Update ancientmetagenome-environmental_libraries.tsv

[jfy133]

Pull Request

This PR is for a

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

For the following list(s):

• [ ] 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

• [ ] Publication is published (preprints currently not accepted)?
• [ ] Checked the publication is not already in the database?
• [ ] Checked samples in this publication are not previously published data (newly re-sequenced metagenomes are OK!)?
• [ ] Samples are shotgun metagenomes (hostassociated-singlegenome may also contain whole-genome enriched data)?
• [ ] 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)?
• [ ] 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):

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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 ┏━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━┳━━━━━━━━━┳━━━━━━━━┓ ┃ ┃ Line ┃ ┃ ┃ ┃ Offending value ┃ number ┃ Column ┃ Error ┃ ┡━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━╇━━━━━━━━━╇━━━━━━━━┩ │ ERS14240319,ERS14240320 │ 519 │ archiv… │ 'ERS14 │ │ │ │ │ 240319 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240320 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ │ ERS14240309,ERS14240310,ERS14240311,ERS14240312 │ 516 │ archiv… │ 'ERS14 │ │ │ │ │ 240309 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240310 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240311 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240312 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ │ ERS14240306,ERS14240307,ERS14240308 │ 515 │ archiv… │ 'ERS14 │ │ │ │ │ 240306 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240307 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240308 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ │ ERS14240317,ERS14240318 │ 518 │ archiv… │ 'ERS14 │ │ │ │ │ 240317 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240318 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ │ ERS14240303,ERS14240304,ERS14240305 │ 514 │ archiv… │ 'ERS14 │ │ │ │ │ 240303 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240304 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240305 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ │ ERS14240313,ERS14240314,ERS14240315,ERS14240316 │ 517 │ archiv… │ 'ERS14 │ │ │ │ │ 240313 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240314 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240315 │ │ │ │ │ ,ERS14 │ │ │ │ │ 240316 │ │ │ │ │ ' │ │ │ │ │ does │ │ │ │ │ not │ │ │ │ │ match │ │ │ │ │ '^[\\S │ │ │ │ │ ]+$' │ └──────────────────────────────────────────────────┴────────┴─────────┴────────┘ 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 !

[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 !