+%22name[%E2%80%A6]Microbiome+Data+Collaborative%22+%7D&plan%5Btemplate_id%5D=1321 | Rejected status code: 302 Found (configurable with "accept" option): Redirects may have been limited by "max-redirects".

💬 @eecavanna: I visited the URL in my web browser and saw a banner about having to sign in. I Assume that's why the link checker took issue with this.

Errors in _build/html/reference/software_development/index.html

• [429] https://www.gnu.org/software/make/ | Rejected status code: 429 Too Many Requests (configurable with "accept" option)
• [429] https://www.gnu.org/software/make/manual/html_node/Phony-Targets.html | Rejected status code: 429 Too Many Requests (configurable with "accept" option)
• [429] https://www.gnu.org/software/make/manual/html_node/Rule-Example.html | Rejected status code: 429 Too Many Requests (configurable with "accept" option)

💬 @eecavanna: I consider these to be a non-issue and assume it's just a case of the gnu.org web server being configured to prevent frequent visits from "bots" (such as the link checker).

Errors in _build/html/runtime/admin/index.html

• [404] https://www.nersc.gov/systems/spin/ | Rejected status code: 404 Not Found (configurable with "accept" option)

💬 @eecavanna: Maybe NERSC restructured their site over time and didn't add a redirect from the old URL to the new URL. Here's an overview about Spin: https://docs.nersc.gov/services/spin/

Errors in _build/html/runtime/howto-guides/author-changesheets/index.html

• [404] https://microbiomedata.github.io/nmdc-schema/doi/ | Rejected status code: 404 Not Found (configurable with "accept" option)

💬 @eecavanna: Looks like the schema docs URLs are case sensitive. I do see a page about a class named Doi at: https://microbiomedata.github.io/nmdc-schema/Doi/

Errors in _build/html/runtime/nb/wf_automation/index.html

• [404] https://microbiomedata.github.io/nmdc-schema/Activity/ | Rejected status code: 404 Not Found (configurable with "accept" option)

💬 @eecavanna: I think this is just outdated documentation in the Runtime repo (this page gets pulled from the nmdc-runtime repo). I vaguely remember the "Activity" class being removed as part of the Berkeley schema overhaul.

Errors in _build/html/runtime/tutorials/metadata-in/index.html

• [404] https://api.microbiomedata.org/nmdcschema/biosample_set/fake | Rejected status code: 404 Not Found (configurable with "accept" option)

💬 @eecavanna: The Runtime docs do contain that URL (as an example), here, followed by a note acknowledging that it might not work anymore.

Errors in _build/html/workflows/chapters/2_Read_Based_Taxonomy/index.html

• [404] https://github.com/poeli/GOTTCHA2 | Rejected status code: 404 Not Found (configurable with "accept" option)
• [404] https://github.com/poeli/GOTTCHA2/blob/master/LICENSE | Rejected status code: 404 Not Found (configurable with "accept" option)

Errors in _build/html/workflows/chapters/3_Metagenome_Reads_QC/index.html

• [404] https://github.com/microbiomedata/ReadsQC/blob/documentation/input.json | Rejected status code: 404 Not Found (configurable with "accept" option)
• [302] https://jgi.doe.gov/data-and-tools/bbtools/ | Rejected status code: 302 Found (configurable with "accept" option): Redirects may have been limited by "max-redirects".

Errors in _build/html/workflows/chapters/4_Metagenome_Assembly/index.html

• [302] https://jgi.doe.gov/data-and-tools/bbtools/ | Rejected status code: 302 Found (configurable with "accept" option): Redirects may have been limited by "max-redirects".

Errors in _build/html/workflows/chapters/5_Metagenome_and_Metatranscriptome_Annotation/index.html

• [403] https://doi.org/10.1128/msystems.00804-20 | Rejected status code: 403 Forbidden (configurable with "accept" option)
• [404] https://portal.nersc.gov/cfs/m3408/test_data/metaT/SRR11678315.fastq.gz | Rejected status code: 404 Not Found (configurable with "accept" option)

Errors in _build/html/workflows/chapters/6_Metagenome_Assembled_Genome/index.html

• [403] https://doi.org/10.1093/bioinformatics/btz848 | Rejected status code: 403 Forbidden (configurable with "accept" option)

Errors in _build/html/workflows/chapters/7_Metatranscriptome_Workflow_Overview/index.html

• [302] https://jgi.doe.gov/data-and-tools/bbtools/ | Error (cached)

Errors in _build/html/workflows/chapters/8_Metatranscriptome_Reads_QC/index.html

• [302] https://jgi.doe.gov/data-and-tools/bbtools/ | Error (cached)
• [302] https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/data-preprocessing/ | Rejected status code: 302 Found (configurable with "accept" option): Redirects may have been limited by "max-redirects".

Errors in _build/html/workflows/chapters/12_GCMS_Metabolomics/index.html

• [404] https://github.com/microbiomedata/metaMS/blob/master/docs/index.rst | Rejected status code: 404 Not Found (configurable with "accept" option)

Errors in _build/html/workflows/chapters/13_LCMS_Metabolomics/index.html

• [404] https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst | Rejected status code: 404 Not Found (configurable with "accept" option)
• [404] https://github.com/microbiomedata/metaMS/blob/master/wdl/metaMS_lcmsmetabolomics.wdl | Rejected status code: 404 Not Found (configurable with "accept" option)
• [502] https://gnps-external.ucsd.edu/gnpslibrary | Rejected status code: 502 Bad Gateway (configurable with "accept" option)

Errors in _build/html/workflows/chapters/15_LCMS_Lipidomics/index.html

• [404] https://github.com/microbiomedata/metaMS/blob/master/docs/index_lipid.rst | Rejected status code: 404 Not Found (configurable with "accept" option)

Redirects per input

Show/hide redirects

Redirects in _build/html/_hooks/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/_hooks/README.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/_hooks/README.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2F_hooks%2FREADME.md

Redirects in _build/html/_templates/footer.html

• [200] https://microbiomedata.org/privacy | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://microbiomedata.org/privacy --[307]--> https://www.lbl.gov/terms-and-conditions/web-privacy-notice/

Redirects in _build/html/explanation/community_conversations/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/explanation/community_conversations.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/explanation/community_conversations.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fexplanation%2Fcommunity_conversations.md

Redirects in _build/html/explanation/fair_data/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/explanation/fair_data.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/explanation/fair_data.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fexplanation%2Ffair_data.md
• [200] https://www.go-fair.org/implementation-networks/overview/fair-microbiome/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://www.go-fair.org/implementation-networks/overview/fair-microbiome/ --[301]--> https://www.go-fair.org/implementation-networks/overview/implementation-networks-archive/fair-microbiome/
• [200] https://www.nature.com/articles/sdata201618 | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: https://www.nature.com/articles/sdata201618 --[303]--> https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fsdata201618 --[302]--> https://idp.nature.com/transit?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fsdata201618&code=1d0e3f5d-041b-499e-baf4-554889786120 --[302]--> https://www.nature.com/articles/sdata201618?error=cookies_not_supported&code=1d0e3f5d-041b-499e-baf4-554889786120

Redirects in _build/html/howto_guides/api_gui/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/api_gui.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/api_gui.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fhowto_guides%2Fapi_gui.md
• [200] https://microbiomedata.github.io/nmdc-schema/DataObject | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://microbiomedata.github.io/nmdc-schema/DataObject --[301]--> https://microbiomedata.github.io/nmdc-schema/DataObject/
• [200] https://w3id.org/nmdc/Biosample | Redirect: Followed 6 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/Biosample --[307]--> https://api.microbiomedata.org/objects/Biosample --[307]--> https://api.microbiomedata.org/objects/Biosample --[307]--> https://microbiomedata.github.io/nmdc-schema/Biosample --[307]--> https://microbiomedata.github.io/nmdc-schema/Biosample --[301]--> https://microbiomedata.github.io/nmdc-schema/Biosample/ --[301]--> https://microbiomedata.github.io/nmdc-schema/Biosample/
• [200] https://w3id.org/nmdc/DataObject/ | Redirect: Followed 5 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/DataObject/ --[307]--> https://api.microbiomedata.org/objects/DataObject/ --[307]--> http://api.microbiomedata.org/objects/DataObject --[308]--> https://api.microbiomedata.org/objects/DataObject --[307]--> https://microbiomedata.github.io/nmdc-schema/DataObject --[301]--> https://microbiomedata.github.io/nmdc-schema/DataObject/
• [200] https://w3id.org/nmdc/PlannedProcess/ | Redirect: Followed 5 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/PlannedProcess/ --[307]--> https://api.microbiomedata.org/objects/PlannedProcess/ --[307]--> http://api.microbiomedata.org/objects/PlannedProcess --[308]--> https://api.microbiomedata.org/objects/PlannedProcess --[307]--> https://microbiomedata.github.io/nmdc-schema/PlannedProcess --[301]--> https://microbiomedata.github.io/nmdc-schema/PlannedProcess/
• [200] https://w3id.org/nmdc/Study | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/Study --[307]--> https://api.microbiomedata.org/objects/Study --[307]--> https://microbiomedata.github.io/nmdc-schema/Study --[301]--> https://microbiomedata.github.io/nmdc-schema/Study/

Redirects in _build/html/howto_guides/data_plan/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/data_plan.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/data_plan.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fhowto_guides%2Fdata_plan.md
• [200] https://w3id.org/nmdc/nmdc | Redirect: Followed 2 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/nmdc --[307]--> https://microbiomedata.github.io/nmdc-schema --[301]--> https://microbiomedata.github.io/nmdc-schema/

Redirects in _build/html/howto_guides/globus/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/globus.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/globus.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fhowto_guides%2Fglobus.md
• [200] https://globus.org/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://globus.org/ --[301]--> https://www.globus.org/

Redirects in _build/html/howto_guides/portal_guide/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/portal_guide.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/portal_guide.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fhowto_guides%2Fportal_guide.md
• [200] https://microbiomedata.org/nmdc-data-use-policy | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://microbiomedata.org/nmdc-data-use-policy --[301]--> https://microbiomedata.org/nmdc-data-use-policy/

Redirects in _build/html/howto_guides/submit2nmdc/index.html

• [200] https://apps.apple.com/app/apple-store/id6575364655?pt=278434&ct=docs&mt=8 | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://apps.apple.com/app/apple-store/id6575364655?pt=278434&ct=docs&mt=8 --[301]--> https://apps.apple.com/us/app/nmdc-field-notes/id6575364655?ct=docs&pt=278434
• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/submit2nmdc.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/howto_guides/submit2nmdc.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Fhowto_guides%2Fsubmit2nmdc.md

Redirects in _build/html/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/index.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/index.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Findex.md
• [200] https://microbiomedata.org/contact | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://microbiomedata.org/contact --[301]--> https://microbiomedata.org/contact/

Redirects in _build/html/reference/data_portal/index.html

• [200] https://docs.celeryq.dev/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.celeryq.dev/ --[302]--> https://docs.celeryq.dev/en/stable/
• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/reference/data_portal.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/reference/data_portal.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Freference%2Fdata_portal.md

Redirects in _build/html/reference/software_development/index.html

• [200] https://claude.ai/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://claude.ai/ --[307]--> https://claude.ai/login
• [200] https://docs.pytest.org/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.pytest.org/ --[302]--> https://docs.pytest.org/en/stable/
• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/reference/software_development.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/reference/software_development.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Freference%2Fsoftware_development.md
• [200] https://jaws-docs.readthedocs.io/en/latest/Resources/best_practices.html | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://jaws-docs.readthedocs.io/en/latest/Resources/best_practices.html --[302]--> https://jaws-docs.jgi.doe.gov/en/latest/Resources/best_practices.html
• [200] https://nodejs.org/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://nodejs.org/ --[307]--> https://nodejs.org/en

Redirects in _build/html/runtime/admin/index.html

• [200] https://github.com/orgs/microbiomedata/teams/architecture-wg | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/orgs/microbiomedata/teams/architecture-wg --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Forgs%2Fmicrobiomedata%2Fteams%2Farchitecture-wg
• [200] https://www.nersc.gov/live-status/motd/ | Redirect: Followed 2 redirects resolving to the final status of: OK. Redirects: https://www.nersc.gov/live-status/motd/ --[301]--> https://www.nersc.gov/live-status/motd --[301]--> https://www.nersc.gov/users/status

Redirects in _build/html/runtime/explanation/identifiers/index.html

• [200] https://w3id.org/nmdc/Biosample | Redirect: Followed 6 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/Biosample --[307]--> https://api.microbiomedata.org/objects/Biosample --[307]--> https://api.microbiomedata.org/objects/Biosample --[307]--> https://microbiomedata.github.io/nmdc-schema/Biosample --[307]--> https://microbiomedata.github.io/nmdc-schema/Biosample --[301]--> https://microbiomedata.github.io/nmdc-schema/Biosample/ --[301]--> https://microbiomedata.github.io/nmdc-schema/Biosample/
• [200] https://w3id.org/nmdc/id | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: https://w3id.org/nmdc/id --[307]--> https://api.microbiomedata.org/objects/id --[307]--> https://microbiomedata.github.io/nmdc-schema/id --[301]--> https://microbiomedata.github.io/nmdc-schema/id/

Redirects in _build/html/runtime/howto-guides/claim-and-run-jobs/index.html

• [200] https://docs.dagster.io/concepts/ops-jobs-graphs/jobs-graphs | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/ops-jobs-graphs/jobs-graphs --[308]--> https://docs.dagster.io/guides/build/ops/graphs
• [200] https://docs.dagster.io/concepts/ops-jobs-graphs/ops | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/ops-jobs-graphs/ops --[308]--> https://docs.dagster.io/guides/build/ops
• [200] https://docs.dagster.io/concepts/partitions-schedules-sensors/sensors | Redirect: Followed 2 redirects resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/partitions-schedules-sensors/sensors --[308]--> https://docs.dagster.io/guides/automate/sensors --[308]--> https://docs.dagster.io/guides/automate/sensors
• [200] https://docs.dagster.io/concepts/repositories-workspaces/repositories | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/repositories-workspaces/repositories --[308]--> https://docs.dagster.io/api/dagster/repositories

Redirects in _build/html/runtime/howto-guides/create-triggers/index.html

• [200] https://docs.dagster.io/concepts/partitions-schedules-sensors/sensors | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/partitions-schedules-sensors/sensors --[308]--> https://docs.dagster.io/guides/automate/sensors

Redirects in _build/html/runtime/howto-guides/update-sensors-ops/index.html

• [200] https://docs.dagster.io/concepts/resources | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/concepts/resources --[308]--> https://docs.dagster.io/guides/build/external-resources
• [200] https://docs.dagster.io/deployment/executors | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/deployment/executors --[308]--> https://docs.dagster.io/guides/operate/run-executors
• [200] https://docs.dagster.io/deployment/run-launcher | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/deployment/run-launcher --[308]--> https://docs.dagster.io/deployment/execution/run-launchers
• [200] https://docs.dagster.io/guides/deploy/code-locations/workspace-yaml | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.dagster.io/guides/deploy/code-locations/workspace-yaml --[308]--> https://docs.dagster.io/guides/build/projects/workspaces/workspace-yaml

Redirects in _build/html/runtime/nb/api_access_via_python/index.html

• [200] https://github.com/microbiomedata/nmdc-runtime/issues/new | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/nmdc-runtime/issues/new --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fnmdc-runtime%2Fissues%2Fnew

Redirects in _build/html/runtime/tutorials/json/index.html

• [200] https://docs.mongodb.com/manual/tutorial/query-documents/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.mongodb.com/manual/tutorial/query-documents/ --[301]--> https://www.mongodb.com/docs/manual/tutorial/query-documents/

Redirects in _build/html/runtime/tutorials/metadata-in/index.html

• [200] https://docs.mongodb.com/v4.4/reference/command/delete/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://docs.mongodb.com/v4.4/reference/command/delete/ --[301]--> https://www.mongodb.com/docs/v4.4/reference/command/delete/
• [200] https://gist.github.com/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://gist.github.com/ --[302]--> https://gist.github.com/starred

Redirects in _build/html/tutorials/nav_data_portal/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/tutorials/nav_data_portal.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/tutorials/nav_data_portal.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Ftutorials%2Fnav_data_portal.md

Redirects in _build/html/tutorials/submission_portal/index.html

• [200] https://github.com/microbiomedata/docs/edit/main/content/home/src/tutorials/submission_portal.md | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/docs/edit/main/content/home/src/tutorials/submission_portal.md --[302]--> https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2Fmicrobiomedata%2Fdocs%2Fedit%2Fmain%2Fcontent%2Fhome%2Fsrc%2Ftutorials%2Fsubmission_portal.md

Redirects in _build/html/workflows/chapters/2_Read_Based_Taxonomy/index.html

• [200] http://ccb.jhu.edu/software/kraken2 | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: http://ccb.jhu.edu/software/kraken2 --[308]--> https://ccb.jhu.edu/software/kraken2 --[301]--> http://ccb.jhu.edu/software/kraken2/ --[308]--> https://ccb.jhu.edu/software/kraken2/
• [200] http://www.ccb.jhu.edu/software/centrifuge | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: http://www.ccb.jhu.edu/software/centrifuge --[308]--> https://www.ccb.jhu.edu/software/centrifuge --[301]--> http://www.ccb.jhu.edu/software/centrifuge/ --[308]--> https://www.ccb.jhu.edu/software/centrifuge/

Redirects in _build/html/workflows/chapters/4_Metagenome_Assembly/index.html

• [200] https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/ --[301]--> https://www.ncbi.nlm.nih.gov/genbank/genome_agp_specification/

Redirects in _build/html/workflows/chapters/5_Metagenome_and_Metatranscriptome_Annotation/index.html

• [200] http://reusabledata.org/cath | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/cath --[301]--> https://reusabledata.org/cath
• [200] http://reusabledata.org/cogs | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/cogs --[301]--> https://reusabledata.org/cogs
• [200] http://reusabledata.org/kegg-ftp | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/kegg-ftp --[301]--> https://reusabledata.org/kegg-ftp
• [200] http://reusabledata.org/pfam | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/pfam --[301]--> https://reusabledata.org/pfam
• [200] http://reusabledata.org/rfam | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/rfam --[301]--> https://reusabledata.org/rfam
• [200] http://reusabledata.org/smart | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/smart --[301]--> https://reusabledata.org/smart
• [200] http://reusabledata.org/supfam | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/supfam --[301]--> https://reusabledata.org/supfam
• [200] http://reusabledata.org/tigrfams | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://reusabledata.org/tigrfams --[301]--> https://reusabledata.org/tigrfams

Redirects in _build/html/workflows/chapters/6_Metagenome_Assembled_Genome/index.html

• [200] http://reusabledata.org/cogs | Redirect: Followed 2 redirects resolving to the final status of: OK. Redirects: http://reusabledata.org/cogs --[301]--> https://reusabledata.org/cogs --[301]--> https://reusabledata.org/cogs
• [200] http://www.microbesonline.org/fasttree/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://www.microbesonline.org/fasttree/ --[301]--> https://microbesonline.org/fasttree/
• [200] http://www.microbesonline.org/fasttree/FastTree.c | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: http://www.microbesonline.org/fasttree/FastTree.c --[301]--> https://microbesonline.org/fasttree/FastTree.c
• [200] https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-209 | Redirect: Followed 4 redirects resolving to the final status of: OK. Redirects: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-8-209 --[301]--> https://link.springer.com/article/10.1186/1471-2105-8-209 --[303]--> https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1186%2F1471-2105-8-209 --[302]--> https://idp.springer.com/transit?redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1186%2F1471-2105-8-209&code=66039242-7a03-442c-9c09-6ef07c4790d3 --[302]--> https://link.springer.com/article/10.1186/1471-2105-8-209?error=cookies_not_supported&code=66039242-7a03-442c-9c09-6ef07c4790d3
• [200] https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02155-4 | Redirect: Followed 4 redirects resolving to the final status of: OK. Redirects: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02155-4 --[301]--> https://link.springer.com/article/10.1186/s13059-020-02155-4 --[303]--> https://idp.springer.com/authorize?response_type=cookie&client_id=springerlink&redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1186%2Fs13059-020-02155-4 --[302]--> https://idp.springer.com/transit?redirect_uri=https%3A%2F%2Flink.springer.com%2Farticle%2F10.1186%2Fs13059-020-02155-4&code=06acc71f-7ba3-45e5-9bac-9b42d493f776 --[302]--> https://link.springer.com/article/10.1186/s13059-020-02155-4?error=cookies_not_supported&code=06acc71f-7ba3-45e5-9bac-9b42d493f776
• [200] https://github.com/microbiomedata/nmdc-schema/files/14377315/nmdc_wfmag-11-6scpgx92.1_heatmap.pdf | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/nmdc-schema/files/14377315/nmdc_wfmag-11-6scpgx92.1_heatmap.pdf --[302]--> https://objects.githubusercontent.com/github-production-repository-file-5c1aeb/354168085/14377315?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20260220%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20260220T023907Z&X-Amz-Expires=300&X-Amz-Signature=bb96230c7107f7ece80ebe698c34df61a4052eba347857a4b1dd049c2f2d8041&X-Amz-SignedHeaders=host&response-content-disposition=attachment%3Bfilename%3Dnmdc_wfmag-11-6scpgx92.1_heatmap.pdf&response-content-type=application%2Fpdf
• [200] https://github.com/microbiomedata/nmdc-schema/files/14377316/nmdc_wfmag-11-6scpgx92.1_barplot.pdf | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/nmdc-schema/files/14377316/nmdc_wfmag-11-6scpgx92.1_barplot.pdf --[302]--> https://objects.githubusercontent.com/github-production-repository-file-5c1aeb/354168085/14377316?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20260220%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20260220T023906Z&X-Amz-Expires=300&X-Amz-Signature=b8b5b5a648366d553a87aae1718ad61449e4f25bae9d482b4385de8f1c71cbe0&X-Amz-SignedHeaders=host&response-content-disposition=attachment%3Bfilename%3Dnmdc_wfmag-11-6scpgx92.1_barplot.pdf&response-content-type=application%2Fpdf
• [200] https://github.com/psf/requests/blob/master/LICENSE | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/psf/requests/blob/master/LICENSE --[302]--> https://github.com/psf/requests/blob/main/LICENSE
• [200] https://github.com/PyMySQL/PyMySQL/blob/master/LICENSE | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/PyMySQL/PyMySQL/blob/master/LICENSE --[302]--> https://github.com/PyMySQL/PyMySQL/blob/main/LICENSE
• [200] https://github.com/user-attachments/assets/fee36f54-914c-45f7-bc07-379b4da4ea72 | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/user-attachments/assets/fee36f54-914c-45f7-bc07-379b4da4ea72 --[302]--> https://github-production-user-asset-6210df.s3.amazonaws.com/737589/354722121-fee36f54-914c-45f7-bc07-379b4da4ea72.png?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20260220%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20260220T023906Z&X-Amz-Expires=300&X-Amz-Signature=0519399abbab35fc926f7dcecfce347d4f215cee2566d1119c5c41c7b0a0a5af&X-Amz-SignedHeaders=host
• [200] https://github.com/user-attachments/files/16498858/MetaG_test_ko_matrix.txt | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/user-attachments/files/16498858/MetaG_test_ko_matrix.txt --[302]--> https://objects.githubusercontent.com/github-production-repository-file-5c1aeb/265964562/16498858?X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Credential=AKIAVCODYLSA53PQK4ZA%2F20260220%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Date=20260220T023906Z&X-Amz-Expires=300&X-Amz-Signature=5023e45e0db2702f55e63f87359b81a6367118e11df3fc85ec5d72e70c69eb09&X-Amz-SignedHeaders=host&response-content-disposition=attachment%3Bfilename%3DMetaG_test_ko_matrix.txt&response-content-type=text%2Fplain
• [200] https://opensource.org/licenses/MIT | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://opensource.org/licenses/MIT --[301]--> https://opensource.org/license/MIT
• [200] https://www.nature.com/articles/s41579-020-0377-0 | Redirect: Followed 3 redirects resolving to the final status of: OK. Redirects: https://www.nature.com/articles/s41579-020-0377-0 --[303]--> https://idp.nature.com/authorize?response_type=cookie&client_id=grover&redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41579-020-0377-0 --[302]--> https://idp.nature.com/transit?redirect_uri=https%3A%2F%2Fwww.nature.com%2Farticles%2Fs41579-020-0377-0&code=e9d757e8-6eff-416a-901d-00b5c922e60c --[302]--> https://www.nature.com/articles/s41579-020-0377-0?error=cookies_not_supported&code=e9d757e8-6eff-416a-901d-00b5c922e60c
• [200] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323987/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323987/ --[301]--> https://pmc.ncbi.nlm.nih.gov/articles/PMC6323987/

Redirects in _build/html/workflows/chapters/10_Metatranscriptome_Expression/index.html

• [200] https://readthedocs.org/ | Redirect: Followed 5 redirects resolving to the final status of: OK. Redirects: https://readthedocs.org/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://app.readthedocs.org/welcome/
• [200] https://www.sphinx-doc.org/ | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://www.sphinx-doc.org/ --[302]--> https://www.sphinx-doc.org/en/master/

Redirects in _build/html/workflows/chapters/11_Metaproteomics/index.html

• [200] https://opensource.org/licenses/BSD-2-Clause | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://opensource.org/licenses/BSD-2-Clause --[301]--> https://opensource.org/license/BSD-2-Clause
• [200] https://readthedocs.org/ | Redirect: Followed 5 redirects resolving to the final status of: OK. Redirects: https://readthedocs.org/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://app.readthedocs.org/welcome/
• [200] https://www.sphinx-doc.org/ | Redirect: Followed 2 redirects resolving to the final status of: OK. Redirects: https://www.sphinx-doc.org/ --[302]--> https://www.sphinx-doc.org/en/master/ --[302]--> https://www.sphinx-doc.org/en/master/

Redirects in _build/html/workflows/chapters/12_GCMS_Metabolomics/index.html

• [200] https://github.com/microbiomedata/metaMS/tree/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf | Redirect: Followed 1 redirect resolving to the final status of: OK. Redirects: https://github.com/microbiomedata/metaMS/tree/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf --[301]--> https://github.com/microbiomedata/metaMS/blob/master/data/raw_data/GCMS_FAMES_01_GCMS-01_20191023.cdf
• [200] https://readthedocs.org/ | Redirect: Followed 6 redirects resolving to the final status of: OK. Redirects: https://readthedocs.org/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org --[302]--> https://app.readthedocs.org/welcome/ --[302]--> https://about.readthedocs.com/?ref=app.readthedocs.org

Full Github Actions output

[eecavanna]

Hi @aclum, the link checker on GitHub Actions is working again. This ticket was created by it just now. It shows the results of scanning all the HTML documents that make up the current website. I'll insert my own comments above, now, (preceded by a 💬 emoji) in an attempt to make the errors more actionable.

[aclum]

None of these appear to be from the recent updates so let's divvy these up to go over in the next documentation meeting. cc @ssarrafan