Thanks, @Debjit Pramanik. I independently tested the sample-selection fix using real Pf8 P. falciparum data from four Kilifi samples. The new regression test and existing phylogeny subworkflow test both passed, and all 72 genotype-to-consensus comparisons matched. I also noticed your note about duplicate FASTA headers. I'd be happy to investigate this as a separate follow-up, particularly for the multi-contig Plasmodium use case.