-c option MUMi

[nataliesilmon]

Hi,

When I use -M option to report MUM indexes, not all of the genomes are included - so I tried to use -c option to force include all genomes in the directory, but then get

Traceback (most recent call last):
  File "<string>", line 876, in <module>
AttributeError: 'str' object has no attribute 'close'

Is there another way of getting MUMi for all genomes? When running parsnp without -M option a file called all.mumi is generated but this doesn't include file names. recruitedgenomes.lst contains file names and MUMi, but only for those that were recruited (which is not the entire dataset).