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stianlagstad / chimeraviz

chimeraviz is an R package that automates the creation of chimeric RNA visualizations.
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Failed to create EnsDb #97

Open taot2007 opened 1 year ago

taot2007 commented 1 year ago

Hi stianlagstad,

I tried to create EnsDb from a downloaded .gtf file using "edbSqliteFile <- ensDbFromGtf(gtf = "Homo_sapiens.GRCh38.104.gtf")", and here is the error information:

Processing chromosomes ... Fetch seqlengths from ensembl ... Error in readLines(curl(my_url)) : Server denied you to change to the given directory In addition: Warning message: In ensDbFromGRanges(GTF, outfile = outfile, path = path, organism = organism, : I'm missing column(s): 'entrezid'. The corresponding database column(s) will be empty! Error in readLines(curl(my_url)) : Server denied you to change to the given directory Error in readLines(curl(my_url)) : Server denied you to change to the given directory Error in readLines(curl(my_url)) : Server denied you to change to the given directory Error in readLines(curl(my_url)) : Server denied you to change to the given directory FAIL

Look like a connection issue. Do you have any idea on this? Do you have a ready-to-use .sqlite file for GRCh38.104? Thanks so much!

stianlagstad commented 1 year ago

Hi @taot2007 , would you be able to share the download link for that exact .gtf file? So that I may be able to reproduce the issue locally.