Long2023

[DianaSpurite]

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): 10.1371/journal.ppat.1011538

This is to close #1103

Checklist

• [x] Publication is published (preprints currently not accepted)?
• [x] Checked the publication is not already in the database?
• [x] 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/1106

[github-actions[bot]]

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	kidney stone	material	607	'kidney stone' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.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	sample_name	2742	None is not of type 'string'
Schema Validation Error	AccuPrime Pfx DNA	library_polymerase	2742	'AccuPrime Pfx 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	None	sample_name	2743	None is not of type 'string'
Schema Validation Error	AccuPrime Pfx DNA	library_polymerase	2743	'AccuPrime Pfx 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	None	sample_name	2744	None is not of type 'string'
Schema Validation Error	AccuPrime Pfx DNA	library_polymerase	2744	'AccuPrime Pfx 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]]

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	kidney stone	material	607	'kidney stone' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.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	sample_name	2742	None is not of type 'string'
Schema Validation Error	None	sample_name	2743	None is not of type 'string'
Schema Validation Error	None	sample_name	2744	None is not of type 'string'

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

[github-actions[bot]]

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	kidney stone	material	607	'kidney stone' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.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]

checks should go through once the enum PR is checked and merged

[github-actions[bot]]

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	kidney stone	material	607	'kidney stone' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/material.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]]

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]]

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