Re: Differences in output between old version and new version of Mauve I think the problem may be an SML file format conflict between the old and new versions.Â  The SML files in the new version store inexact match information, while the old version stored exact match information.Â  In order to test whether this is in fact part of the problem, try deleting the files ending with .sml in the /home/william/sequences/mauve/ directory before running the old version. Note that the new Mauve release automatically recognizes old format .sml files and updates them automatically.Â  So, the old .sml format should never be a problem for the newer Mauve. -Aaron wmccaig@nyc.rr.com wrote: Aaron, Thank you for the quick response to my questions, I do appreciate it.  I am, in fact, registered with the mailing list, though I have not received any messages before this one.  I had re-registered this morning, just in case. Following is the information from the output of Mauve which I mentioned in my earlier message.  This is utilizing the older version of Mauve.  The reason I am confused is because I can run the newer version with no problems, but get this message with the old version. I've had this happen on several machines.  I am uncertain if there is a conflict or not with having both versions installed at the same time.  At any rate, here is the information.  Thank you again for your help. William Executing:  ./mauveAligner -o /home/william/mauve_output/279_B31_JD1_N40/279_B31_JD1_N40 --i sland-size=50 --island-output=/home/william/mauve_output/279_B31_JD1_N40/279_B31 _JD1_N40.islands --backbone-size=50 --max-backbone-gap=50 --backbone-output=/hom e/william/mauve_output/279_B31_JD1_N40/279_B31_JD1_N40.backbone --id-matrix=/hom e/william/mauve_output/279_B31_JD1_N40/279_B31_JD1_N40.id_matrix --output-alignm ent=/home/william/mauve_output/279_B31_JD1_N40/279_B31_JD1_N40.alignment --outpu t-guide-tree=/home/william/mauve_output/279_B31_JD1_N40/279_B31_JD1_N40.guide_tr ee /home/william/sequences/mauve/279-plasmids-Assembly-9-28-04.fas /home/william /sequences/mauve/279-plasmids-Assembly-9-28-04.fas.sml /home/william/sequences/m auve/Borrelia_burgdorferi_B31.genome /home/william/sequences/mauve/Borrelia_burg dorferi_B31.genome.sml /home/william/sequences/mauve/JD1-Assembly-9-28-04.fas /h ome/william/sequences/mauve/JD1-Assembly-9-28-04.fas.sml /home/william/sequences /mauve/N40-Assembly-10-3-04.fas /home/william/sequences/mauve/N40-Assembly-10-3- 04.fas.sml  Sequence loaded successfully. /home/william/sequences/mauve/279-plasmids-Assembly-9-28-04.fas 523576 base pair s. Sequence loaded successfully. /home/william/sequences/mauve/Borrelia_burgdorferi_B31.genome 1519856 base pairs . Sequence loaded successfully. /home/william/sequences/mauve/JD1-Assembly-9-28-04.fas 1518917 base pairs. Sequence loaded successfully. /home/william/sequences/mauve/N40-Assembly-10-3-04.fas 1342546 base pairs. Using 21-mers for initial seeds Creating sorted mer list Create time was: 1 seconds. Creating sorted mer list Create time was: 1 seconds. Creating sorted mer list Create time was: 1 seconds. Creating sorted mer list Create time was: 1 seconds. 0%..99%..Exited with code: 139 ----- Original Message ----- From: Aaron Darling <darling@cs.wisc.edu> Date: Tuesday, January 25, 2005 3:45 pm Subject: Re: Differences in output between old version and new version of Mauve    William, Thanks for the e-mail.  As you guessed, the difference in the  number of  Intervals between Mauve versions results from both more sensitive  alignment and a file format change. The output from the new version of Mauve includes an Interval entry  for  every unaligned region in addition to intervals for the aligned  regions.  This was done to support the sequence similarity display  in  the latest version. If your previous alignment had 57 intervals and the new one has  359, 287  of which are unaligned intervals, it sounds like 15 intervals can  be  attributed to greater sensitivity in the new aligner version. Yes, I agree it's wasteful to include entries containing nothing  but  gaps as part of the unaligned intervals.  A future Mauve release  may  economize the file format. As for the exiting with error codes, this message is somewhat  misleading.  The actual error code number has no significance.  The  relevant error should be displayed in the text of the log window.   If  you can send me a copy of the error message text I can try to help  you  track down the problem. -Aaron William McCaig wrote:      Hello there, I'm having a problem with the Mauve alignment program and was         wondering if       someone could help me to figure out what exactly is going on.  I         was using an       older version of Mauve, 20040708, and recently switched to the         newest one,       20041216. The problem is as follows: Running both versions with the exact same 4 alignment files, at         the default       settings, produces two different sets of results.  In the old         version, for       instance, I wind up with an IntervalCount of 57, while with the         newer version       it's 359.  I'm not certain if the default settings changed between         the two       versions, or if this is a result of the "inexact seeds" resulting         in "more       sensitive alignments" that was mentioned in the ChangeLog.   However, I have also noticed a number of Intervals located near         the end of       the .alignment file that appear to contain an entry for only one         of the four       sequences.  That is, one sequence has an entry and the other three         are       nothing but gaps.  This is in the newer output file generated and         is not       located in the old one at all.  Is there some setting I am missing         that       changed between Versions that would result in this output.  Doing         a count of       the intervals, there are 287 or so of these Interval entries.          Perhaps I'm       not understanding the exact format of the MultiFASTA output file,         but it       seems kind of pointless to have an entry where the sequences you         are       comparing to are all gaps.   I believe that these entries make no difference when it comes to         using the       Java Viewer that is included with Mauve, but I actually need the         .alignment       output file. Also, a number of times I have gotten an exit status with error         code 139.  I'm       not certain what that or any of the other codes mean.  I can't         figure out       exactly what is going wrong, except it appears to happen on one of         my       machines with one version and not on another.   Any help at all with this would be greatly appreciated.   Thank you, in advance, William ############################################################# This message is sent to you because you are subscribed to  the mailing list <gel-software@svm.vetmed.wisc.edu>. 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