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Old 12-29-2011, 10:49 AM   #3
Location: Sydney, Australia

Join Date: May 2010
Posts: 65

The problems you're experiencing are happening because you've used the wrong command-line syntax for mauveAligner. The command-line syntax is documented in the manual, please read it carefully. mauveAligner requires one to specify a sequence file followed by a name for a genome-specific index file (.sslist or .sml) for that sequence that the software will create. By neglecting to include a path for the .sslist file and instead giving the next sequence name immediately, the software took that file to be the desired path for the .sslist and tried to write the index there.

tirohia, you should be running mauveAligner as:
mauveAligner --output=something NC_004578.fna NC_004578.fna.sslist Nz1334-contigs.fa Nz1334-contigs.fa.sslist

tomiczeek, your command should be:
./mauveAligner --output=jb50vsSpmito.mauve --output-alignment=jb50vsSpmito.alignment jb50contigs.fa jb50contigs.fa.sslist Sp.may2011.extras_mito.fasta Sp.may2011.extras_mito.fasta.sslist

Both of you will need to check that your sequence files are intact as they may have been overwritten by incorrect use of mauveAligner.

2nd, unless you have a compelling reason I would strongly suggest using progressiveMauve instead of mauveAligner. mauveAligner requires manual tuning of its parameters and is generally nowhere near as accurate as progressiveMauve. See this paper for details:

Finally, there's a chance that the .sslist created by some versions of mauveAligner may be unreadable by progressiveMauve and it may cause a mysterious crash. If that seems to be happening and your .sslist were created by mauveAligner just delete them and progressiveMauve will recreate them. It only takes a few seconds.
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