Error opening DB in gap4

2012-10-13
2013-04-18
  • John F Wolters

    John F Wolters - 2012-10-13

    I am having issues opening a database converted from a caf file generated using MIRA

    When attempting to open the file using the gap4 interface, only the version.aux file is visible, and not the version file.

    When attempting to open the file via the command line
    e.g gap4 TESTRUN1_FILTERED.0

    I get the following error:
    jwolter1@bravo:~/SeqFinishing$ gap4 TESTRUN1_FILTERED.0
    WARNING! Database has lock file, but is no longer in use.
    WARNING! Taking ownership of lock.
    Fri 12 Oct 21:17:11 2012 Success
    Fri 12 Oct 21:17:11 2012 invalid type
    Fri 12 Oct 21:17:11 2012 reading record 186245
    Fri 12 Oct 21:17:11 2012 /tmp/staden-2.0.0b9-src/build/../gap4/gap-io.c:174
    Gap4 has found an unrecoverable error - These are usually bugs.
    Please submit all errors at https://sourceforge.net/projects/staden/

    Any help would be greatly appreciated.

     
  • Andrew Whitwham

    Andrew Whitwham - 2012-10-15

    Hello,

    Just seeing the aux file in the gap4 open file window is normal.

    Did you use caf2gap to convert the caf file into gap4?

    Thanks,

    Andrew

     
  • John F Wolters

    John F Wolters - 2012-10-15

    Yes,

    The settings I used were straight from the MIRA manual (with a different project name):
    caf2gap -project c227-11 -ace c227-11-clrc_filteredx500y8.caf

    The output was a PROJECTNAME.0 file and a PROJECTNAME.0.aux file

     
  • James Bonfield

    James Bonfield - 2012-10-15

    Have you do any editing of the gap4 database between running caf2gap and getting this error? If not then we can assume caf2gap or the CAF file itself are in error. If you have edited then it's probably something in gap4 which broke.  If it's the CAF file or caf2gap itself then is the issue reproducable (ie by running caf2gap again)?

    On a different note, you can try "copy_db -v -f TESTRUN1_FILTERED.0 TESTRUN1_FILTERED.F" to create a new copy (version F). The -f option of copy_db attempts to fix data corruptions during the copy. It's not foolproof, but it may work. The alternative (which also may or may not work) is gap2caf followed by caf2gap to fix issues.

     

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