getGFFSet function CRASHES R session
0
0
Entering edit mode
Matan G. ▴ 60
@matan-g-22483
Last seen 3.3 years 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 • 794 views
ADD COMMENT

Login before adding your answer.

Traffic: 776 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6