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  1. Bug Repository
  2. BUG-183

Z mays latest genome very slow to load

          Details

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

            IGB 6.2.2

            Description

            Initial loading of genome often is slow. Need instructions to reproduce.

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                relates to

                Task - A task that needs to be done. BUG-647 Server bugs

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

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                  ann.loraine Ann Loraine added a comment -

                  I tested the 6.6 branch Revision: 9368

                  I reset prefs to default, launched the branch (using ant run) and then selected Z_mays_B73_Mar_2010.

                  It took about three minutes for Z_mays_B73_Mar_2010 gene models to load with RNA-Seq data sets included in the annots.xml file.

                  Next, I removed the data sets from the annots.xml file (by updating the annots.xml to an earlier revision, e.g.,

                  [aloraine@cci-vm12 Z_mays_B73_Mar_2010]$ svn up -r316 annots.xml
                  U annots.xml
                  Updated to revision 316.
                  [aloraine@cci-vm12 Z_mays_B73_Mar_2010]$ more annots.xml
                  <files>
                  <file name="Z_mays_B73_Mar_2010.bed.gz" title="Maize Transcripts 5b release" des
                  cription="Annotations from MaizeSequence.org, filtered gene set 5b release" url="h
                  ttp://www.maizegenome.org" load_hint="Whole Sequence" label_field="id"/> </files>

                  It took then less than a minute to load the gene models.

                  Is this about what you would expect?

                  Show
                  ann.loraine Ann Loraine added a comment - I tested the 6.6 branch Revision: 9368 I reset prefs to default, launched the branch (using ant run) and then selected Z_mays_B73_Mar_2010. It took about three minutes for Z_mays_B73_Mar_2010 gene models to load with RNA-Seq data sets included in the annots.xml file. Next, I removed the data sets from the annots.xml file (by updating the annots.xml to an earlier revision, e.g., [aloraine@cci-vm12 Z_mays_B73_Mar_2010] $ svn up -r316 annots.xml U annots.xml Updated to revision 316. [aloraine@cci-vm12 Z_mays_B73_Mar_2010] $ more annots.xml <files> <file name="Z_mays_B73_Mar_2010.bed.gz" title="Maize Transcripts 5b release" des cription="Annotations from MaizeSequence.org, filtered gene set 5b release" url="h ttp://www.maizegenome.org" load_hint="Whole Sequence" label_field="id"/> </files> It took then less than a minute to load the gene models. Is this about what you would expect?
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                  hiralv Hiral Vora (Inactive) added a comment -

                  I have added a fix that should have improved the speed. Please test it from preview against current release.

                  Make sure that you clear your cache and preferences in each test.

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - I have added a fix that should have improved the speed. Please test it from preview against current release. Make sure that you clear your cache and preferences in each test.
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                  ann.loraine Ann Loraine added a comment -

                  I'm here at work today.
                  I cleared my cache and reset prefs to defaults.
                  I launched IGB r9368.
                  It's fast as can be expected!

                  Show
                  ann.loraine Ann Loraine added a comment - I'm here at work today. I cleared my cache and reset prefs to defaults. I launched IGB r9368. It's fast as can be expected!
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed version 6.7.0(9754) on Windows

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                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed version 6.7.0(9754) on Windows
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed Version 6.7.0 on Mac

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                  anuj Anuj Puram (Inactive) added a comment - Passed Version 6.7.0 on Mac
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                  smylapur Vineeth Mylapur (Inactive) added a comment -

                  Passed 7.0 (11928) on windows.

                  Show
                  smylapur Vineeth Mylapur (Inactive) added a comment - Passed 7.0 (11928) on windows.

                    People

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

                      • Created:
                        Updated:
                        Resolved: