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grp-bork / spire_contribute

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Missing assemblies #6

Closed snayfach closed 8 months ago

snayfach commented 8 months ago

For some studies, the link to download the assemblies .tar file is broken:

Larson_2022_elderly Panwar_2020_lake_Antarctica Cao_2023_goat Bell_2018_groundwater McKay_2021_coalbed Castro-Nallar_2023_Patagonia_fjords Wang_2022_elderly_osteoporosis Fujimoto_2021_FMT_rCDI Zhong_2023_virus_Arctic Liang_2020_adenomatous_polyps PRJNA309119_Eurytemora_copepod_water Aylward_2012_ant_fungus

For example: wget https://swifter.embl.de/~fullam/spire/compiled/Aylward_2012_ant_fungus_spire_v1_assemblies.tar

--2023-12-26 23:17:13-- https://swifter.embl.de/~fullam/spire/compiled/Aylward_2012_ant_fungus_spire_v1_assemblies.tar Resolving swifter.embl.de (swifter.embl.de)... 194.94.44.56 Connecting to swifter.embl.de (swifter.embl.de)|194.94.44.56|:443... connected. HTTP request sent, awaiting response... 404 Not Found 2023-12-26 23:17:14 ERROR 404: Not Found.

For other studies, the link is fine, but there are missing assemblies from the tarball. Here's one example:

wget https://swifter.embl.de/~fullam/spire/compiled/Avila-Herrera_2020_astronaut_ISS_spire_v1_assemblies.tar
tar -xvf Avila-Herrera_2020_astronaut_ISS_spire_v1_assemblies.tar
ls Avila-Herrera_2020_astronaut_ISS | grep SAMN10252997

Overall there are 3660 samples between these two categories

snayfach commented 8 months ago

There are also studies where the tarball is empty. Here's one example: https://spire.embl.de/study/Boktor_2022_PD_RUMC?page=1

And here's the full list:

Boktor_2022_PD_RUMC Boktor_2022_PD_TBC Bowerman_2021_rodent Derosa_2022_NSCLC Ekwanzala_2020_wastewater Haifer_2022_FMT_donors Jo_2022_PD Kim_2021_Korea Lee_2022_melanoma Leung_2022_liver_NAFLD Liu_2022_CRC_China Mao_2022_PD Matson_2018_melanoma McCulloch_2022_melanoma Peters_2019_melanoma Pleasure-Ateba_2020_dog Podlesny_2022_FMT_UC Qian_2020_PD Riquelme_2021_wastewater Routy_2018_PD1 Thomas_2019_CRC_Italy Wallen_2022_PD

fullama commented 8 months ago

Thanks for the detailed report! The tar file permissions should all be fixed now.. the missing assemblies in the tars are most likely one that failed to assemble - i will add that to the list of changes to make to the site so these samples are flagged.

The studies where the tarball was empty i have removed from the site as they were mistakenly labelled as ready for release.