Multiple samples per library cause issue with AMDirT viewer

[ZoePochon]

Hi there!
I selected all the ancient leprosy samples and downloaded the different tables and I noticed that Neukamm2020 was absent. I went back to AMDirT viewer and when you click on "Neukamm2020" (for the leprosy hit at least but maybe for the other one too) and click on the validate selection button, nothing happens. This might be a bug in AncientMetagenomeDir rather than AMDirT, I'm not sure.

[jfy133]

Hm interesting... how did you load the viewer? Via CLI or the online version?

[ZoePochon]

Via the command line.

[jfy133]

I can replicate, but there is nothing in the console... not sure what's happening

[jfy133]

@maxibor (ignore previous now-deleted ping), do you know how we could debug this? Both the DOI and PRJ files resolve on the respective websites... (the only thing I could imagine being an issue)

[maxibor]

@jfy133 @ZoePochon I can't replicate, all is fine with me.
Maybe it was a temporary ENA api disruption ?

[jfy133]

@maxibor and I just tested again and he was looking at the wrong table, investigating gain

[maxibor]

Ok, finally poinpointed the true source of the issue.
Turns out that some libraries were uploaded to ENA in a very unorthodox way: normally, there should be only one sample accession id (ERS...) per library (and multiple libraries per sample).
We'll have to think about how to handle this, as it is not respecting the ENA data model.

Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1630	ENA	PRJEB33848	ERS3635976,ERS3636087,ERS3636088,ERS3636089	Abusir1630b	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 2500	PAIRED	WGS	1675402	ERR4374948	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/008/ERR4374948/ERR4374948_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/008/ERR4374948/ERR4374948_2.fastq.gz	926be06d766f617d530dd86c2c923a98;ef3b1912569503c4bec4393c467af101	107051806;105518845
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1630	ENA	PRJEB33848	ERS3635976,ERS3636087,ERS3636088,ERS3636089	Abusir1630UDG1	double	Phusion Hot Start High-Fidelity DNA	full-udg	Illumina HiSeq 4000	SINGLE	WGS	22570691	ERR4375144	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/004/ERR4375144/ERR4375144.fastq.gz	bc31466e2ba83f27902b3e517bf739b3	785130427
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1630	ENA	PRJEB33848	ERS3635976,ERS3636087,ERS3636088,ERS3636089	Abusir1630UDG2	double	Phusion Hot Start High-Fidelity DNA	full-udg	Illumina HiSeq 4000	SINGLE	WGS	27168496	ERR4383828	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/008/ERR4383828/ERR4383828.fastq.gz	41ea60645b38e218d841674673dbfb47	962482754
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1630	ENA	PRJEB33848	ERS3635976,ERS3636087,ERS3636088,ERS3636089	Abusir1630UDG3	double	Phusion Hot Start High-Fidelity DNA	full-udg	Illumina HiSeq 4000	SINGLE	WGS	25875319	ERR4383829	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/009/ERR4383829/ERR4383829.fastq.gz	cabe84183a942517ed31bd06f815d7f0	917944806
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 2500	PAIRED	WGS	2920994	ERR4374011	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/001/ERR4374011/ERR4374011_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/001/ERR4374011/ERR4374011_2.fastq.gz	e7ec3c7fb29e40d16710081d2feb8994;933b05c122f2c4899b7a0a470d7533fb	223979315;224820846
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s_deeper_sequencing_1	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	7498748	ERR4386594	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/004/ERR4386594/ERR4386594_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/004/ERR4386594/ERR4386594_2.fastq.gz	4c1532173ff5167f5f11722a51266c7e;882cf017a4d2ecba66596d28f5b098a8	470376358;513240544
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s_deeper_sequencing_3	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	2094918	ERR4388102	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/002/ERR4388102/ERR4388102_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/002/ERR4388102/ERR4388102_2.fastq.gz	b3a7f685a18bcc3e7ab40d0511400adc;7bb00d39f98a28f5a3fb619426a3696f	74381752;81080489
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s_deeper_sequencing_4	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	2043769	ERR4388107	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/007/ERR4388107/ERR4388107_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/007/ERR4388107/ERR4388107_2.fastq.gz	588ffe4bca41e2c72cca79959ca06ffd;266ffb4a7ce4c2d4f31343e7654ded18	73500339;86160084
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s_deeper_sequencing_2	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	68309897	ERR4388231	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/001/ERR4388231/ERR4388231_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/001/ERR4388231/ERR4388231_2.fastq.gz	acece4818ab416324da0cf63402b0a12;3c0efafafecda2de2e1ea5966546b5f5	2507959022;2979964842
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543s_deeper_sequencing_5	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	85981168	ERR4388236	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/006/ERR4388236/ERR4388236_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/006/ERR4388236/ERR4388236_2.fastq.gz	66d091524a34f078c98572d36f533f02;0306df7f63723b81354b84658d7ca86b	3787231452;3997582586
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543b_deeper_sequencing_1	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	1151423	ERR4384927	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/007/ERR4384927/ERR4384927_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/007/ERR4384927/ERR4384927_2.fastq.gz	c74c1c0c0a2ed8599bd6d461a2b7c633;f94e0d0abbf5d0cdfa025950450ece20	75049432;86890431
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543b_deeper_sequencing_2	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	3669179	ERR4385800	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/000/ERR4385800/ERR4385800_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/000/ERR4385800/ERR4385800_2.fastq.gz	102a24929948a9c8a36fd97bc413a1db;ab3352a7943ac95861386137174be48b	232629449;265766157
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543b_deeper_sequencing_3	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	12607106	ERR4385809	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/009/ERR4385809/ERR4385809_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/009/ERR4385809/ERR4385809_2.fastq.gz	6f41a2eb226ae091f5423fdc98391b04;96d6ba2c095cba635fdfff04a5963bc3	794112413;899207544
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543b_deeper_sequencing_4	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 4000	PAIRED	WGS	72657115	ERR4386569	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/009/ERR4386569/ERR4386569_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR438/009/ERR4386569/ERR4386569_2.fastq.gz	e7f72ba102c6ad019068109dc3cb6d19;b0ed5a76e625b70479a02af4e35a6042	2811157094;3327301183
Neukamm2020	2020	10.1186/s12915-020-00839-8	Abusir1543	ENA	PRJEB33848	ERS3636018,ERS3636097,ERS3636099,ERS3636100,ERS3636098,ERS3636101,ERS3636093,ERS3636094,ERS3636095,ERS3636096,ERS3636025	Abusir1543b	double	Phusion Hot Start High-Fidelity DNA	none	Illumina HiSeq 2500	PAIRED	WGS	3702377	ERR4374008	fastq_all	ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/008/ERR4374008/ERR4374008_1.fastq.gz;ftp.sra.ebi.ac.uk/vol1/fastq/ERR437/008/ERR4374008/ERR4374008_2.fastq.gz	6c48b43d0690b87dc343c185eb95d85a;38f5f85d17cb6dc960e3fb88f3856b11	302008916;300798534

ancientsinglegenome-hostassociated_libraries.tsv#L1103-L1119

[jfy133]

Further info in this case: there is multiple samples in one library, but each library has a unique sample ID 🙄