Closed DianaSpurite closed 9 months ago
AMDirT, version 1.4.6
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 |
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
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 |
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
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 |
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
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
AMDirT, version 1.4.6
Invalid dataset ancientmetagenome-hostassociated_samples.tsv
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
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
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
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.
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.
Thanks @DianaSpurite, I will check that.
You are right @DianaSpurite , these samples were only sampled in 1993 and 2012. I guess we can discard these two samples. Any objections @jfy133 ?
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.
AMDirT, version 1.4.6
ancientmetagenome-hostassociated_samples.tsv
is valid
ancientsinglegenome-hostassociated_samples.tsv
is valid
ancientmetagenome-environmental_samples.tsv
is valid
ancientmetagenome-hostassociated_libraries.tsv
is valid
ancientsinglegenome-hostassociated_libraries.tsv
is valid
ancientmetagenome-environmental_libraries.tsv
is valid
Adding Maddison2023 samples
Pull Request
This PR is for a
For the following list(s):
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
github-bot
)?@SPAAM-community/ancientmetagenomedir
?/assets/enums
, e.g. material or archive)? If so the corresponding PR is here: https://github.com/SPAAM-community/AncientMetagenomeDir/pull/1121