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I get 19220 genomes being downloaded. Also, I get the following messages
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015034605.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040095.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040335.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040615.1'
I would really appreciate your thoughts on what could explain the difference.
The text was updated successfully, but these errors were encountered:
sskashaf
changed the title
Some RefSeq genomes not being download
Some RefSeq genomes not being downloaded
Nov 2, 2020
Hello,
When I download the assembly summary for refseq
wget ftp:https://ftp.ncbi.nlm.nih.gov/genomes/refseq/bacteria/assembly_summary.txt
and select for the complete genomes
awk -F '\t' '{if($12=="Complete Genome") print $20}' assembly_summary.txt > assembly_summary_complete_genomes.txt
I get 21530 genomes.
When I do a dry run using ncbi-genome-download 0.3.0,
ncbi-genome-download --dry-run bacteria --section refseq -l complete
I get 19220 genomes being downloaded. Also, I get the following messages
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015034605.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040095.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040335.1'
WARNING: Skipping entry, as it has no ftp directory listed: 'GCF_015040615.1'
I would really appreciate your thoughts on what could explain the difference.
The text was updated successfully, but these errors were encountered: