getGFFSet function CRASHES R session
Entering edit mode
Matan G. ▴ 50
Last seen 2.5 years ago

Hi all,

I'm trying to run the following example taken from:

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 ''
    Something went wrong when trying to access the FTP site ''. 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 '' currently available?
    Error: '/tmp/RtmpoaclqZ/assembly_summary_archaea_refseq.txt' does not exist.
    In addition: Warning message:
    In download.file(url, ...) :
      URL '': 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.


getGFF NCBI biomartr biomaRt • 592 views

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