DianaSpurite commented 1 year ago

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): doi.org/10.1038%2Fs41467-023-39950-z

This is to close #1099

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/1112

github-actions[bot] commented 1 year 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	Citrus aurantiifolia	sample_host	608	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	608	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	609	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	609	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	610	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	610	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	611	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	611	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	612	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	612	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	613	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	613	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	614	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	614	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	615	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	616	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	616	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	617	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	618	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	618	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	619	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [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	sample_name	2744	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2744	'unknown' 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	NextSeq500	instrument_model	2744	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2745	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2745	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2746	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2746	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2747	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2747	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2748	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2748	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2749	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2749	'unknown' 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	NextSeq500	instrument_model	2749	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2750	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2750	'unknown' 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	NextSeq500	instrument_model	2750	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2751	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2751	'unknown' 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	NextSeq500	instrument_model	2751	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2752	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2752	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2753	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2753	'unknown' 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	NextSeq500	instrument_model	2753	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2754	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2754	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2755	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2755	'unknown' 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	NextSeq500	instrument_model	2755	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 1 year ago

Github is being a little difficult for me atm, will correct the errors when it responds better

github-actions[bot] commented 1 year 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	Citrus aurantiifolia	sample_host	608	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	608	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	609	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	609	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	610	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	610	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	611	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	611	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	612	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	612	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	613	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	613	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	614	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	614	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	615	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	616	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	616	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	617	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	618	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	618	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	619	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [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	sample_name	2744	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2744	'unknown' 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	NextSeq500	instrument_model	2744	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2745	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2745	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2746	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2746	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2747	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2747	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2748	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2748	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2749	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2749	'unknown' 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	NextSeq500	instrument_model	2749	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2750	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2750	'unknown' 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	NextSeq500	instrument_model	2750	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2751	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2751	'unknown' 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	NextSeq500	instrument_model	2751	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2752	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2752	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2753	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2753	'unknown' 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	NextSeq500	instrument_model	2753	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2754	None is not of type 'string'
Schema Validation Error	NextSeq500	instrument_model	2754	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]
Schema Validation Error	None	sample_name	2755	None is not of type 'string'
Schema Validation Error	unknown	library_polymerase	2755	'unknown' 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	NextSeq500	instrument_model	2755	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

github-actions[bot] commented 1 year 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	Citrus aurantiifolia	sample_host	608	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	608	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	609	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	609	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	610	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	610	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	611	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	611	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	612	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	612	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	613	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	613	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	614	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	614	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	615	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	616	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	616	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	617	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	618	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	618	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	619	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [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	NextSeq500	instrument_model	2744	'NextSeq500' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/instrument_model.json[/link]

Ancient Metagenome Environmental

ancientmetagenome-environmental_libraries.tsv is valid

DianaSpurite commented 1 year ago

Couple of notes

As discussed coordinates rough as for some sample collections only country was listed
Six samples sequenced according to BEST protocol, for those, I think, I got the library_polymerase; for other six samples TrueSeqNano protocol in which I couldn't find anything about library amplification. Looked at other papers, but also didn't find anything specific - only comparison to the BEST protocol. But since it was an unrelated paper I didn't date to state the same polymerase.
Separate library names not listed, I cannot recall what we did in such case when the library names match sample names 1:1
Lastly - there was a mention of library treatment, but I understood that the context is related to the two different types of protocols and NOT the udg treatment. I could be wrong.

github-actions[bot] commented 1 year 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	Citrus aurantiifolia	sample_host	608	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	608	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	609	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	609	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	610	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	610	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	611	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	611	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	612	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	612	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	613	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	613	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus aurantiifolia	sample_host	614	'Citrus aurantiifolia' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	614	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	615	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	616	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	616	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	617	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Citrus medica	sample_host	618	'Citrus medica' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	618	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/singlegenome_species.json[/link]
Schema Validation Error	Xanthomonas citri pv. citri	singlegenome_species	619	'Xanthomonas citri pv. citri' is not an accepted value.
				Please check [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 1 year 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 1 year ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

ancientmetagenome-hostassociated_samples.tsv is valid

Ancient Single Genome Host Associated

Traceback (most recent call last): File "/opt/hostedtoolcache/Python/3.9.18/x64/bin/AMDirT", line 8, in sys.exit(cli()) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/core.py", line 1157, in call return self.main(args, kwargs) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/core.py", line 1078, in main rv = self.invoke(ctx) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/core.py", line 1688, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/core.py", line 1434, in invoke return ctx.invoke(self.callback, ctx.params) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/core.py", line 783, in invoke return __callback(args, *kwargs) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/click/decorators.py", line 33, in new_func return f(get_current_context(), args, kwargs) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/AMDirT/cli.py", line 78, in validate run_validation(kwargs, **ctx.obj) File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/AMDirT/validate/init.py", line 27, in run_validation v.check_duplicate_dois() File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/AMDirT/validate/application/init.py", line 16, in check_duplicate_dois project_dois = self.dataset.groupby("project_name")[ File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pandas/core/frame.py", line 8872, in groupby return DataFrameGroupBy( File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pandas/core/groupby/groupby.py", line 1274, in init grouper, exclusions, obj = get_grouper( File "/opt/hostedtoolcache/Python/3.9.18/x64/lib/python3.9/site-packages/pandas/core/groupby/grouper.py", line 1009, in get_grouper raise KeyError(gpr) KeyError: 'project_name'

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 commented 1 year ago

Refined some Lat:Lon, Dates, and Polymerase

github-actions[bot] commented 1 year 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

SPAAM-community / AncientMetagenomeDir

Campos2023 #1113

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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

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

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

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

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

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

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