Hi Norhan, if your goal is to do a progressiveMauve alignment on the command-line, your best bet will be a command like this:
./progressiveMauve --output=fifty_isolates.alignment Autumn2013_ALT_17.gbk Spring2012_ALT_27.gbk there's no need to use mauveAligner to make an identity matrix for progressiveMauve, it will calculate that on its own. But if you want to try it anyway, you'll need to move the --id-matrix parameter earlier in the command. The sequences & SMLs need to come at the end of the mauveAligner command. Best, -Aaron On Fri, 2015-02-27 at 00:17 +1100, Norhan Mahfouz wrote: > Hi every one, > 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?! > P.S. I'm using mauve only to get the identity matrix as an input to > progressive mauve > -- Aaron E. Darling, Ph.D. Associate Professor, ithree institute University of Technology Sydney Australia http://darlinglab.org twitter: @koadman UTS CRICOS Provider Code: 00099F DISCLAIMER: This email message and any accompanying attachments may contain confidential information. If you are not the intended recipient, do not read, use, disseminate, distribute or copy this message or attachments. If you have received this message in error, please notify the sender immediately and delete this message. Any views expressed in this message are those of the individual sender, except where the sender expressly, and with authority, states them to be the views of the University of Technology Sydney. Before opening any attachments, please check them for viruses and defects. Think. Green. Do. Please consider the environment before printing this email. ------------------------------------------------------------------------------ Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
