Problem: mutation report /wish.exe

Jake
2005-12-27
2013-04-18
  • Jake
    Jake
    2005-12-27

    When I try to produce mutation report from GAP4 commands menu I usually sooner or later get windows error message: "wish.exe encountered a problem and needs to close, please send us an error report". After sending or not and error report the whole gap closes down, however, the BUSSY file stays present in the directory with the database.

    Few times it happened that the gap just shut down without any error message, but leaving behind the BUSSY file.
    Few times it also happened, that the program created mutation_report directory, sometime empty, sometime with several png files included, once or twice even with the index file before closing down.

    Anybody any ideas what's going on?

    I'm running Staden package 1-6-0 on Windows XP SP2, on Compaq Pressario V2010US. I installed the Staden package from the provided msi file.

    Thanks a lot for any help and advice!!!

    Jake

     
    • James Bonfield
      James Bonfield
      2006-01-03

      It's almost certainly a bug. I find debugging on windows a total nightmare to be honest though, but with luck I'll be able to trigger the same problem on unix too.

      Does it always happen with the same input database? If it's easy to reproduce with a given data set then having access to that data set would greatly improve the chances of finding and fixing the bug.

      James

       
    • Jake
      Jake
      2006-01-05

      It happened with multiple databases. Recently I provided one of the databases to E.Akhunov (UC Davis) and he had the same problem using my database, however when he build-up the database from the trace files on his instalation of Staden, he was able to produce mutation report without problem. So it may be problem specific to my system???
      In light of this I'm going to get it running under Linux (hopefully).

      I will provide the database as well as original trace files, if you still want to have a look into it. Are there some other information/files, which would help you with this? Where should I send the files?

      Jake
      hadam"et"ksu.edu

      Jakub Hadam
      Dept. of Plant Pathology
      Kansas State University

       
    • James Bonfield
      James Bonfield
      2006-01-10

      It's certainly the case that the windows version works slightly differently for the html mutation report. For starters it produces greyscale images and unfortunately that's an issue with the Tk library the GUI is based on rather than Gap4 itself. So linux is better in that respect.

      I'm somewhat busy on another project right now, but feel free to mail files to jkbonfield@sourceforge.net and I think they'll get through OK. If not I'll contact you directly.

       
    • I experienced the same problem in a Windows installation if I selected to view the mutation report based on sequence or the second option (don't remember what it is) rather than leaving the default. If I left the default selections when I generated the mutation report, it worked. However, I found it odd that the mutation report shows the opposite strand numbering than the contig editor, and also showed several mutations other than the one's shown in the 'show SNPs' window.
      Phil Morin (phillip.morin@noaa.gov)

       
    • I have experienced the same problem.
      Pity, because it is a feature of the program that would really be useful to me!