biomartr::getGenome() issue
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9 days ago
qstefano ▴ 20

Hello there,

For the past few weeks I've been having trouble downloading assembly genomes with the biomartr::getGenome() function. Below my code:

getGenome(db="refseq", organism="GCF_000008865.2", reference=TRUE, gunzip = TRUE)

The ftp link to the file is detected but not downloaded:

The FTP link: 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/GCF_000008865.2_ASM886v2_genomic.fna.gz' seems not to be available at the moment. This might be due to an instable internet connection, a firewall issue, or wrong organism name. Could you please try to re-run the function to see whether it works now? The FTP link: 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/md5checksums.txt' seems not to be available at the moment. This might be due to an instable internet connection, a firewall issue, or wrong organism name. Could you please try to re-run the function to see whether it works now? Genome download of Escherichia_coli_O157:H7_str._Sakai is completed! The download session seems to have timed out at the FTP site 'https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/008/865/GCF_000008865.2_ASM886v2/GCF_000008865.2_ASM886v2_genomic.fna.gz'. This could be due to an overload of queries to the databases. Please restart this function to continue the data retrieval process or wait for a while before restarting this function in case your IP address was logged due to an query overload on the server side. Error: Please provide a valid file path to your genome assembly file.

I did some tests and ruled out that it is a firewall or connection issue. I also tried changing organism and parameters.

Suggestions? Thanks

RefSeq R Assembly NCBI Package • 79 views
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