I am trying to run a few hundred samples through NextStrain in a global background from GISAID. I include the sample names in the “include.txt” file, and see them added back in on the log files. The samples show up in the sequence-diagnostics.tsv output and each has an associated align_#.txt, but none of the jsons seem to include the samples. The log files do not indicate that they were filtered out. The samples all have >99% complete genomes and the metadata was carefully defined to match the standards.
Can you help me figure out why the samples don’t appear in the json output files?