C14Bos2014

[KaHea-21]

Pull Request

To update issue #1222

C14 data needs reviewing and entered into missing fields

This PR is for a

• New Publication(s)
• Correction

For the following list(s):

• ancientmetagenome-environmental (README)
• ancientmetagenome-hostassociated (README)
• ancientsinglegenome-hostassociated (README)

This is to close

PR Workflow

1. Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
2. Wait for checks for sample metdata to pass
3. (If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
4. (Once passed) comment on this PR @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! (may take a minute or so to get the comment with the file)
5. Fill in the template, and verify autofilled data correct!
6. Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
7. Wait for checks for library metadata to pass
8. Request review!

Pre-review checklist (new publications)

• 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 and not amplicon data
  • Note: 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)?
• Once sample table validation completed Library metadata has been added
  • Use @spaam-bot please autofill <table_name> <project_id> to get a half-filled template! May take a minute or so to get the comment with the file
  • Fill in template, and verify autofill data correct!
  • Once filled in, append(!) the new rows to the end of the corresponding library metadata file
• Changelog is updated to include the publication under 'Added'?

[github-actions]

amdirt, version 1.6.5

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

Dates

Ancient Single Genome Host Associated

Invalid dataset ancientsinglegenome-hostassociated_dates.tsv

Error	Source	Column	Row	Message
Schema Validation Error	ShCal13	calibration_curve	27	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	CALIB	calibration_software	27	'CALIB' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json[/link]
Schema Validation Error	ShCal13	calibration_curve	28	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	ShCal13	calibration_curve	29	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	ShCal13	calibration_curve	30	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	CALIB	calibration_software	30	'CALIB' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json[/link]
Schema Validation Error	ShCal13	calibration_curve	31	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	CALIB	calibration_software	31	'CALIB' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_software.json[/link]
Schema Validation Error	ShCal13	calibration_curve	32	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]
Schema Validation Error	ShCal13	calibration_curve	33	'ShCal13' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/c14_calibration_curve.json[/link]

[aidaanva]

@yaxalponce Please change the field of multiple dates to false, since the elements were only dated once. Leave only the calibrated dates with OxCal since they are the ones that were used for subsequent analysis. Once the changes has been done request my rereview.