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Some RefSeq genomes not being downloaded #139

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sskashaf opened this issue Nov 2, 2020 · 0 comments
Open

Some RefSeq genomes not being downloaded #139

sskashaf opened this issue Nov 2, 2020 · 0 comments

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@sskashaf
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sskashaf commented Nov 2, 2020

Hello,

When I download the assembly summary for refseq

wget ftp://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.

@sskashaf sskashaf changed the title Some RefSeq genomes not being download Some RefSeq genomes not being downloaded Nov 2, 2020
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