org.h2.jdbc.JdbcSQLException: Table "frequency" not found; SQL statement: SELECT rsid, dbSNPmaf, espEAmaf, espAAmaf, espAllmaf, exacAFRmaf, exacAMRmaf, exacEASmaf, exacFINmaf, exacNFEmaf, exacOTHmaf, exacSASmaf FROM frequency WHERE chromosome = ? AND position = ? AND ref = ? AND alt = ? ORDER BY dbsnpmaf desc, espeamaf desc, espaamaf desc, espallmaf desc [42102-192]

GitHub | visze | 3 months ago
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Root Cause Analysis

  1. org.h2.jdbc.JdbcSQLException

    Table "frequency" not found; SQL statement: SELECT rsid, dbSNPmaf, espEAmaf, espAAmaf, espAllmaf, exacAFRmaf, exacAMRmaf, exacEASmaf, exacFINmaf, exacNFEmaf, exacOTHmaf, exacSASmaf FROM frequency WHERE chromosome = ? AND position = ? AND ref = ? AND alt = ? ORDER BY dbsnpmaf desc, espeamaf desc, espaamaf desc, espallmaf desc [42102-192]

    at org.h2.message.DbException.getJdbcSQLException()
  2. H2 Database Engine
    JdbcConnection.prepareStatement
    1. org.h2.message.DbException.getJdbcSQLException(DbException.java:345)
    2. org.h2.message.DbException.get(DbException.java:179)
    3. org.h2.message.DbException.get(DbException.java:155)
    4. org.h2.command.Parser.readTableOrView(Parser.java:5388)
    5. org.h2.command.Parser.readTableFilter(Parser.java:1257)
    6. org.h2.command.Parser.parseSelectSimpleFromPart(Parser.java:1896)
    7. org.h2.command.Parser.parseSelectSimple(Parser.java:2044)
    8. org.h2.command.Parser.parseSelectSub(Parser.java:1890)
    9. org.h2.command.Parser.parseSelectUnion(Parser.java:1711)
    10. org.h2.command.Parser.parseSelect(Parser.java:1699)
    11. org.h2.command.Parser.parsePrepared(Parser.java:445)
    12. org.h2.command.Parser.parse(Parser.java:317)
    13. org.h2.command.Parser.parse(Parser.java:289)
    14. org.h2.command.Parser.prepareCommand(Parser.java:254)
    15. org.h2.engine.Session.prepareLocal(Session.java:560)
    16. org.h2.engine.Session.prepareCommand(Session.java:501)
    17. org.h2.jdbc.JdbcConnection.prepareCommand(JdbcConnection.java:1202)
    18. org.h2.jdbc.JdbcPreparedStatement.<init>(JdbcPreparedStatement.java:73)
    19. org.h2.jdbc.JdbcConnection.prepareStatement(JdbcConnection.java:290)
    19 frames
  3. org.monarchinitiative.exomiser
    DefaultFrequencyDao.getFrequencyData
    1. org.monarchinitiative.exomiser.core.dao.DefaultFrequencyDao.createPreparedStatement(DefaultFrequencyDao.java:113)
    2. org.monarchinitiative.exomiser.core.dao.DefaultFrequencyDao.getFrequencyData(DefaultFrequencyDao.java:90)
    2 frames
  4. Java RT
    Method.invoke
    1. sun.reflect.GeneratedMethodAccessor27.invoke(Unknown Source)
    2. sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    3. java.lang.reflect.Method.invoke(Method.java:498)
    3 frames
  5. Spring AOP
    ReflectiveMethodInvocation.proceed
    1. org.springframework.aop.support.AopUtils.invokeJoinpointUsingReflection(AopUtils.java:333)
    2. org.springframework.aop.framework.ReflectiveMethodInvocation.invokeJoinpoint(ReflectiveMethodInvocation.java:190)
    3. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:157)
    3 frames
  6. Spring Context
    CacheInterceptor.invoke
    1. org.springframework.cache.interceptor.CacheInterceptor$1.invoke(CacheInterceptor.java:52)
    2. org.springframework.cache.interceptor.CacheAspectSupport.invokeOperation(CacheAspectSupport.java:345)
    3. org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:414)
    4. org.springframework.cache.interceptor.CacheAspectSupport.execute(CacheAspectSupport.java:327)
    5. org.springframework.cache.interceptor.CacheInterceptor.invoke(CacheInterceptor.java:61)
    5 frames
  7. Spring AOP
    JdkDynamicAopProxy.invoke
    1. org.springframework.aop.framework.ReflectiveMethodInvocation.proceed(ReflectiveMethodInvocation.java:179)
    2. org.springframework.aop.framework.JdkDynamicAopProxy.invoke(JdkDynamicAopProxy.java:213)
    2 frames
  8. com.sun.proxy
    $Proxy43.getFrequencyData
    1. com.sun.proxy.$Proxy43.getFrequencyData(Unknown Source)
    1 frame
  9. org.monarchinitiative.exomiser
    PassOnlyAnalysisRunner.lambda$5
    1. org.monarchinitiative.exomiser.core.factories.VariantDataServiceImpl.getVariantFrequencyData(VariantDataServiceImpl.java:70)
    2. org.monarchinitiative.exomiser.core.filters.FrequencyDataProvider.provideVariantData(FrequencyDataProvider.java:36)
    3. org.monarchinitiative.exomiser.core.filters.AbstractFilterDataProvider.runFilter(AbstractFilterDataProvider.java:48)
    4. org.monarchinitiative.exomiser.core.filters.AbstractFilterDataProvider.runFilter(AbstractFilterDataProvider.java:1)
    5. org.monarchinitiative.exomiser.core.filters.SimpleVariantFilterRunner.runFilterAndAddResult(SimpleVariantFilterRunner.java:83)
    6. org.monarchinitiative.exomiser.core.filters.SimpleVariantFilterRunner.run(SimpleVariantFilterRunner.java:79)
    7. org.monarchinitiative.exomiser.core.analysis.PassOnlyAnalysisRunner.lambda$5(PassOnlyAnalysisRunner.java:71)
    7 frames
  10. Java RT
    ReferencePipeline.forEach
    1. java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    2. java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    3. java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
    4. java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
    5. java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    6. java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    7. java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    8. java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    9. java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    9 frames
  11. org.monarchinitiative.exomiser
    PassOnlyAnalysisRunner.lambda$1
    1. org.monarchinitiative.exomiser.core.analysis.PassOnlyAnalysisRunner.lambda$1(PassOnlyAnalysisRunner.java:71)
    1 frame
  12. Java RT
    ReferencePipeline.collect
    1. java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:174)
    2. java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    3. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    4. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    5. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    6. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    7. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    8. java.util.stream.ForEachOps$ForEachOp$OfRef.accept(ForEachOps.java:184)
    9. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    10. java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:175)
    11. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    12. java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1374)
    13. java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
    14. java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    15. java.util.stream.ForEachOps$ForEachOp.evaluateSequential(ForEachOps.java:151)
    16. java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(ForEachOps.java:174)
    17. java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    18. java.util.stream.ReferencePipeline.forEach(ReferencePipeline.java:418)
    19. java.util.stream.ReferencePipeline$7$1.accept(ReferencePipeline.java:270)
    20. java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
    21. java.util.Iterator.forEachRemaining(Iterator.java:116)
    22. java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
    23. java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
    24. java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
    25. java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
    26. java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
    27. java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
    27 frames
  13. org.monarchinitiative.exomiser
    Exomiser.run
    1. org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.loadAndFilterVariants(AbstractAnalysisRunner.java:170)
    2. org.monarchinitiative.exomiser.core.analysis.AbstractAnalysisRunner.run(AbstractAnalysisRunner.java:111)
    3. org.monarchinitiative.exomiser.core.Exomiser.run(Exomiser.java:60)
    3 frames
  14. de.charite.compbio
    Main.main
    1. de.charite.compbio.exomiserbenchmark.exomiser.ExomiserAnalysis.run(ExomiserAnalysis.java:35)
    2. de.charite.compbio.exomiserbenchmark.Main.runBenchmark(Main.java:226)
    3. de.charite.compbio.exomiserbenchmark.Main.run(Main.java:108)
    4. de.charite.compbio.exomiserbenchmark.Main.main(Main.java:92)
    4 frames