DianaSpurite commented 11 months ago

Adding Maddison2023 samples

Pull Request

This PR is for a

[x] New Publication(s)
[ ] Correction

For the following list(s):

[ ] ancientmetagenome-environmental (README)
[x] ancientmetagenome-hostassociated (README)
[ ] ancientsinglegenome-hostassociated (README)

New Publication

Publication Information

This pull request is to add samples from the following publication(s): 10.1371/journal.pone.0291540

This is to close #1116

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'?
[x] Pull request has passed validation checks (see automated comment from github-bot)?
[x] Review requested from @SPAAM-community/ancientmetagenomedir?
[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: https://github.com/SPAAM-community/AncientMetagenomeDir/pull/1121

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Dataset Parsing Error	ancientmetagenome-hostassociated_samples.tsv	-	-	Error tokenizing data. C error: Expected 16 fields in line 1403, saw 17

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

DianaSpurite commented 11 months ago

As I understood the library protocol the authors used is this: https://www.neb.com/en/-/media/nebus/files/manuals/manuale7103-e7645.pdf?rev=de09eaf8fcdf45e0ac8a66bf6fee75fb&hash=FC51B96E7568B4482CF1B5217EF04E31

I didn't find anything familiar to library polymerase there

github-actions[bot] commented 11 months ago

AMDirT, version 1.4.6

Samples

Ancient Metagenome Host Associated

Invalid dataset ancientmetagenome-hostassociated_samples.tsv

Error	Source	Column	Row	Message
Schema Validation Error	Lithobates pipiens	sample_host	1403	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1404	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1405	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1406	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1407	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1408	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1409	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1410	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1411	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1412	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]
Schema Validation Error	Lithobates pipiens	sample_host	1413	'Lithobates pipiens' is not an accepted value.
				Please check [link=https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json]https://spaam-community.github.io/AncientMetagenomeDir/assets/enums/sample_host.json[/link]

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

DianaSpurite commented 11 months ago

Quick comment

the host species are updated to a newer genus, so Lithobates pipiens instead of Rana pipiens :https://github.com/SPAAM-community/AncientMetagenomeDir/pull/1121
validation checks should pass then, once that PR is merged into master

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

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

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

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

alexhbnr commented 9 months ago

Hi @jfy133, I have reviewed the PR and made some changes to it. Mainly, I have added two samples that were previously missing for a reason I am not aware. So maybe you just briefly check whether these changes look correct to you and then I merge the PR into the master branch.

DianaSpurite commented 9 months ago

I have added two samples that were previously missing for a reason I am not aware.

I think those were very modern samples, if I'm not wrong.

alexhbnr commented 9 months ago

Thanks @DianaSpurite, I will check that.

alexhbnr commented 9 months ago

You are right @DianaSpurite , these samples were only sampled in 1993 and 2012. I guess we can discard these two samples. Any objections @jfy133 ?

jfy133 commented 9 months ago

No, that's how we've done it for young samples in other publications, so discarding is fine.

The only exception is the environmental samples when you have distinct/defined sequence.

github-actions[bot] commented 9 months ago

AMDirT, version 1.4.6

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

SPAAM-community / AncientMetagenomeDir

Madison2023 #1123

Pull Request

New Publication

Publication Information

Checklist

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

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

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

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

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

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

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