White2021 #1084

DianaSpurite · 2023-06-19T07:05:59Z

Pull Request

This PR is for a

New Publication(s)
Correction

For the following list(s):

ancientmetagenome-environmental (README)
ancientmetagenome-hostassociated (README)
ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

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

This is to close #740

Checklist

Publication is published (preprints currently not accepted)?
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!)?
Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
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)?
Changelog is updated to include the publication under 'Added'?
Pull request has passed validation checks (see automated comment from github-bot)?
Review requested from @SPAAM-community/ancientmetagenomedir?
(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: Update singlegenome_species for White 2021.json #1086

adding White 2021 samples

adding White 2021 libraries

Added White 2021 samples

Adding White 2021 libraries. Certain entries missing (weren't in the ENA tables)

removed White 2021 samples from metagenome host associated

Removing White 2021 libraries from the metagenome hostassociated

github-actions · 2023-06-19T07:08:12Z

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	Treponema denticola	singlegenome_species	591	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	592	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	593	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	594	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	595	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	596	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	597	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	598	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	599	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	600	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	601	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	602	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Duplicated Row Error	(595, 600)	-	-	Rows (595, 600) are duplicated
Duplicated Row Error	(583, 588)	-	-	Rows (583, 588) are duplicated
Duplicated Row Error	(589, 594)	-	-	Rows (589, 594) are duplicated

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	AmpliTaq Gold	library_polymerase	2280	'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	None	download_sizes	2280	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2281	'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	None	download_sizes	2281	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2282	'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	None	download_sizes	2282	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2283	'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	None	download_sizes	2283	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2284	'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	None	download_sizes	2284	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2285	'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	None	download_sizes	2285	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2286	'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	None	download_sizes	2286	None is not of type 'string'
Schema Validation Error	AmpliTaq Gold	library_polymerase	2287	'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	None	download_sizes	2287	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-06-19T07:08:32Z

Added the White samples to singlegenome and removed from metagenome. There are several entries missing in the libraries which were not included in the ENA table

jfy133 · 2023-06-19T07:40:22Z

There are several entries missing in the libraries which were not included in the ENA table

What do you mean here? As in libraries in the paper but the data hasn't been uploaded?

Is this also why you have validation errors?

DianaSpurite · 2023-06-19T12:09:47Z

The ENA table didn't contain all the information, e.g., download sizes

errors for the samples are due to enums, some duplication and also library_polymerase is not entered correctly
working on it

github-actions · 2023-06-19T13:46:05Z

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	Treponema denticola	singlegenome_species	591	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	592	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	593	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	594	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	595	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	596	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	597	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	598	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	599	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	600	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	601	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	602	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Duplicated Row Error	(595, 600)	-	-	Rows (595, 600) are duplicated
Duplicated Row Error	(583, 588)	-	-	Rows (583, 588) are duplicated
Duplicated Row Error	(589, 594)	-	-	Rows (589, 594) are duplicated

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	None	download_sizes	2280	None is not of type 'string'
Schema Validation Error	None	download_sizes	2281	None is not of type 'string'
Schema Validation Error	None	download_sizes	2282	None is not of type 'string'
Schema Validation Error	None	download_sizes	2283	None is not of type 'string'
Schema Validation Error	None	download_sizes	2284	None is not of type 'string'
Schema Validation Error	None	download_sizes	2285	None is not of type 'string'
Schema Validation Error	None	download_sizes	2286	None is not of type 'string'
Schema Validation Error	None	download_sizes	2287	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2023-06-19T13:59:26Z

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	Treponema denticola	singlegenome_species	590	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	591	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	592	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	593	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	594	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	595	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	596	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	597	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	598	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	599	'Porphyromonas gingivalis' is not an accepted value.
				Please check [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	None	download_sizes	2280	None is not of type 'string'
Schema Validation Error	None	download_sizes	2281	None is not of type 'string'
Schema Validation Error	None	download_sizes	2282	None is not of type 'string'
Schema Validation Error	None	download_sizes	2283	None is not of type 'string'
Schema Validation Error	None	download_sizes	2284	None is not of type 'string'
Schema Validation Error	None	download_sizes	2285	None is not of type 'string'
Schema Validation Error	None	download_sizes	2286	None is not of type 'string'
Schema Validation Error	None	download_sizes	2287	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-06-19T14:02:14Z

Enums added, duplicates removed, spelling errors fixed.

library names, read count, md5s and download sizes not available in the tsv from ENA

added white 2021

github-actions · 2023-06-19T14:11:53Z

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	Treponema denticola	singlegenome_species	590	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	591	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	592	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	593	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Treponema denticola	singlegenome_species	594	'Treponema denticola' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	595	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	596	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	597	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	598	'Porphyromonas gingivalis' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Porphyromonas gingivalis	singlegenome_species	599	'Porphyromonas gingivalis' is not an accepted value.
				Please check [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	None	download_sizes	2280	None is not of type 'string'
Schema Validation Error	None	download_sizes	2281	None is not of type 'string'
Schema Validation Error	None	download_sizes	2282	None is not of type 'string'
Schema Validation Error	None	download_sizes	2283	None is not of type 'string'
Schema Validation Error	None	download_sizes	2284	None is not of type 'string'
Schema Validation Error	None	download_sizes	2285	None is not of type 'string'
Schema Validation Error	None	download_sizes	2286	None is not of type 'string'
Schema Validation Error	None	download_sizes	2287	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite · 2023-06-20T08:02:58Z

Correction for my previous comment - library names are available on the ENA table, but they are the same as the sample names. There was a procedure for this - I remember taking a part of one the links and using that as a library name, but I cannot recall which link and which part.

DianaSpurite · 2023-06-20T11:30:29Z

The download links I have added are not correct. The correct ones are not available at https://www.ebi.ac.uk/ena/browser/view/PRJEB49091

jfy133 · 2023-06-23T07:26:13Z

…Dir into White2021

github-actions · 2023-12-04T13:41:25Z

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	None	download_sizes	2868	None is not of type 'string'
Schema Validation Error	None	download_sizes	2869	None is not of type 'string'
Schema Validation Error	None	download_sizes	2870	None is not of type 'string'
Schema Validation Error	None	download_sizes	2871	None is not of type 'string'
Schema Validation Error	None	download_sizes	2872	None is not of type 'string'
Schema Validation Error	None	download_sizes	2873	None is not of type 'string'
Schema Validation Error	None	download_sizes	2874	None is not of type 'string'
Schema Validation Error	None	download_sizes	2875	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions · 2024-10-02T09:18:59Z

AMDirT, version 1.6.2

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

jfy133

Wow, thius took a while. Sorry about that!

One formatting change, and removed samples that had basically no genomic coverage (and thus not analysed further).

DianaSpurite and others added 11 commits November 8, 2022 13:23

Update CHANGELOG.md

5ce7626

Merge branch 'master' into White2021

ad33e23

Update check_dataset.yml

134fa4d

Update ancientmetagenome-hostassociated_samples.tsv

5d78535

adding White 2021 samples

Update ancientmetagenome-hostassociated_libraries.tsv

a82ef28

adding White 2021 libraries

Merge branch 'master' into White2021

0513105

Merge branch 'master' into White2021

f7a085f

Update ancientsinglegenome-hostassociated_samples.tsv

7af85cb

Added White 2021 samples

Update ancientsinglegenome-hostassociated_libraries.tsv

23d988b

Adding White 2021 libraries. Certain entries missing (weren't in the ENA tables)

Update ancientmetagenome-hostassociated_samples.tsv

78e5648

removed White 2021 samples from metagenome host associated

Update ancientmetagenome-hostassociated_libraries.tsv

8a6a534

Removing White 2021 libraries from the metagenome hostassociated

Update ancientsinglegenome-hostassociated_libraries.tsv

0965751

Update ancientsinglegenome-hostassociated_samples.tsv

9cb00b3

Update CHANGELOG.md

af136da

added white 2021

DianaSpurite requested a review from jfy133 June 22, 2023 09:45

DianaSpurite marked this pull request as draft June 23, 2023 07:25

jfy133 force-pushed the master branch 2 times, most recently from d2b8d05 to 5d105e9 Compare July 28, 2023 07:20

Merge branch 'master' of github.com:SPAAM-community/AncientMetagenome…

cf066ea

…Dir into White2021

jfy133 force-pushed the master branch 9 times, most recently from 223e767 to c16a3da Compare March 21, 2024 16:32

jfy133 force-pushed the master branch from 418ed01 to e87c37d Compare March 25, 2024 08:34

alexhbnr added 3 commits September 25, 2024 11:09

Merge branch 'master' into White2021

54d5411

Update library info after new upload of seq data to ENA

1ee1060

Update CHANGELOG.md

7b3fe00

jfy133 marked this pull request as ready for review September 25, 2024 10:36

alexhbnr and others added 5 commits September 25, 2024 13:36

Merge branch 'master' into White2021

49225bf

Fix CHANGELOG

541dce4

Merge branch 'master' into White2021

f41bfab

Fix Lat:Lon precision and remove non-genome samples

12d570d

Remove low-coverage genomes

4ea1d15

jfy133 approved these changes Oct 2, 2024

View reviewed changes

jfy133 merged commit 705bc8e into master Oct 2, 2024
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jfy133 deleted the White2021 branch October 2, 2024 09:19

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White2021 #1084

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White2021 #1084

White2021 #1084

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DianaSpurite commented Jun 19, 2023 • edited Loading

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github-actions bot commented Jun 19, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Jun 19, 2023

jfy133 commented Jun 19, 2023 • edited Loading

DianaSpurite commented Jun 19, 2023

github-actions bot commented Jun 19, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

github-actions bot commented Jun 19, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Jun 19, 2023

github-actions bot commented Jun 19, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

DianaSpurite commented Jun 20, 2023

DianaSpurite commented Jun 20, 2023

jfy133 commented Jun 23, 2023

github-actions bot commented Dec 4, 2023

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

github-actions bot commented Oct 2, 2024

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

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DianaSpurite commented Jun 19, 2023 •

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