Hello Karthik, On Sat, 2014-11-15 at 10:43 +1100, Hullahalli, Karthik wrote: > Dear Support Group, > > I have aligned 78 Enterococcus faecalis genomes, and I am currently trying to > construct a phylogenetic tree based on the alignment file in XMFA format. > This alignment was done on a computer running Windows 7, and we have problems > that occur when we try to manipulate this file (specifically with > StripSubsetLCBs) on a different computer running a UNIX environment. > StripSubsetLCBs claims that the length of sequence described in the FASTA > header is different from the length of sequence that is actually read.
Without seeing the exact error message copied & pasted from your terminal it's a bit hard to key in on what's gone wrong. Still, there are several potential pitfalls when moving an alignment from one computer to another. In particular, the XMFA stores the locations of input sequence files as the first few lines. stripSubsetLCBs needs to access these files, and if it's unable to find them it may run into trouble. There are also potential issues with dos vs. unix end of line characters and filesystem paths. The best advice I can give to workaround these issues is to run the initial alignment with all files (input sequences and output) in the current working directory, so that system-specific pathnames are unnecessary, e.g. don't give paths on the aligner command-line, just filenames. Then when you move the files to unix, move all of the files together, and convert the end of lines with dos2unix. You might also try running stripSubsetLCBs on the same windows machine where the alignment was calculated. 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. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://pubads.g.doubleclick.net/gampad/clk?id=154624111&iu=/4140/ostg.clktrk _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
