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  1. Bug Repository
  2. BUG-274

Loading local .CHP file throws error on Windows

    Details

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

      Windows v9908

      Description

      1. Open IGB
      2. No species loaded
      3. Drag and drop in local .CHP file (attached)
      Throws error in console:

      MainWorkspaceManager:itemStateChanged hit
      MainWorkspaceManager:itemStateChanged hit
      Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
      WARNING: BGZF file has invalid uncompressedLength: -216092498
      java.lang.RuntimeException: BGZF file has invalid uncompressedLength: -216092498
      at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:376)
      at net.sf.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:361)
      at net.sf.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:109)
      at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:234)
      at net.sf.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:159)
      at com.affymetrix.genometryImpl.util.GeneralUtils.unzipFile(GeneralUtils.java:451)
      at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:602)
      at com.affymetrix.genometryImpl.util.LocalUrlCacher.convertURIToFile(LocalUrlCacher.java:589)
      at com.affymetrix.igb.featureloader.QuickLoad.getGenome(QuickLoad.java:379)
      at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:273)
      at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
      at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
      at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
      at javax.swing.SwingWorker$1.call(Unknown Source)
      at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
      at java.util.concurrent.FutureTask.run(Unknown Source)
      at javax.swing.SwingWorker.run(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
      at java.lang.Thread.run(Unknown Source)
      Caused by: java.lang.NegativeArraySizeException
      at net.sf.samtools.util.BlockCompressedInputStream.inflateBlock(BlockCompressedInputStream.java:374)
      ... 19 more
      Jan 23, 2012 1:24:05 PM com.affymetrix.igb.featureloader.QuickLoad logException
      WARNING: null
      java.lang.NullPointerException
      at com.affymetrix.igb.featureloader.QuickLoad.addMethodsToFeature(QuickLoad.java:306)
      at com.affymetrix.igb.featureloader.QuickLoad.loadAndAddAllSymmetries(QuickLoad.java:286)
      at com.affymetrix.igb.featureloader.QuickLoad.access$000(QuickLoad.java:46)
      at com.affymetrix.igb.featureloader.QuickLoad$1.runInBackground(QuickLoad.java:194)
      at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:38)
      at javax.swing.SwingWorker$1.call(Unknown Source)
      at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
      at java.util.concurrent.FutureTask.run(Unknown Source)
      at javax.swing.SwingWorker.run(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
      at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
      at java.lang.Thread.run(Unknown Source)
      MainWorkspaceManager:itemStateChanged hit
      MainWorkspaceManager:itemStateChanged hit

        Attachments

          Issue Links

            Activity

            kkubiak Katharine Kubiak (Inactive) created issue -
            hiralv Hiral Vora (Inactive) made changes -
            Field Original Value New Value
            Assignee Hiral Vora [ hiralv ] David Norris [ david ]
            david David Norris (Inactive) made changes -
            Assignee David Norris [ david ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            alyssa Alyssa Gulledge (Inactive) made changes -
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
            kkubiak Katharine Kubiak (Inactive) made changes -
            Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Open [ 1 ] Resolved [ 5 ]
            Assignee Alyssa Gulledge [ alyssa ]
            Resolution Fixed [ 1 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Status Resolved [ 5 ] Closed [ 6 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Project IGB 6.7 [ 10040 ] Bug Repository [ 10030 ]
            Key IGBB-229 BUG-274
            fwang4 Fuquan Wang (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            Assignee Fuquan Wang [ fwang4 ]
            fwang4 Fuquan Wang (Inactive) made changes -
            Assignee Fuquan Wang [ fwang4 ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
            fwang4 Fuquan Wang (Inactive) made changes -
            Comment [ Failed for 7.0.0 (11884) Mac:

            Arabidopsis file shows - "CHP file is in legacy format, cannot be loaded"
            TisMap.. files show - "Couldn't find genome data on server for CHP file, genome = Unknown Genome 1" ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
            kkubiak Katharine Kubiak (Inactive) made changes -
            Assignee Katharine Kubiak [ kkubiak ] Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] 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 ]
            richard Richard Linchangco (Inactive) made changes -
            Resolution Fixed [ 1 ]
            Status Closed [ 6 ] Reopened [ 4 ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Link This issue relates to BUG-622 [ BUG-622 ]
            richard Richard Linchangco (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ]
            alyssa Alyssa Gulledge (Inactive) made changes -
            Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
            hiralv Hiral Vora (Inactive) made changes -
            Assignee Hiral Vora [ hiralv ] 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 ]

              People

              • Assignee:
                Unassigned
                Reporter:
                kkubiak Katharine Kubiak (Inactive)
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                Dates

                • Created:
                  Updated:
                  Resolved: