If it was flagged for sequencing, don't complain.
species_path = genome_map.get(species, None)
logging.debug("Looked for genome '%s' got location '%s'" % (species, species_path))
species_path = genome_map.get(species, None)
logging.debug("Looked for genome '%s' got location '%s'" % (species, species_path))
- if species_path is None:
+ if not is_sequencing and species_path is None:
no_genome_msg = "Forcing lanes %s to sequencing as there is no genome for %s"
logging.warning(no_genome_msg % (lane_numbers, species))
is_sequencing = True
no_genome_msg = "Forcing lanes %s to sequencing as there is no genome for %s"
logging.warning(no_genome_msg % (lane_numbers, species))
is_sequencing = True