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While trying to fetch genomes from GenBank I had an issue with a lot of genomes from GenBank. One example:
#BiocManager::install("Biostrings")
#BiocManager::install("biomaRt")
i#nstall.packages("biomartr", dependencies = TRUE)
biomartr::getGenome("GCA_000689275.1", db = "genbank")
Result:
> biomartr::getGenome("GCA_000689275.1", db = "genbank")
-> Starting genome retrieval of 'GCA_000689275.1' from genbank ...
Unfortunately no GENOME file could be found for organism 'GCA_000689275.1'. Thus, the download of this organism has been omitted. Have you tried to specify 'reference = FALSE' ?
[1] "Not available"
Hello,
While trying to fetch genomes from GenBank I had an issue with a lot of genomes from GenBank. One example:
Result:
Although the same genome is available at ncbi: https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_000689275.1/
I cannot figure out where this problem might be coming from, specially that it is not happening with ALL the genomes from GenBank..
Thank you for the help!
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