SPAAM-community / AncientMetagenomeDir

Repository containing lists of all published ancient metagenomic (and related) samples and libraries

http://www.spaam-community.org/AncientMetagenomeDir/

Creative Commons Attribution 4.0 International

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Hodgkins2023 #1117

Closed DianaSpurite closed 9 months ago

DianaSpurite commented 11 months ago

Adding Hodgkind2023 samples

Pull Request

This PR is for a

[x] New Publication(s)
[ ] Correction

For the following list(s):

[ ] ancientmetagenome-environmental (README)
[ ] ancientmetagenome-hostassociated (README)
[x] ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s):

This is to close #1109

Checklist

[x] Publication is published (preprints currently not accepted)?
[x] Checked the publication is not already in the database?
[ ] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
[x] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
[x] Checked the list follows conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)?
[x] Changelog is updated to include the publication under 'Added'?
[x] Pull request has passed validation checks (see automated comment from github-bot)?
[x] Review requested from @SPAAM-community/ancientmetagenomedir?
[x] (If applicable) Made a separate PR to add new categories to controlled lists (stored under /assets/enums, e.g. material or archive)? If so the corresponding PR is here: https://github.com/SPAAM-community/AncientMetagenomeDir/pull/1118

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	2 paired fastq	library_name	2759	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2762	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2764	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2809	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2811	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2812	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2813	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2814	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2815	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2816	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2817	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2818	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2819	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2820	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2821	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2822	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2823	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2824	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2825	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2826	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2827	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2828	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2829	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2830	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	2 paired fastq	library_name	2759	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2762	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2764	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2809	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2811	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2812	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2813	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2814	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2815	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2816	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2817	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2818	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2819	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2820	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2821	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2822	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2823	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2824	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2825	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2826	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2827	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2828	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2829	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	AmpliTaq Gold	library_polymerase	2830	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	2 paired fastq	library_name	2759	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2762	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2764	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2809	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 11 months ago

I'll leave a bunch of comments with information later today to help with reviewing process

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	2 paired fastq	library_name	2759	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2762	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	2 paired fastq	library_name	2764	'2 paired fastq' does not match '^[\S]+$'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2809	'AmpliTaq Gold' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Clostridium tetani	singlegenome_species	608	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	609	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	610	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	611	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	612	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	613	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	614	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	615	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	616	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	617	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	618	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	619	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	620	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	621	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	622	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	623	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	624	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	625	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	626	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	627	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	628	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	629	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	630	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	631	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	632	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	633	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	634	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	635	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	636	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	637	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	638	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	639	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	640	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	641	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	642	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	643	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	644	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Clostridium tetani	singlegenome_species	645	'Clostridium tetani' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 11 months ago

When the species PR is approved the commit should become validated

DianaSpurite commented 11 months ago

For the reviewer(s):

SAMPLES:

All sample information is taken from Hodgkins 2023 publication supplementary table and main text, including sample age, sample material and coordinates (shortened in some cases to 3 decimals). Excluding PRJ numbers, SRS/ERS numbers and subsequently which archive.
Tenerife-004-Tooth sample age not provided, therefore I set it the same as the age of the other sample from the same site
For Vác-Mummy-Tissue sample, the material was stated to be "left chest extract", so I set it as simply "tissue"
Pericues-BC28-Bone sample age left as 550 as I wasn't sure if I should round up or down

DianaSpurite commented 11 months ago

For the reviewer(s):

LIBRARIES:

Links to all the original studies for each sample are available in the Hodgkins supplementary table "Supp Data 2"

I looked for the information here:

Sanganji-A1-Tooth and Sanganji-A2-Tooth: https://pubmed.ncbi.nlm.nih.gov/27581845/ -> ENA -> supplementary information -> Listed protocol
Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth: https://doi.org/10.1016/j.jasrep.2017.12.025 -> ENA -> main text -> Listed protocol (Meyer and Kircher, 2010)
Augsburg-Tooth -> our records sample: "1343UnTal85"
Tenerife-011-Tooth; Tenerife-004-Tooth; GranCanaria-005-Tooth; GranCanaria-008-Tooth; Tenerife-012-Tooth; Tenerife-013-Tooth: https://pubmed.ncbi.nlm.nih.gov/29107554/ -> main text -> ENA
Tepos_35-Tooth: https://pubmed.ncbi.nlm.nih.gov/29335577/ unfortunately I didn't note this one for some reason..
Cueva_de_los_Lagos-Tooth: https://pubmed.ncbi.nlm.nih.gov/29531053/ -> main text -> ENA -> Kircher et.al protocol, age for this sample middle from the listed "late Bronze Age"
Yámana-Tooth: https: //pubmed.ncbi.nlm.nih.gov/29632188/ -> ENA -> suplement table
Vác-Mummy-Tissue: our records, sample "92-A1"
Chinchorro-Mummy-Bone and Pericues-BC28-Bone: https://pubmed.ncbi.nlm.nih.gov/26198033/ -> ENA -> supplementary information
Marseille-Tooth -> our records, sample "OBS107"
Barcelona-3031-Tooth -> our records, sample "Barcelona3031"
SLC-France-Tooth: https://pubmed.ncbi.nlm.nih.gov/30478041/ -> didn't note, unfortunately
Karolva-Tooth: https://pubmed.ncbi.nlm.nih.gov/31594508/ ->ENA -> supplementary information
Abusir1655-Tooth; Abusir1595-Tooth; Abusir1668-Tooth; Abusir1671-Tooth; Abusir1607-Tooth: https://pubmed.ncbi.nlm.nih.gov/32859198/ -> ENA -> main text -> listed protocols
Dacaozi-Tooth: https://pubmed.ncbi.nlm.nih.gov/32483115/ -> ENA -> main text -> listed protocols (36, 37)
Riga_Cemetery-Tooth -> our recoreds, sample "G701"
Chincha-UC12-12-Tooth; Chincha-UC12-24-Tooth; Chincha-UC8-8168-Tooth: https://pubmed.ncbi.nlm.nih.gov/32661160/ -> ENA -> main text -> protocol ref. 71 -> in that protocol ref. 2 & 3, not sure about polymerase for this sample
Chiribaya_Alta-Bone and El_Yaral-Bone-> our records samples "sample 54" and "sample 64", however, library treatment appeared to mismatch in our records and the Hodgkins 2023 supplement table. Main text in the original publication didn't state anything about treatment: https://pubmed.ncbi.nlm.nih.gov/25141181/
Peru-NA40-Bone; Peru-NA42-Bone: https://pubmed.ncbi.nlm.nih.gov/24568772/ -> ENA -> main text -> listed protocol (KAPA)
Pueblo_Bonito-Tooth: https://pubmed.ncbi.nlm.nih.gov/28221340/ -> ENA, layout listed as paired, but appears to be single is 3 of the libraries
Gniezno-Tooth: https://pubmed.ncbi.nlm.nih.gov/28609785/ -> ENA -> protocol Meyer and Kircher. ref. 73, I listed "single stranded" but was confused about it
Punta_Candelero-Tooth: https://pubmed.ncbi.nlm.nih.gov/31710665/ -> ENA -> protocol Meyer and Kircher, fastq assumed for this sample
Sample age and library treatment from Hodgkins 2023 UNLESS info comes from "our records".
Our records simply copied everything from archive information to download sizes.

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 11 months ago

Sample age calculated considering 1950 as the present time

iseultj commented 11 months ago

Hi Diana, Thanks for doing this! I noticed a couple of things:

For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.

For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?

For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)

For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....

For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.

Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.

Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA Polymerase DNA	library_polymerase	2870	'HotStarTaq DNA Polymerase DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA	library_polymerase	2868	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2869	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2870	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2871	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2872	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2873	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2874	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2875	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2876	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2877	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2878	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2879	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2880	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2881	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_libraries.tsv

Error	Source	Column	Row	Message
Schema Validation Error	HotStarTaq DNA	library_polymerase	2868	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2869	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2870	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2871	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2872	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2873	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2874	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2875	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2876	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2877	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2878	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2879	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2880	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]
Schema Validation Error	HotStarTaq DNA	library_polymerase	2881	'HotStarTaq DNA' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/library_polymerase.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 11 months ago

Hi Diana, Thanks for doing this! I noticed a couple of things:

For Sanganji-A1-Tooth and Sanganji-A2-Tooth, it says the polymerase is unknown- I checked the Qiagen multiplex PCR handbook, and it looks like they use a HotStarTaq polymerase, but I'm not sure if that's what they actually used.

For Deir-Rifeh-KNIII-Tooth and Deir-Rifeh-KNII-Tooth - you put half-udg but I can't find any reference to it in the original paper?

For Tepos, I think the polymerases used were Accuprime (Taq) polymerase and then further amplification with Herculase II Fusion DNA Polymerase (agilent)

For the Chincha samples, it might be best to leave the polymerase as unknown? I wasn't able to figure it out either....

For Chiribaya_Alta-Bone and El_Yaral-Bone-in the supplement, it does state it's UDG treated, so I think ok to leave as is.

Finally, for Pueblo_Bonito-Tooth, in the main text it also says it was paired, so I don't know what's going on with the library layout.

Thanks for going through all of these and leaving the details for me, it made reviewing so much easier!

I have addressed all these points, so I think it's good to go now. Thankfully, this issue was much easier than anticipated due to coordinates being available and James's suggestion to indicate exactly where in original publications the info could be found! Thank you both for your help along the process and with reviewing!

DianaSpurite commented 9 months ago

I am also requesting a review from you @alexhbnr as you are at it at the moment. This is already revised and there are comments and changes made. If you have a moment, could you please have a look and merge this also?

DianaSpurite commented 9 months ago

the sample(s?) excluded from the table here are previously sequenced

alexhbnr commented 9 months ago

I will review it properly at the beginning of next week @DianaSpurite. I started reviewing it yesterday and realised that all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al. I have contacted @jfy133 about how we should handle the publication DOIs of the samples as the samples have been previously published (see Supp. Data Table 2). @jfy133 pointed me to check the previous publications that had the same issue, e.g. Bieker2020 and the Oetzi publication. I will do this next week.

DianaSpurite commented 9 months ago

all DOIs are pointing to the paper by Caruana et al. instead of Hodgkins et al.

yes, that sound like my mistake, I mixed up at the beginning of working with this publication.

Thank you for looking into this, let me know if I can help.

alexhbnr commented 9 months ago

Hi @DianaSpurite and @iseultj,

I went through your review and have a few questions/comments that I am not completely sure about:

For the samples Sanganji-A1-Tooth and Sanganji-A2-Tooth, you have listed that your polymerase that was used for the library amplification was HotStarTaq DNA (see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up with HotStarTaq DNA instead?
For the sample Tepos_35-Tooth, there is already an entry from the original publication, so I would suggest to copy the info from there.
All references to the protocol "Meyer and Kircher, 2010" should have the "Phusion Hot Start High-Fidelity DNA" polymerase, as this is the one listed in their protocol.
For the Dacaozi-Tooth sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".

If you could please check the first question, I would then approve the review and we can merge with the master branch.

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 9 months ago

For the samples Sanganji-A1-Tooth and Sanganji-A2-Tooth, you have listed that your polymerase that was used for the library amplification was HotStarTaq DNA (see also comment by @iseultj). What I found in the Suppl. Materials is a link to this study (https://doi.org/10.1126/science.1211177) and they stated that they use two rounds of PCR amplification, one time with AmpliTaq Gold and once with Phusion. So I am puzzled how you ended up with HotStarTaq DNA instead?

I had set it to 'Unknown' initially, exactly because they state two, and my competence level is rather low when it comes to the sequencing methods, so I corrected it according to the review.

For the sample Tepos_35-Tooth, there is already an entry from the original publication, so I would suggest to copy the info from there.

I will check and do so.

All references to the protocol "Meyer and Kircher, 2010" should have the "Phusion Hot Start High-Fidelity DNA" polymerase, as this is the one listed in their protocol.

Can you please confirm - does this mean for Deir-Rifeh; Cueva_de_los_Lagos and Punta_Candelero samples?

For the Dacaozi-Tooth sample, the two protocols that are listed were only used for the DNA extraction steps but not for the library preparation steps. From their description of the library protocol steps, it is not apparent, which protocol they used. I would therefore propose to set it to "Unknown".

Will fix this too

If you could please check the first question, I would then approve the review and we can merge with the master branch.

alexhbnr commented 9 months ago

@DianaSpurite for points 2 to 4, I should have already done this, so nothing to worry there at the moment. Thanks for clarifying question 1. I will wait for @iseultj's feedback and then go ahead.

Thanks @DianaSpurite for putting all the work in the first place. That was a beast of a publication to add to AMDir.

iseultj commented 9 months ago

Hi, the HotStart Taq was my mistake - I was looking at their SM where they include the following as modifications to the Rasmussen protocol: A first round PCR was set up with Multiplex PCR kit (Qiagen) as follows: 5 µl DNA library, 25 µl Mix, 20-100 nM each Multiplexing PCR primer, and H2O up to 50 µl... I looked at the multiplex PCR (qiagen) handbook to find it, but to be honest I wasn't clear whether they used the HotStart Taq or the enzymes used in the Rasmussen paper - maybe Unknown is the best way forward? Sorry for neglecting this PR, and thanks so much to both of you for both doing all the work and finishing it off!

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_samples.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_samples.tsv is valid

Libraries

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_libraries.tsv is valid

Ancient Single Genome Host Associated

ancientsinglegenome-hostassociated_libraries.tsv is valid

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid