Hi Kevin, I hope this doesn't find you too late. Reply below... On Wed, 2014-06-11 at 15:52 +1000, Kevin Kocot wrote: > uqkkocot@barrine3:~> progressiveMauve --seed-family --seed-weight=11 > --backbone-output=backbone_output --output=output.mauve seq1 > Amphimedon_queenslandica_genomic_scaffolds.fa seq2 > Mnemiopsis_leidyi_genomic_scaffolds.fa seq3 > Monosiga_brevicollis_genomic_scaffolds.fa seq4 > Nematostella_vectensis_genomic_scaffolds.fa seq5 > Pleurobrachia_bachei_genomic_scaffolds.fa seq6 > Trichoplax_adhaerens_genomic_scaffolds.fa > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > > Searching with seed pattern 111001001010100100111 > > Searching with seed pattern 1110101001001010111 > > Searching with seed pattern 1111001010101001111 > done > Floating point exception > > Thanks! > Kevin
The FileNotOpened error message suggests that progressiveMauve wasn't able to read one of the files you've asked it to align. Can you confirm whether the file "seq1" exists and contains fasta sequence? If you meant to just align the *.fa files, then the correct command-line syntax for progressiveMauve would be to omit the seq1 seq2 etc. Some other notes: a seed weight of 11 might be a bit small for these genomes, probably it would be better to go with whatever progressiveMauve selects as a default at least for a first attempt. The --seed-family option will improve the ability to detect homology at higher sequence divergence, but comes at the cost of speed. I am not sure whether it will be worthwhile for the genomes you've got. Best, -Aaron -- 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. ------------------------------------------------------------------------------ Open source business process management suite built on Java and Eclipse Turn processes into business applications with Bonita BPM Community Edition Quickly connect people, data, and systems into organized workflows Winner of BOSSIE, CODIE, OW2 and Gartner awards http://p.sf.net/sfu/Bonitasoft _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
