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  1. Bug Repository
  2. BUG-180

problem with genomic sequence viewer on IGB 6.6 release

    Details

    • Type: Bug
    • Status: Closed (View Workflow)
    • Priority: Major
    • Resolution: Fixed
    • Labels:
      None
    • Environment:

      Integrated Genome Browser, version: 6.6.0 (9170)
      IGB 6.6 release

      Description

      This may well be a data bug, but if it is, we should help IGB recover when such bugs come up.

      I noticed this when trying to load sequence data for viewing in the sequence viewer.

      To repeat:

      (1) Reset prefs to defaults
      (2) Choose species Zea mays
      (3) Choose genome Z_mays_B73_Mar_2009
      (4) Click Sequence 1 (note - it is large!)
      (5) Zoom in on a feature
      (6) Right-click and choose "view genomic sequence" option
      (7) Wait. When I did this at home a few times, IGB just hung and I had to use "Force Quit" on my Mac to shut IGB down. When I did this just now at work, IGB hung for a few seconds and then a window opened bearing the error message:

      "Some error, ocurred, Please raise a bug request."

      The message contained an "OK" button. I clicked it.

      IGB then returned to its normal state, but it appeared the requested sequence had loaded. The genomic sequence viewer did not open, however.

      Here is the error message from the console:

      Completed loading sequence for 1 : 221,299,576 - 221,303,944 from IGB Quickload QuickLoad

      -------------------------------------------------------
      Can not open sequence viewer: Some error ocurred, Please raise a bug request
      -------------------------------------------------------

      Completed loading sequence for 1 : 221,299,576 - 221,304,578 from IGB Quickload QuickLoad

      -------------------------------------------------------
      Can not open sequence viewer: Some error ocurred, Please raise a bug request
      -------------------------------------------------------

        Attachments

        1. sv-ATG.png
          150 kB
          Ann Loraine
        2. sv-ATG.png
          150 kB
          Ann Loraine
        3. SV-bug.png
          681 kB
          Ann Loraine

          Issue Links

            Activity

            Hide
            alyssa Alyssa Gulledge (Inactive) added a comment -

            Everything looks fine. Closing this bug.

            Show
            alyssa Alyssa Gulledge (Inactive) added a comment - Everything looks fine. Closing this bug.
            Hide
            kkubiak Katharine Kubiak (Inactive) added a comment -

            Passed v9770 Windows

            Show
            kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9770 Windows
            Hide
            anuj Anuj Puram (Inactive) added a comment -

            Passed version 6.7.0(9791) on Mac

            Show
            anuj Anuj Puram (Inactive) added a comment - Passed version 6.7.0(9791) on Mac
            Hide
            smylapur Vineeth Mylapur (Inactive) added a comment -

            genome Z_mays_B73_Mar_2009 is not available.

            Instead I used the latest Z_mays_B73_Mar_2010.It takes few min to open the view sequence but works well.

            Passed 7.0 (11928) on windows.

            Show
            smylapur Vineeth Mylapur (Inactive) added a comment - genome Z_mays_B73_Mar_2009 is not available. Instead I used the latest Z_mays_B73_Mar_2010.It takes few min to open the view sequence but works well. Passed 7.0 (11928) on windows.
            Hide
            richard Richard Linchangco (Inactive) added a comment -

            Passed V.13526, Mac, Java 1.06.0_37

            Show
            richard Richard Linchangco (Inactive) added a comment - Passed V.13526, Mac, Java 1.06.0_37

              People

              • Assignee:
                Unassigned
                Reporter:
                ann.loraine Ann Loraine
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                Dates

                • Created:
                  Updated:
                  Resolved: