I am trying to use mauve via command line for whole genome alignment;
./mauveAligner --weight=300 --output-alignment=fifty_isolates.alignment Autumn2013_ALT_17.gbk 1.gbk.sml Spring2012_ALT_27.gbk 2.gbk.sml --id-matrix= id_matrix.txt
I get this error:
Error: Each sequence file must have a corresponding SML file specified.
Indeed the sml files are non existent, however, and I quote the manual:
"Each sequence must have a corresponding Sorted Mer List (SML) file name given. If the SML file does not exist,
mauveAligner will create it."
Nothing in the options is related to SML file creation, what's the catch?!