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  1. User Support
  2. HELP-275

IGB and Oxford Nanopore Long reads....

          Details

          • Type: Support
          • Status: To-Do (View Workflow)
          • Priority: Major
          • Resolution: Unresolved
          • Labels:
            None

            Description

            From: Nicholas Schurch (Staff) <N.Schurch@dundee.ac.uk>
            To: "Norris, David" <dcnorris@uncc.edu>; "Ann.Loraine@uncc.edu" <Ann.Loraine@uncc.edu>,
            Mason Meyer <mmeyer20@uncc.edu>
            Date: \Mon, Aug 7, 2017 at 10:43 AM
            Subject: IGB and Oxford Nanopore Long reads....

            I was wondering if you had any experience trying to view long read RNA alignments from Oxford Nanopore or Pacbio in IGB. I have some ON DRS data that I've aligned with gmap. The bam alignments looks good from the aligner. When I load it in IGB everything slows to a crawl. Ona really small window with only one-or-two genes in it its 10s seconds to load and seconds to do anything else. With a large region it becomes unusable.

            I think the issue is related to parsing and understanding the long complex cigar strings for the long reads (they are error prone and indel heavy). If I have the console open when I load them I get lots of instances of 'String index out of range' like this:

            java.lang.StringIndexOutOfBoundsException: String index out of range: 143
            at java.lang.String.substring(String.java:1963)
            at com.affymetrix.genometry.symmetry.impl.BAMSym.interpretCigar(BAMSym.java:489)
            at com.affymetrix.genometry.symmetry.impl.BAMSym.getBaseQuality(BAMSym.java:440)
            at com.affymetrix.genometry.symmetry.impl.BAMSym.access$100(BAMSym.java:27)
            at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getBaseQuality(BAMSym.java:166)
            at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.getAverageQuality(BAMSym.java:177)
            at com.affymetrix.genometry.symmetry.impl.BAMSym$BamChildSingletonSeqSym.cloneProperties(BAMSym.java:222)
            at com.affymetrix.igb.tiers.TierLabelManager.determineProps(TierLabelManager.java:738)
            at com.affymetrix.igb.view.SeqMapView.determineProps(SeqMapView.java:2236)
            at com.affymetrix.igb.property.PropertyView.getPropertiesRow(PropertyView.java:234)
            at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2087)
            at com.affymetrix.igb.view.SeqMapView.setToolTip(SeqMapView.java:2045)
            at com.affymetrix.igb.view.SeqMapViewMouseListener.oldToolTip(SeqMapViewMouseListener.java:210)
            at com.affymetrix.igb.view.SeqMapViewMouseListener.mouseMoved(SeqMapViewMouseListener.java:192)
            at com.affymetrix.genoviz.widget.NeoWidget.heardMouseEvent(NeoWidget.java:1339)
            at com.affymetrix.genoviz.widget.NeoMap.heardMouseEvent(NeoMap.java:1589)
            at com.affymetrix.genoviz.widget.NeoAbstractWidget.mouseMoved(NeoAbstractWidget.java:827)
            at com.affymetrix.genoviz.bioviews.View.heardMouseEvent(View.java:978)
            at com.affymetrix.genoviz.bioviews.View.mouseMoved(View.java:887)
            at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329)
            at java.awt.AWTEventMulticaster.mouseMoved(AWTEventMulticaster.java:329)
            at java.awt.Component.processMouseMotionEvent(Component.java:6580)
            at javax.swing.JComponent.processMouseMotionEvent(JComponent.java:3342)
            at java.awt.Component.processEvent(Component.java:6304)
            at java.awt.Container.processEvent(Container.java:2236)
            at java.awt.Component.dispatchEventImpl(Component.java:4891)
            at java.awt.Container.dispatchEventImpl(Container.java:2294)
            at java.awt.Component.dispatchEvent(Component.java:4713)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
            at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4538)
            at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466)
            at java.awt.Container.dispatchEventImpl(Container.java:2280)
            at java.awt.Window.dispatchEventImpl(Window.java:2750)
            at java.awt.Component.dispatchEvent(Component.java:4713)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
            at java.awt.EventQueue.access$500(EventQueue.java:97)
            at java.awt.EventQueue$3.run(EventQueue.java:709)
            at java.awt.EventQueue$3.run(EventQueue.java:703)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
            at java.awt.EventQueue$4.run(EventQueue.java:731)
            at java.awt.EventQueue$4.run(EventQueue.java:729)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
            at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
            at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
            at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
            at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
            at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

            Any ideas what the problem is? I can probably send you the bam file to take a look at tomorrow if that'd help....

            Cheers,

            Nick Schurch

            Senior Bioinformatician,
            The Barton Group,
            Division of Computational Biology
            School of Life Sciences
            University of Dundee,
            Dundee, Scotland, UK, DD1 5EH.
            www.compbio.dundee.ac.uk

            Tel: +44 1382 388707
            Fax: +44 1382 345 893
            Twitter: @nickschurch
            The University of Dundee is registered Scottish charity: No.SC015096

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                relates to

                Bug - A problem which impairs or prevents the functions of the product. IGBF-1173 IGB slows down when viewing Oxford Nanopore Long reads

                • Major - Major loss of function.
                • Closed

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                  mason Mason Meyer (Inactive) added a comment -

                  From: "Ann.Loraine@uncc.edu" <Ann.Loraine@uncc.edu>
                  To: Nicholas Schurch (Staff) <N.Schurch@dundee.ac.uk>"Norris, David" <dcnorris@uncc.edu>;
                  Mason Meyer <mmeyer20@uncc.edu>
                  Date: Mon, Aug 7, 2017 at 12:07 PM
                  Subject: Re: IGB and Oxford Nanopore Long reads....

                  Thanks Nick for letting us know about this.
                  Yes, please - send us a simple BAM file we can use for debugging.
                  David is no longer working on the project so you can leave him off future emails.
                  Mason - can you make an issue in Jira for this?
                  We'll do our best to sort it out!

                  Yours,

                  Ann

                  Show
                  mason Mason Meyer (Inactive) added a comment - From: "Ann.Loraine@uncc.edu" <Ann.Loraine@uncc.edu> To: Nicholas Schurch (Staff) <N.Schurch@dundee.ac.uk>"Norris, David" <dcnorris@uncc.edu>; Mason Meyer <mmeyer20@uncc.edu> Date: Mon, Aug 7, 2017 at 12:07 PM Subject: Re: IGB and Oxford Nanopore Long reads.... Thanks Nick for letting us know about this. Yes, please - send us a simple BAM file we can use for debugging. David is no longer working on the project so you can leave him off future emails. Mason - can you make an issue in Jira for this? We'll do our best to sort it out! Yours, Ann
                  Hide
                  Permalink
                  mason Mason Meyer (Inactive) added a comment -

                  From: Mason Meyer <mmeyer20@uncc.edu>
                  To:Nicholas Schurch (Staff) <N.Schurch@dundee.ac.uk>, "Ann.Loraine@uncc.edu" <Ann.Loraine@uncc.edu>
                  Date: Mon, Aug 7, 2017 at 3:35 PM
                  Subject: Re: IGB and Oxford Nanopore Long reads....

                  Hello,

                  I have created IGBF-1175 (IGB slows down when viewing Oxford Nanopore Long reads), as requested.

                  Thanks for letting us know about this issue, Nick. Please send the simple BAM file whenever you have a chance and I will use it to look into the issue.

                  Thanks again,

                  Mason Meyer
                  IGB Support Specialist

                  Show
                  mason Mason Meyer (Inactive) added a comment - From: Mason Meyer <mmeyer20@uncc.edu> To:Nicholas Schurch (Staff) <N.Schurch@dundee.ac.uk>, "Ann.Loraine@uncc.edu" <Ann.Loraine@uncc.edu> Date: Mon, Aug 7, 2017 at 3:35 PM Subject: Re: IGB and Oxford Nanopore Long reads.... Hello, I have created IGBF-1175 (IGB slows down when viewing Oxford Nanopore Long reads), as requested. Thanks for letting us know about this issue, Nick. Please send the simple BAM file whenever you have a chance and I will use it to look into the issue. Thanks again, Mason Meyer IGB Support Specialist

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                      Reporter:
                      mason Mason Meyer (Inactive)
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                        Updated: