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]

Samebug tips1

Check if you're not creating unused SQL entities, as it might cause this exception.

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Solutions on the web1234

  • via GitHub by visze
    , 5 months ago
    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]
  • Table "journal" not found; SQL statement: select "sequence_number" from "journal" where "persistence_id" = ? order by "sequence_number" desc limit 1 [42102-192]
  • Table "journal" not found; SQL statement: select "sequence_number" from "journal" where "persistence_id" = ? order by "sequence_number" desc limit 1 [42102-191]
  • Stack trace

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

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