C14-Guinet_2025 by ZoePochon · Pull Request #1719 · SPAAM-community/AncientMetagenomeDir

ZoePochon · 2026-02-06T16:27:08Z

Pull Request

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 #1666

PR Workflow

Open this PR with sample metadata on the samples metadata sheet (:tada: you're already here!)
Wait for checks for sample metdata to pass
(If checks fail) make corrections, and push changes to this branch (no need to open a new PR!)
(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)
Fill in the template, and verify autofilled data correct!
Once filled in, append(!) the new rows from the TEMPLATE file to the end of the corresponding library metadata file, and update this PR
Wait for checks for library metadata to pass
Only for ancientsinglegenome-hostassociated: fill the dates table
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
For ancientsinglegenome-hostassociated: fill the dates table!
Changelog is updated to include the publication under 'Added'?

github-actions · 2026-02-06T16:31:49Z

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

ancientsinglegenome-hostassociated_dates.tsv is valid

ZoePochon · 2026-02-06T16:32:09Z

There are some samples that were dated according to molecular clock but I did not add them since there was no column category for it.

However, I think we should consider adding a column for molecular clock dating values.

KaHea-21 · 2026-02-27T13:45:59Z

 Sabin2020	2020	10.1098/rstb.2019.0576	MAM001	Homo sapiens	PRJNA640385	SRS7054140	TRUE	FALSE	594	DNE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	unknown	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	M13	Mammuthus primigenius	PRJEB78615	ERS21099302	TRUE	TRUE	11700-0	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	Ua	13370	NR	NR	NR	tooth	7910	80	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	L389	Mammuthus primigenius	PRJEB78615	ERS21099221	TRUE	TRUE	11700-0	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	Ua	13364	NR	NR	NR	tooth	4335	60	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK012	Mammuthus primigenius	PRJEB78615	ERS21099451	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA


Suggested change

Guinet2025 2025 10.1016/j.cell.2025.08.003 FK012 Mammuthus primigenius PRJEB78615 ERS21099451 TRUE TRUE 129000-11700 FALSE supplement table 1 10.1016/j.cell.2025.08.003 FALSE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

Guinet2025 2025 10.1016/j.cell.2025.08.003 FK012 Mammuthus primigenius PRJEB78615 ERS21099451 TRUE FALSE 129000-11700 DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

KaHea-21 · 2026-02-27T13:47:28Z

+Guinet2025	2025	10.1016/j.cell.2025.08.003	M13	Mammuthus primigenius	PRJEB78615	ERS21099302	TRUE	TRUE	11700-0	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	Ua	13370	NR	NR	NR	tooth	7910	80	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	L389	Mammuthus primigenius	PRJEB78615	ERS21099221	TRUE	TRUE	11700-0	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	Ua	13364	NR	NR	NR	tooth	4335	60	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK012	Mammuthus primigenius	PRJEB78615	ERS21099451	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK033	Mammuthus primigenius	PRJEB78615	ERS21099082	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA


Suggested change

Guinet2025 2025 10.1016/j.cell.2025.08.003 FK033 Mammuthus primigenius PRJEB78615 ERS21099082 TRUE TRUE 129000-11700 FALSE supplement table 1 10.1016/j.cell.2025.08.003 FALSE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

Guinet2025 2025 10.1016/j.cell.2025.08.003 FK033 Mammuthus primigenius PRJEB78615 ERS21099082 TRUE FALSE 129000-11700 DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

KaHea-21 · 2026-02-27T13:48:00Z

+Guinet2025	2025	10.1016/j.cell.2025.08.003	L389	Mammuthus primigenius	PRJEB78615	ERS21099221	TRUE	TRUE	11700-0	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	Ua	13364	NR	NR	NR	tooth	4335	60	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK012	Mammuthus primigenius	PRJEB78615	ERS21099451	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK033	Mammuthus primigenius	PRJEB78615	ERS21099082	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	MD228	Mammuthus primigenius	PRJEB78615	ERS21099095	TRUE	TRUE	774100–129000	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA


Suggested change

Guinet2025 2025 10.1016/j.cell.2025.08.003 MD228 Mammuthus primigenius PRJEB78615 ERS21099095 TRUE TRUE 774100–129000 FALSE supplement table 1 10.1016/j.cell.2025.08.003 FALSE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

Guinet2025 2025 10.1016/j.cell.2025.08.003 MD228 Mammuthus primigenius PRJEB78615 ERS21099095 TRUE FALSE 774100–129000 DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

KaHea-21 · 2026-02-27T13:48:35Z

+Guinet2025	2025	10.1016/j.cell.2025.08.003	FK001	Mammuthus primigenius	PRJEB78615	ERS21099439	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	NR	NR	NR	NR	NR	bone	33800	250	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	MD024	Mammuthus primigenius	PRJEB78615	ERS21099141	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	TRUE	NR	OxA	38760	NR	NR	NR	bone	17627	77	-99999	-99999	-99999	-99999	FALSE	NR	NR	NR	NR	NR	-99999	-99999	-99999	-99999	-99999	FALSE	DNE	DNE	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	MD213	Mammuthus primigenius	PRJEB78615	ERS21099090	TRUE	TRUE	129000-11700	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA
+Guinet2025	2025	10.1016/j.cell.2025.08.003	P033	Mammuthus sp.	PRJEB78615	ERS21099510,ERS21099509	TRUE	TRUE	1200000-800000	FALSE	supplement table	1	10.1016/j.cell.2025.08.003	FALSE	DNE	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	NA	NA	NA	DNE	DNE	DNE	DNE	DNE	DNE	NA	NA	NA	DNE	NA	DNE	DNE	NA	NA	NA	NA	NA


Suggested change

Guinet2025 2025 10.1016/j.cell.2025.08.003 P033 Mammuthus sp. PRJEB78615 ERS21099510,ERS21099509 TRUE TRUE 1200000-800000 FALSE supplement table 1 10.1016/j.cell.2025.08.003 FALSE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

Guinet2025 2025 10.1016/j.cell.2025.08.003 P033 Mammuthus sp. PRJEB78615 ERS21099510,ERS21099509 TRUE FALSE 1200000-800000 DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

Update ancientmetagenome-hostassociated_dates.tsv

7629bc3

ZoePochon changed the title ~~Update ancientmetagenome-hostassociated_dates.tsv~~ C14-Guinet_2025 Feb 6, 2026

Merge branch 'master' into Guinet_2025

a00c757

ZoePochon requested a review from aidaanva February 6, 2026 16:32

KaHea-21 self-requested a review February 27, 2026 13:43

KaHea-21 reviewed Feb 27, 2026

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KaHea-21 requested changes Feb 27, 2026

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ZoePochon added the Ready for Review label Mar 27, 2026

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C14-Guinet_2025#1719

C14-Guinet_2025#1719
ZoePochon wants to merge 2 commits intomasterfrom
Guinet_2025

ZoePochon commented Feb 6, 2026

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github-actions Bot commented Feb 6, 2026

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ZoePochon commented Feb 6, 2026

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	Guinet2025 2025 10.1016/j.cell.2025.08.003 FK012 Mammuthus primigenius PRJEB78615 ERS21099451 TRUE TRUE 129000-11700 FALSE supplement table 1 10.1016/j.cell.2025.08.003 FALSE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA
	Guinet2025 2025 10.1016/j.cell.2025.08.003 FK012 Mammuthus primigenius PRJEB78615 ERS21099451 TRUE FALSE 129000-11700 DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE DNE NA NA NA NA NA NA DNE DNE DNE DNE DNE DNE NA NA NA DNE NA DNE DNE NA NA NA NA NA

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ZoePochon commented Feb 6, 2026

Pull Request

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Pre-review checklist (new publications)

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github-actions Bot commented Feb 6, 2026

Samples

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Libraries

Ancient Metagenome Host Associated

Ancient Single Genome Host Associated

Ancient Metagenome Environmental

Dates

Ancient Single Genome Host Associated

Uh oh!

ZoePochon commented Feb 6, 2026

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