Open ZoePochon opened 10 months ago
Hm interesting... how did you load the viewer? Via CLI or the online version?
Via the command line.
I can replicate, but there is nothing in the console... not sure what's happening
@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)
@jfy133 @ZoePochon I can't replicate, all is fine with me. Maybe it was a temporary ENA api disruption ?
@maxibor and I just tested again and he was looking at the wrong table, investigating gain
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
Further info in this case: there is multiple samples in one library, but each library has a unique sample ID :roll_eyes:
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.