Question: Mauve aligner without SML files
gravatar for norhanmahfouz
5.7 years ago by
norhanmahfouz0 wrote:

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?!

next-gen alignment • 2.0k views
ADD COMMENTlink modified 5.7 years ago • written 5.7 years ago by norhanmahfouz0

problem solved!

ADD REPLYlink written 5.7 years ago by norhanmahfouz0

Hey, I realize this was a long time ago, but I'm having the same problem and keep running into roadblocks. How did you solve it?

ADD REPLYlink written 5.1 years ago by Pryce Michener10
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