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Issue with getGenome() from GenBank database #111

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GeorgeAlehandro opened this issue Mar 29, 2024 · 0 comments
Open

Issue with getGenome() from GenBank database #111

GeorgeAlehandro opened this issue Mar 29, 2024 · 0 comments

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@GeorgeAlehandro
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Hello,

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"

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!

@GeorgeAlehandro GeorgeAlehandro changed the title Issue with GetGenome() from GenBank database Issue with getGenome() from GenBank database Mar 29, 2024
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