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metadata option unworking

See original GitHub issue

version of ncbi-genome-download

0.2.11

command

python3 ncbi-genome-download/ncbi-genome-download-runner.py --verbose --genus "Kluyvera" --metadata
-table data.tsv --format fasta -p 10 --retries 1 bacteria

result

All genomes are downloaded but the data.tsv file doesnt contains the metadata, only the header.

cat data.tsv 

assembly_accession	bioproject	biosample	wgs_master	excluded_from_refseq	refseq_category	relation_to_type_material	taxid	species_taxid	organism_name	infraspecific_name	isolate	version_status	assembly_level	release_type	genome_rep	seq_rel_date	asm_name	submitter	gbrs_paired_asm	paired_asm_comp	ftp_path	local_filename

Issue Analytics

State:
Created 4 years ago
Comments:5 (4 by maintainers)

Top GitHub Comments

1reaction

kblincommented, Jan 7, 2020

As a workaround, you can run ncbi-genome-download in single-process mode, that will fix writing the metadata table.

0reactions

kblincommented, Jan 7, 2020

Yeah, I agree. It’s just not trivial to fix after the recent change to also parallelize the download checking, but I would like to fix it.

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