found incorrect link for genome #27
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Note that this actually can cause us to download the wrong genome (v1 instead of v2) if that accession is not suppressed. I found this was the case for test accession |
This was referenced May 13, 2024
bluegenes
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May 13, 2024
- fixes #27 - allows `ftp_path` input that would be gotten from assembly_summary file - makes input csv format more restrictive: requires column names ["accession", "name", "ftp_path"], though `ftp_path` entries are optional. `ftp_path` is the `ftp_path` that can be obtained from NCBI assembly summary files
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When we try to find the link to download
GCA_000193795.2,directsketchfound the following link: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/193/795/GCA_000193795.1_ASM19379v1/GCA_000193795.1_ASM19379v1_genomic.fna.gz. Note that the folder https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/193/795/GCA_000193795.1_ASM19379v1/ does indeed exist, but this.1assembly is suppressed, so the download fails.When I looked up the genome via NCBI, I found the v2 genome is available at : https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/193/795/GCA_000193795.2_ASM19379v2/GCA_000193795.2_ASM19379v2_genomic.fna.gz
so this script found the v1 folder, instead of the v2 folder, causing the download to fail.
To fix this, look into the link + version check here: https://github.com/sourmash-bio/sourmash_plugin_directsketch/blob/main/src/directsketch.rs#L106-L125
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