The two archaeal sequences are lost for different reasons: •

GB_GCA_964441565.1~CAYTWW010000004.1

has 10 Ns at 856-865. It's lost already at the

BIOPYTHON_REMOVEN

step. • `GB_GCA_902827205.1~LR792634.1`is lost in

FILTERGAPPY

not because it's gappy, but because the genome is reported as "contaminated" in the NCBI

assembly_summary_genbank.txt

(the

excluded_from_refseq

field). Joining in this info and using it to filter was a crucial step in getting rid of the S. aureus sequences assigned to E. coli. The

FILTERGAPPY

module has an unfortunate name. It's because it evolved from filtering gappy via selecting a number of good sequences, to becoming a much stronger filtering step.