Re: Differences in output between old version and new version of Mauve 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  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 . > >To unsubscribe, E-mail to:  > >To switch to the DIGEST mode, E-mail to  digest@svm.vetmed.wisc.edu>>To switch to the INDEX mode, E-mail to  >  > >Send administrative queries to   request@svm.vetmed.wisc.edu>> > >   > > >  > ############################################################# > This message is sent to you because you are subscribed to >  the mailing list . > To unsubscribe, E-mail to:  > To switch to the DIGEST mode, E-mail to  digest@svm.vetmed.wisc.edu>To switch to the INDEX mode, E-mail to  >  > Send administrative queries to   request@svm.vetmed.wisc.edu> >