getGFFSet function CRASHES R session
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Matan G. ▴ 40
@matan-g-22483
Last seen 5 months ago

Hi all,

I'm trying to run the following example taken from: https://rdrr.io/cran/biomartr/man/getGFFSet.html

library(biomartr)
getGFFSet("refseq", organisms = c("Arabidopsis thaliana", 
                                      "Arabidopsis lyrata", 
                                      "Capsella rubella"))

Running it online results in the following:

Starting GFF retrieval of the following GFFs: Arabidopsis thaliana, Arabidopsis lyrata, Capsella rubella ...
Generating folder set_GFF ...




Starting GFF retrieval of 'Arabidopsis thaliana' from refseq ...


It seems that this is the first time you run this command for refseq.
Thus, 'assembly_summary.txt' files for all kingdoms will be retrieved from refseq. 
Don't worry this has to be done only once if you don't restart your R session.


    trying URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt'
    Something went wrong when trying to access the FTP site 'ftp://ftp.ncbi.nlm.nih.gov/'. Sometimes the internet connection isn't stable and re-running the function might help. Otherwise, could there be an issue with the firewall?. Is the the FTP site 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt' currently available?
    Error: '/tmp/RtmpoaclqZ/assembly_summary_archaea_refseq.txt' does not exist.
    In addition: Warning message:
    In download.file(url, ...) :
      URL 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/archaea/assembly_summary.txt': status was 'Couldn't resolve host name'
    Execution halted

Running it locally on R studio just crashes and aborting session.

How can it be solved.

Best

getGFF NCBI biomartr biomaRt • 153 views
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