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

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-608 Sequence viewer bugs

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

                  Ascending order - Click to sort in descending order
                  ann.loraine Ann Loraine created issue -
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                  ann.loraine Ann Loraine added a comment -

                  This worked okay for Arabidopsis data - which are being distributed via bnib and DAS, I believe.

                  Show
                  ann.loraine Ann Loraine added a comment - This worked okay for Arabidopsis data - which are being distributed via bnib and DAS, I believe.
                  ann.loraine Ann Loraine made changes -
                  Field Original Value New Value
                  Environment IGB 6.6 release Integrated Genome Browser, version: 6.6.0 (9170)
                  IGB 6.6 release
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  The problem seems to affect any sequence other than UNKNOWN in mays.

                  Show
                  ann.loraine Ann Loraine added a comment - The problem seems to affect any sequence other than UNKNOWN in mays.
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Can you reproduce this?

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Can you reproduce this?
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited

                  I got the beachball of death.... and will likely need to force quit from Chr 1. chr 10 just worked...

                  Something is wrong with the data set - I tried to move from chromosome 10 to chromosome 9 and got 4 NPEs

                  Meanwhile, everything else from phytosome works fine

                  Ann's comment: Did you check everything?

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited I got the beachball of death.... and will likely need to force quit from Chr 1. chr 10 just worked... Something is wrong with the data set - I tried to move from chromosome 10 to chromosome 9 and got 4 NPEs Meanwhile, everything else from phytosome works fine Ann's comment: Did you check everything?
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  ann.loraine Ann Loraine added a comment -

                  I think it is a data problem. I tried it with the new maize release and there was no problem at all.
                  I will re-create the sequence file and try again.

                  Show
                  ann.loraine Ann Loraine added a comment - I think it is a data problem. I tried it with the new maize release and there was no problem at all. I will re-create the sequence file and try again.
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  I got the same problem with Glycine max August 2010. I think this a general problem having to do with the 2bit file format.

                  Show
                  ann.loraine Ann Loraine added a comment - I got the same problem with Glycine max August 2010. I think this a general problem having to do with the 2bit file format.
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  I checked the 2bit file using twoBitInfo. It should be fine. The file sizes match between a newly recreated file and the one currently deployed on QL. So I don't think it is a data file issue.

                  Show
                  ann.loraine Ann Loraine added a comment - I checked the 2bit file using twoBitInfo. It should be fine. The file sizes match between a newly recreated file and the one currently deployed on QL. So I don't think it is a data file issue.
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  I also see some strange behavior that reminds me of what Micheal has mentioned. I tried to launch the Sequence Viewer on this gene model: AC229699_21.1 (M_truncatula_Mar_2009) and got some dashes appearing in the Sequence Viewer. (See attached.)

                  Show
                  ann.loraine Ann Loraine added a comment - I also see some strange behavior that reminds me of what Micheal has mentioned. I tried to launch the Sequence Viewer on this gene model: AC229699_21.1 (M_truncatula_Mar_2009) and got some dashes appearing in the Sequence Viewer. (See attached.)
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  Shows Sequence Viewer displaying dashes when it should not.

                  Show
                  ann.loraine Ann Loraine added a comment - Shows Sequence Viewer displaying dashes when it should not.
                  ann.loraine Ann Loraine made changes -
                  Attachment SV-bug.png [ 10391 ]
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  Getting error for:

                  O_sativa_japonica_Jun_2009
                  P_persica_Apr_2010
                  P_patens_Jan_2008

                  What I did was:

                  Selected the genome.
                  Double-clicked a gene model to zoom on it.
                  Right-clicked and selected View Genome Sequence in Sequence Viewer
                  A new window opened asking me if I want to load the sequence - I clicked "yes"
                  A new window opened with an error message:

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

                  I clicked OK, and the sequence loaded.

                  Show
                  ann.loraine Ann Loraine added a comment - Getting error for: O_sativa_japonica_Jun_2009 P_persica_Apr_2010 P_patens_Jan_2008 What I did was: Selected the genome. Double-clicked a gene model to zoom on it. Right-clicked and selected View Genome Sequence in Sequence Viewer A new window opened asking me if I want to load the sequence - I clicked "yes" A new window opened with an error message: "Some error occurred, Please raise a bug request." I clicked OK, and the sequence loaded.
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  I have added a fix for this bug.

                  "I also see some strange behavior that reminds me of what Micheal has mentioned. I tried to launch the Sequence Viewer on this gene model: AC229699_21.1 (M_truncatula_Mar_2009) and got some dashes appearing in the Sequence Viewer. (See attached.)"

                  Bug fix should have also fixed similar error for other species too.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - I have added a fix for this bug. "I also see some strange behavior that reminds me of what Micheal has mentioned. I tried to launch the Sequence Viewer on this gene model: AC229699_21.1 (M_truncatula_Mar_2009) and got some dashes appearing in the Sequence Viewer. (See attached.)" Bug fix should have also fixed similar error for other species too.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  On trunk v.9316: I have no dashes for any of the listed genomes or genes. I have no error messages.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - On trunk v.9316: I have no dashes for any of the listed genomes or genes. I have no error messages.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  ann.loraine Ann Loraine added a comment -

                  Just a couple of quick notes on sequence viewer, r9320 on trunk. (It may already be fixed in Hiral's copy.)

                  (1) Check show cDNA. The start codon (ATG) is not indicated correctly in the "cDNA" view.

                  (2) Start codon is being shown when user selects a UTR. (See attached file - sv-ATG.png)

                  Show
                  ann.loraine Ann Loraine added a comment - Just a couple of quick notes on sequence viewer, r9320 on trunk. (It may already be fixed in Hiral's copy.) (1) Check show cDNA. The start codon (ATG) is not indicated correctly in the "cDNA" view. (2) Start codon is being shown when user selects a UTR. (See attached file - sv-ATG.png)
                  ann.loraine Ann Loraine made changes -
                  Attachment sv-ATG.png [ 10392 ]
                  ann.loraine Ann Loraine made changes -
                  Attachment sv-ATG.png [ 10393 ]
                  Hide
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r9324.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r9324.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  M. Trunculata is still very buggy across the gene models - some gene models throw the 'some bug occurred' warning, some don't have the start codon boxed in green, some don't have the terminator boxed in red and some are just fine.

                  For O. sativa japonica, I only found 1 out of 10 that had any issue, and it is missing the 'stop' box (Os01g27500.1) but in general it seemed fine.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - M. Trunculata is still very buggy across the gene models - some gene models throw the 'some bug occurred' warning, some don't have the start codon boxed in green, some don't have the terminator boxed in red and some are just fine. For O. sativa japonica, I only found 1 out of 10 that had any issue, and it is missing the 'stop' box (Os01g27500.1) but in general it seemed fine.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Fixed in r9328.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Fixed in r9328.
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  ann.loraine Ann Loraine added a comment - - edited

                  I am checking Medicago truncatula on revision 9329.

                  These gene models worked fine:

                  Medtr1g081230.4
                  AC225519_15.1
                  Medtr4g158240.3

                  Show
                  ann.loraine Ann Loraine added a comment - - edited I am checking Medicago truncatula on revision 9329. These gene models worked fine: Medtr1g081230.4 AC225519_15.1 Medtr4g158240.3
                  Hide
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                  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.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.6 [ 10021 ] Bug Repository [ 10030 ]
                  Key IGBA-225 BUG-180
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Katharine Kubiak [ kkubiak ]
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9770 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9770 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
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                  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
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Vineeth Mylapur [ smylapur ]
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                  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.
                  smylapur Vineeth Mylapur (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Vineeth Mylapur [ smylapur ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-26 [ BUG-26 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-608 [ BUG-608 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Priority Blocker [ 1 ] Major [ 3 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-26 [ BUG-26 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Richard Linchangco [ richard ]
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                  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
                  richard Richard Linchangco (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Richard Linchangco [ richard ] Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Closed [ 6 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]

                    People

                    • Assignee:
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                      Reporter:
                      ann.loraine Ann Loraine
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                      Dates

                      • Created:
                        Updated:
                        Resolved: