Kjaer2022

[ktozdogan]

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): Kjaer et al.,2022 10.1038/s41586-022-05453-y

This is to close #1031

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)?
• [ ] Review requested from corresponding team (see list of lists above for each team)?
• [ ] (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:

If you do not know how to check errors in failed validation checks, expand here

Correction

This PR is for

• [ ] ancientmetagenome-hostassociated
• [ ] ancientsinglegenome-hostassociated
• [ ] ancientmetagenome-environmental

Reference

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

This is to close

Description

The issue is:

Checklist

• [ ] Checked the corrected entries follow conventions as described in the corresponding sample type's README file (e.g. using ERS/SRS accession codes for ENA/SRA)
• [ ] Changelog is updated to include the publication under 'Changed'?
• [ ] Pull request has passed validation checks (see automated comment from github-bot)?
• [ ] Review requested from corresponding team (see list of lists above for each team)?

[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 ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ Permafrost │ 513 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 522 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 498 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 489 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 495 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 512 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 515 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 525 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 489 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 514 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 492 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 534 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 537 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 523 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 520 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 527 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 492 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 521 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 510 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 496 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 533 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 504 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 497 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 532 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 518 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 493 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 491 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 538 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 502 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 499 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 490 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 486 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 507 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 508 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 517 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 524 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 536 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 487 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 516 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 511 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 519 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 490 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 535 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 488 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 503 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 500 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 501 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 528 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 529 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 487 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 531 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 491 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ None │ 488 │ feature │ 'None' is not an accepted value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/feature.json │ │ Permafrost │ 530 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 526 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 505 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 506 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 486 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 509 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 494 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.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 ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ Permafrost │ 518 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 498 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 495 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 511 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 506 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 513 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 494 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 519 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 528 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 499 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 522 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 516 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 520 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 497 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 530 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 490 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 532 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 533 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 534 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 514 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 529 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 517 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 538 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 512 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 504 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 486 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 500 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 503 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 501 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 536 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 491 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 515 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 508 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 507 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 526 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 492 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 489 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 510 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 493 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 496 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 487 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 509 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 521 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 525 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 535 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 488 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 523 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 537 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 502 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 527 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 524 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 505 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 531 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.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 ┃ ┡━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩ │ Permafrost │ 487 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 488 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.json │ │ Permafrost │ 486 │ material │ 'Permafrost' is not an accepted │ │ │ │ │ value. │ │ │ │ │ Please check │ │ │ │ │ https://spaam-community.github.io │ │ │ │ │ /AncientMetagenomeDir/assets/enum │ │ │ │ │ s/material.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 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 !

[jfy133]

Thanks @ktozdogan I will do this next Friday :)

[ktozdogan]

1. ✓

2. ✓

3. ✓

4. ✓

5. Information about depth was complicated: Loc -- m a.s.l -- depth acc. ts3.1.1 Loc 50 -- 127 -- none (which looks like -2, although it might make sense acc. Figure1?) Loc 119 -- 116 -- 8 Lok 69 -- 100-103 -- 18 Lok 75, 74a, 74b -- 83 -- none (which makes it around 50 (51 based on loc. 119), which can make sense acc. Figure 1?) Any suggestions?

6. Age: There is this sentence: "However, we discard the older scenario 3 as it contradicts the evidence for continuous sedimentation across Members A and B during a single glacial–interglacial depositional cycle. This leaves two possible scenarios (scenarios 1 and 2), in which scenario 1 supports an age of 1.9 Myr and scenario 2 supports an age of 2.1 Myr." And figure 2 shows members A & B together, and all the DNA data from member B, that's why I put 2 million for all as the average of 2.1 and 1.9. The dates may not be so precise. But I might be interpreting it weirdly. What do you think?

[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 !

[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 !

[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 !