Hi Talia, the XMFA file includes filesystem path references to the original aligned sequences. stripSubsetLCBs tries to read in those sequences, but is unable to open the at least one of the files and that is why it's throwing the FileNotOpened exception. If the sequence files have moved you might try updating the paths in the first few lines of the XMFA with your favorite text editor.
Best, -Aaron On Fri, 2014-04-11 at 08:33 +1000, Talia Karasov wrote: > Hi all, > > I'm having a ridiculous problem, I suspect. > I aligned 25 genomes using progressivemauve. In attempting to subset > the LCBs in the output xmfa file output, I get the following error. > > Here's the command: > > stripSubsetLCBs pre_core.xmfa pre_core.xmfa.bbcols core.xmfa 500 > > > > Here's the error: > > Exception FileNotOpened thrown from > Unknown() in gnFileSource.cpp 67 > Called by Unknown() > Read 86063 backbone entries > seq_count is: 0 > output_ivs.size() 3118 > Segmentation fault: 11 > > > It seems that the bbcols file is recognized, but that the xmfa file > cannot be loaded. The path to the file is correct...I checked this > many times. I changed the permissions on all of these files to full > access, so this is not the issue.I see that several other people have > had this problem, but have yet to find the solution. I've gotten this > same error for several different progressivemauve outputs (for several > different alignments). Any help would be so greatly appreciated! > > Thanks, > > Talia > -- 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. ------------------------------------------------------------------------------ Put Bad Developers to Shame Dominate Development with Jenkins Continuous Integration Continuously Automate Build, Test & Deployment Start a new project now. Try Jenkins in the cloud. http://p.sf.net/sfu/13600_Cloudbees _______________________________________________ Mauve-users mailing list Mauve-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/mauve-users
