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Note that I did not do separate contaminant filtering (which I did for Penstemon), because the parsing code and other downstream steps should knock out contaminants. I can double-check this.
I modified the script from 16S/ITS work for splitting fastq files based on information in their info line, to different files. It is: /project/microbiome/analyses/gtl/HMAX1/demultiplex/splitFastq_manyInputfiles_gbs.pl and I started it running on with 12 hours of wall time (tomorrow is a system maintenance day, so I am seeing whether I can finish before that starts).