gap4 seqmentation fault on Ubuntu 10.04 x64

  • Anonymous - 2010-09-02

    Can anyone help? I get the following errors when I try to open a file with gap4:

    Level 2: DB_Load /home/<user>/GTAGDB/MID3_OUT.1.aux
    Level 1: Gap_Open -1
    Thu 02 Sep 18:25:23 2010 SYSMSG : Success
    Thu 02 Sep 18:25:23 2010 ERROR  : read error
    Thu 02 Sep 18:25:23 2010 COMMENT: reading record 0
    Thu 02 Sep 18:25:23 2010 FILE   : /home/<user>/Desktop/staden-2.0.0b7-src/build.ubuntu/../g/g-request.c:307
    Gap4 has found an unrecoverable error - These are usually bugs.
    Please submit all errors at

    +  Segmentation fault      gap4


  • James Bonfield

    James Bonfield - 2010-09-03

    Hmm. Record 0 is the primary "GDatabase" record which acts as a starting point for all other I/O - it contains things like how many sequences, contigs, annotations, clones, vectors, etc we have along with record numbers for the arrays that hold those contig records IDs, contig ordering, etc. In short - if it's broken you're hosed. HOWEVER - sometimes I see attempts to read record 0 when something has gone wrong, such as uninitialised data (a bug).

    Is this something related to a specific version of Gap4? Could the older ones open it? If so then it's likely a recently introduced bug. If no versions can open it then perhaps it's a corrupted database. Possibly there are also file permission problems, but that normally shows up in other forms with more sensible error messages.

    You may want to try copy_db, eg copy_db -v -f MID3_OUT.1 MID3_OUT.F
    This will attempt to fix the database, correcting problems as it goes. As mentioned above, there are times when it simply isn't possible, but it may give you something sufficient to work with.

  • Nobody/Anonymous

    Thanks for the help, the problem was a combination of user inexperience and brain fade. We tried another database and it works fine.


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