java.lang.ArrayIndexOutOfBoundsException: -4

broadinstitute.org | 6 months ago
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    BaseRecalibrator: Array length mismatch detected. Malformed read — GATK-Forum

    broadinstitute.org | 6 months ago
    java.lang.ArrayIndexOutOfBoundsException: -4
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    broadinstitute.org | 2 years ago
    java.lang.ArrayIndexOutOfBoundsException: -4
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    GitHub | 2 years ago | dweer
    java.lang.ArrayIndexOutOfBoundsException: 0 at net.minecraft.world.chunk.storage.ExtendedBlockStorage.func_ 150819_a(SourceFile:34) at net.minecraft.world.chunk.storage.ExtendedBlockStorage.func_ 76672_e(SourceFile:121) at net.minecraft.world.chunk.storage.AnvilChunkLoader.func_7582 3_a(AnvilChunkLoader.java:441) at net.minecraft.world.chunk.storage.AnvilChunkLoader.checkedRe adChunkFromNBT__Async(AnvilChunkLoader.java:154) at net.minecraft.world.chunk.storage.AnvilChunkLoader.loadChunk __Async(AnvilChunkLoader.java:124) at net.minecraftforge.common.chunkio.ChunkIOProvider.callStage1 (ChunkIOProvider.java:20) at net.minecraftforge.common.chunkio.ChunkIOProvider.callStage1 (ChunkIOProvider.java:12) at net.minecraftforge.common.util.AsynchronousExecutor$Task.ini t(AsynchronousExecutor.java:151) at net.minecraftforge.common.util.AsynchronousExecutor$Task.ini tAsync(AsynchronousExecutor.java:96) at net.minecraftforge.common.util.AsynchronousExecutor$Task.run (AsynchronousExecutor.java:86) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPool Executor.java:1145) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoo lExecutor.java:615)
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    H2 database is corrupt suddenly after a huge number of records is inserted

    Google Groups | 2 years ago | Sourav Mandal
    java.lang.ArrayIndexOutOfBoundsException: 793" [50000-174] at org.h2.message.DbException.getJdbcSQLException(DbException.java:332 <http://h2database.com/html/source.html?file=org/h2/message/DbException.java&line=332&build=174>) at org.h2.message.DbException.get(DbException.java:161 at org.h2.message.DbException.convert(DbException.java:284 <http://h2database.com/html/source.html?file=org/h2/message/DbException.java&line=284&build=174>) at org.h2.table.RegularTable.removeRow(RegularTable.java:394 at org.h2.store.PageStore.redo(PageStore.java:1537 <http://h2database.com/html/source.html?file=org/h2/store/PageStore.java&line=1537&build=174>) at org.h2.store.PageStore.redoDelete(PageStore.java:1511 at org.h2.store.PageLog.recover(PageLog.java:334 <http://h2database.com/html/source.html?file=org/h2/store/PageLog.java&line=334&build=174>) at org.h2.store.PageStore.recover(PageStore.java:1371 at org.h2.store.PageStore.openExisting(PageStore.java:361 <http://h2database.com/html/source.html?file=org/h2/store/PageStore.java&line=361&build=174>) at org.h2.store.PageStore.open(PageStore.java:285 at org.h2.engine.Database.getPageStore(Database.java:2277 <http://h2database.com/html/source.html?file=org/h2/engine/Database.java&line=2277&build=174>) at org.h2.engine.Database.open(Database.java:610 at org.h2.engine.Database.openDatabase(Database.java:236 <http://h2database.com/html/source.html?file=org/h2/engine/Database.java&line=236&build=174>) at org.h2.engine.Database.<init>(Database.java:231 at org.h2.engine.Engine.openSession(Engine.java:56 <http://h2database.com/html/source.html?file=org/h2/engine/Engine.java&line=56&build=174>) at org.h2.engine.Engine.openSession(Engine.java:160 at org.h2.engine.Engine.createSessionAndValidate(Engine.java:139 <http://h2database.com/html/source.html?file=org/h2/engine/Engine.java&line=139&build=174>) at org.h2.engine.Engine.createSession(Engine.java:122 at org.h2.engine.Engine.createSession(Engine.java:28 <http://h2database.com/html/source.html?file=org/h2/engine/Engine.java&line=28&build=174>) at <http://h2database.com/html/source.html?file=org/h2/engine/SessionRemote.java&line=323&build=174>) at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:105 <http://h2database.com/html/source.html?file=org/h2/jdbc/JdbcConnection.java&line=105&build=174>) at org.h2.jdbc.JdbcConnection.<init>(JdbcConnection.java:90 at org.h2.Driver.connect(Driver.java:73 <http://h2database.com/html/source.html?file=org/h2/Driver.java&line=73&build=174>) at org.h2.server.web.WebServer.getConnection(WebServer.java:656 at org.h2.server.web.WebApp.login(WebApp.java:904 <http://h2database.com/html/source.html?file=org/h2/server/web/WebApp.java&line=904&build=174>) at org.h2.server.web.WebApp.process(WebApp.java:209 at org.h2.server.web.WebApp.processRequest(WebApp.java:168 <http://h2database.com/html/source.html?file=org/h2/server/web/WebApp.java&line=168&build=174>) at org.h2.server.web.WebThread.process(WebThread.java:138 at org.h2.server.web.WebThread.run(WebThread.java:94 <http://h2database.com/html/source.html?file=org/h2/server/web/WebThread.java&line=94&build=174>)

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    Root Cause Analysis

    1. java.lang.ArrayIndexOutOfBoundsException

      -4

      at org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon()
    2. org.broadinstitute.sting
      NanoScheduler$MapReduceJob.run
      1. org.broadinstitute.sting.utils.baq.BAQ.calcEpsilon(BAQ.java:158)
      2. org.broadinstitute.sting.utils.baq.BAQ.hmm_glocal(BAQ.java:246)
      3. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:542)
      4. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:595)
      5. org.broadinstitute.sting.utils.baq.BAQ.calcBAQFromHMM(BAQ.java:530)
      6. org.broadinstitute.sting.utils.baq.BAQ.baqRead(BAQ.java:663)
      7. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.calculateBAQArray(BaseRecalibrator.java:428)
      8. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:243)
      9. org.broadinstitute.sting.gatk.walkers.bqsr.BaseRecalibrator.map(BaseRecalibrator.java:112)
      10. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:203)
      11. org.broadinstitute.sting.gatk.traversals.TraverseReadsNano$TraverseReadsMap.apply(TraverseReadsNano.java:191)
      12. org.broadinstitute.sting.utils.nanoScheduler.NanoScheduler$MapReduceJob.run(NanoScheduler.java:468)
      12 frames
    3. Java RT
      Thread.run
      1. java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
      2. java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
      3. java.util.concurrent.FutureTask.run(FutureTask.java:166)
      4. java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
      5. java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
      6. java.lang.Thread.run(Thread.java:679)
      6 frames