SPAAM-community / AncientMetagenomeDir

Repository containing lists of all published ancient metagenomic (and related) samples and libraries
http://www.spaam-community.org/AncientMetagenomeDir/
Creative Commons Attribution 4.0 International
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Add Zimmermann2023 #1091

Closed ktozdogan closed 1 year ago

ktozdogan commented 1 year ago

Pull Request

This PR is for a

For the following list(s):

New Publication

Publication Information

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

This is to close #1066

Checklist

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

Invalid dataset ancientmetagenome-environmental_samples.tsv

Error Source Column Row Message
Schema Validation Error Bering Sea geo_loc_name 559 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 559 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 560 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 560 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 561 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 561 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 562 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 562 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 563 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 563 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 564 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 564 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 565 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 565 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 566 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 566 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 567 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 567 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 568 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 568 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 569 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 569 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 570 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 570 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 571 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 571 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 572 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 572 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 573 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 573 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 574 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 574 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 575 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 575 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 576 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 576 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 577 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 577 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 578 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 578 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 579 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 579 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 580 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 580 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 581 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 581 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 582 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 582 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]
Schema Validation Error Bering Sea geo_loc_name 583 'Bering Sea' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/geo_loc_name.json[/link]
Schema Validation Error marine sediment feature 583 'marine sediment' is not an accepted value.
Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/feature.json[/link]

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

Invalid dataset ancientmetagenome-environmental_libraries.tsv

Error Source Column Row Message
Dataset Parsing Error ancientmetagenome-environmental_libraries.tsv - - Unable to parse string "none" at position 649
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

Invalid dataset ancientmetagenome-environmental_libraries.tsv

Error Source Column Row Message
Dataset Parsing Error ancientmetagenome-environmental_libraries.tsv - - Unable to parse string "none" at position 649
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

jfy133 commented 1 year ago

For libraries: ERR6430824 , ERR6430839, ERR6430845, ERR6430848, are missing There is a ERR6430835 which is not in the ENA table (and with random number of reads And there is ERR6430852 and ERR6430853 in your table and not in the ENA table of samples (the ID in the table has a sample ID that indicates they are blanks).

I have a feeling you've maybe had a freordering and iltering problem?

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

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

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

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

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

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