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ssadedin / ximmer

Ximmer is a system for CNV calling on exome and targeted genomic sequencing
http://ssadedin.github.io/ximmer/
GNU Lesser General Public License v2.1
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Failure in CNVDiagram produces empty js file #36

Open ssadedin opened 4 years ago

ssadedin commented 4 years ago

This error occurred while the Ximmer pipeline was drawing a large number of CNVs in parallel:

CNVDiagram      [22]    INFO    |12:30:05 Caller ed cnvs are: [7843497 - 7844054 (qual=6.59)]
CNVDiagram      [27]    INFO    |12:30:05 Caller ed cnvs are: [7843497 - 7844054 (qual=8.61)]
CNVDiagram      [22]    SEVERE  |12:30:06 Failed to draw CNV chrX:7843497-7844054
Exception:                                                                                                     
java.lang.NullPointerException
        at CNVDiagram$_drawCNV_closure17.doCall(CNVDiagram.groovy:444)
        at CNVDiagram.drawCNV(CNVDiagram.groovy:444)
        at CNVDiagram$_draw_closure10$_closure55.doCall(CNVDiagram.groovy:248)
        at CNVDiagram$_draw_closure10$_closure55.doCall(CNVDiagram.groovy)
        at gngs.Utils.time(Utils.groovy:102)
        at gngs.Utils.time(Utils.groovy)
        at CNVDiagram$_draw_closure10.doCall(CNVDiagram.groovy:246)
        at groovyx.gpars.pa.GParsPoolUtilHelper$_eachParallelPA_closure8.doCall(GParsPoolUtilHelper.groovy:192)
        at com.sun.proxy.$Proxy13.op(Unknown Source)
        at groovyx.gpars.extra166y.AbstractParallelAnyArray$OUPap.leafApply(AbstractParallelAnyArray.java:640)
        at groovyx.gpars.extra166y.PAS$FJOApply.atLeaf(PAS.java:147)
        at groovyx.gpars.extra166y.PAS$FJBase.internalCompute(PAS.java:118)
        at groovyx.gpars.extra166y.PAS$FJBase.compute(PAS.java:106)
        at jsr166y.RecursiveAction.exec(RecursiveAction.java:148)
        at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:305)
        at jsr166y.ForkJoinWorkerThread.execTask(ForkJoinWorkerThread.java:575)
        at jsr166y.ForkJoinPool.scan(ForkJoinPool.java:755)
        at jsr166y.ForkJoinPool.work(ForkJoinPool.java:617)
        at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:369)