Add Perez2022

[Darcy220606]

Pull Request

This PR is for a

• [x] New Publication(s)
• [ ] Correction

For the following list(s):

• [x] ancientmetagenome-environmental (README, ask @thedir-team-dirt for advice)
• [ ] ancientmetagenome-hostassociated (README, ask @thedir-team-bugparty for advice)
• [ ] ancientsinglegenome-hostassociated (README, ask @thedir-team-pathopeeps for advice)

New Publication

Publication Information

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

This is to close

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'?
• [ ] Pull request has passed validation checks (see automated comment from github-bot)?
• [x] Review requested from corresponding team (see list of lists above for each team)?
• [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:

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ hydrothermal system │ 477 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 488 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 482 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 472 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 475 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 479 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 486 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 481 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 483 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 478 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 487 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 476 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 485 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 489 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 484 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 474 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 480 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 471 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 470 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 473 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ └─────────────────────┴─────────────┴─────────┴────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ wetland │ 488 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 484 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 486 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 472 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 477 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 480 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 476 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 478 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 470 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 482 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 473 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 471 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 481 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 485 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 474 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 487 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 489 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 483 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 479 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 475 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ └─────────────────────┴─────────────┴─────────┴────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[Darcy220606]

To @SPAAM-community/thedir-team-dirt. The authors mention two extreme sites: hydrothermal system and wetlands and no other information besides they are terrestrial samples. So i added those two features in the enum features as the other current options are too specific.

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ wetland │ 485 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 482 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 470 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 486 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 475 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 473 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 488 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 489 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 484 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 477 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 480 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 472 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 474 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 479 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 481 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 471 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 487 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 483 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 476 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 478 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ └─────────────────────┴─────────────┴─────────┴────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[jfy133]

To @SPAAM-community/thedir-team-dirt. The authors mention two extreme sites: hydrothermal system and wetlands and no other information besides they are terrestrial samples. So i added those two features in the enum features as the other current options are too specific.

Ok, sounds good to me - however you need to do this as a separate PR into master!

(sorry for the delay getting back to you on this @Darcy220606!)

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ hydrothermal system │ 483 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 476 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 473 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 471 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 488 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 487 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 481 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 484 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 480 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 474 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 477 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 482 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 470 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 475 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 486 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 485 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 478 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ wetland │ 489 │ feature │ 'wetland' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 472 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ │ hydrothermal system │ 479 │ feature │ 'hydrothermal system' is not │ │ │ │ │ an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github │ │ │ │ │ .io/AncientMetagenomeDir/asset │ │ │ │ │ s/enums/feature.json │ └─────────────────────┴─────────────┴─────────┴────────────────────────────────┘ The following type of errors were found: • DatasetValidationError ```

[Darcy220606]

To @SPAAM-community/thedir-team-dirt. The authors mention two extreme sites: hydrothermal system and wetlands and no other information besides they are terrestrial samples. So i added those two features in the enum features as the other current options are too specific.

Ok, sounds good to me - however you need to do this as a separate PR into master!

(sorry for the delay getting back to you on this @Darcy220606!)

Thanks @jfy133 . I made a new PR #1033 to add it.

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json

Errors were found, please unfold below to see errors:

``` Validation Errors were found ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━┓ ┃ Offending value ┃ Line number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━┩ │ -19854.0 │ 484 │ latitude │ -19854.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -90 │ │ -68888.0 │ 485 │ longitude │ -68888.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -180 │ │ -68888.0 │ 484 │ longitude │ -68888.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -180 │ │ microbial,floral,microbial │ 482 │ study_primary_… │ 'microbial,flor │ │ │ │ │ al,microbial' │ │ │ │ │ is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-c │ │ │ │ │ ommunity.github │ │ │ │ │ .io/AncientMeta │ │ │ │ │ genomeDir/asset │ │ │ │ │ s/enums/study_p │ │ │ │ │ rimary_focus.js │ │ │ │ │ on │ │ microbial,floral,microbial │ 485 │ study_primary_… │ 'microbial,flor │ │ │ │ │ al,microbial' │ │ │ │ │ is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-c │ │ │ │ │ ommunity.github │ │ │ │ │ .io/AncientMeta │ │ │ │ │ genomeDir/asset │ │ │ │ │ s/enums/study_p │ │ │ │ │ rimary_focus.js │ │ │ │ │ on │ │ microbial,floral,microbial │ 484 │ study_primary_… │ 'microbial,flor │ │ │ │ │ al,microbial' │ │ │ │ │ is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-c │ │ │ │ │ ommunity.github │ │ │ │ │ .io/AncientMeta │ │ │ │ │ genomeDir/asset │ │ │ │ │ s/enums/study_p │ │ │ │ │ rimary_focus.js │ │ │ │ │ on │ │ -68906.0 │ 482 │ longitude │ -68906.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -180 │ │ microbial,floral,microbial │ 483 │ study_primary_… │ 'microbial,flor │ │ │ │ │ al,microbial' │ │ │ │ │ is not an │ │ │ │ │ accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-c │ │ │ │ │ ommunity.github │ │ │ │ │ .io/AncientMeta │ │ │ │ │ genomeDir/asset │ │ │ │ │ s/enums/study_p │ │ │ │ │ rimary_focus.js │ │ │ │ │ on │ │ -68906.0 │ 483 │ longitude │ -68906.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -180 │ │ -19851.0 │ 483 │ latitude │ -19851.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -90 │ │ -20287.0 │ 485 │ latitude │ -20287.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -90 │ │ -19851.0 │ 482 │ latitude │ -19851.0 is │ │ │ │ │ less than the │ │ │ │ │ minimum of -90 │ └────────────────────────────┴─────────────┴─────────────────┴─────────────────┘ The following type of errors were found: • DatasetValidationError ```

[github-actions[bot]]

ancientMetagenomeDirCheck, version 1.3

Ancient Metagenome Host Associated Samples

Checking ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s.tsv against schema ancientmetagenome-hostassociated/samples/ancientmetagenome-hostassociated_sample s_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Samples

Checking ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples.tsv against schema ancientsinglegenome-hostassociated/samples/ancientsinglegenome-hostassociated_sa mples_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Samples

Checking ancientmetagenome-environmental/samples/ancientmetagenome-environmental_samples. tsv against schema ancientmetagenome-environmental/samples/ancientmetagenome-environmentalsamples schema.json All is good, no errors were found !

Ancient Metagenome Host Associated Libraries

Checking ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries.tsv against schema ancientmetagenome-hostassociated/libraries/ancientmetagenome-hostassociated_libr aries_schema.json All is good, no errors were found !

Ancient Single Genome Host Associated Libraries

Checking ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries.tsv against schema ancientsinglegenome-hostassociated/libraries/ancientsinglegenome-hostassociated libraries_schema.json All is good, no errors were found !

Ancient Metagenome Environmental Libraries

Checking ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies.tsv against schema ancientmetagenome-environmental/libraries/ancientmetagenome-environmental_librar ies_schema.json All is good, no errors were found !