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borenstein-lab / MIMOSA2shiny

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Failed to download_reference_data #1

Closed demonlj closed 4 years ago

demonlj commented 4 years ago 
 download_reference_data(seq_db = "Sequence variants (ASVs)", target_db = "AGORA genomes and models")
ASV_AGORA.tar.gz试开URL’http://elbo-spice.gs.washington.edu/shiny/MIMOSA2shiny/refData/ASV_AGORA.tar.gz'

Error in download.file(paste0(source_url, file_id), destfile = paste0(save_to,  :
  cannot open URL'http://elbo-spice.gs.washington.edu/shiny/MIMOSA2shiny/refData/ASV_AGORA.tar.gz'
 Warning message:
In download.file(paste0(source_url, file_id), destfile = paste0(save_to,  :
  cannot open URL 'https://elbo-spice.gs.washington.edu/shiny/MIMOSA2shiny/refData/ASV_AGORA.tar.gz': HTTP status was '502 Bad Gateway'

would you offer another way to download the reference data?

btw: MIMOSA2 do analysis connection between KEGG metabolomics and taxonomy species, but my data was 16s RNA seqs, which are not reliable at species level. May I just analyze the data at genus level? thank you!

cnoecker commented 4 years ago

Hello, Thanks for your interest in using MIMOSA2. We have observed some intermittent download connection issues with this function - sometimes the connection fails on the first attempt but succeeds if you repeat the same command. You can also download the same data from the links here: https://borenstein-lab.github.io/MIMOSA2shiny/downloads.html# It is also worth noting that we are in the process of migrating our data and application to a larger server, which will change the URL and probably resolve these issues as well.

Regarding your second question, MIMOSA2 can use a variety of strategies to map microbiome taxonomic data to reactions and metabolites with as high a level of resolution as possible, which might depend on your data and environment. You can change the minimum similarity threshold required for a 16S sequence variant to be mapped to a metabolic reconstruction with the "simThreshold" parameter. An alternative strategy is to first run PICRUSt2 on your data to predict KEGG Orthologs for each taxon, and provide the resulting table of inferred KO abundances in each taxa and sample to MIMOSA2.