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GTDB R237

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Donovan H. Parks edited this page Sep 13, 2026 · 25 revisions

Syncing NCBI Genomes

  • sync of Archaea done partially by Pierre and partially by Donovan using different scripts; have settled on the method implemented as ncbi_sync in the GTDB Migration Tk which specifically limits requests per second to minimize errors messages from NCBI

  • Bacterial RefSeq genomes (assembly_summary_bacteria_refseq_nolargeproject.txt):

    • 52,6771 genomes
    • 1 failed
    • 148,760 unchanged
    • used 16 requests per second (--rate 16)
    • 58.5 hours

  • Bacterial GenBank genomes (assembly_summary_bacteria_genbank_nolargeproject.txt):

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