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Merge pull request #2506 from opencb/TASK-6879-dev #1007

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Merge pull request #2506 from opencb/TASK-6879-dev

Merge pull request #2506 from opencb/TASK-6879-dev #1007

GitHub Actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests failed Sep 21, 2024 in 0s

1756 tests run, 107 skipped, 122 failed.

Annotations

Check failure on line 78 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/ClinicalInterpretationAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

ClinicalInterpretationAnalysisTest. 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:228)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:111)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:88)
	at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
	at org.opencb.opencga.analysis.clinical.ClinicalInterpretationAnalysisTest.setUp(ClinicalInterpretationAnalysisTest.java:78)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-12e3a55c-0192-0007-0001-dd5c58e447b9-8954624447207
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 46 more

Check failure on line 51 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/clinical/exomiser/ExomiserInterpretationAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

ExomiserInterpretationAnalysisTest. 

Error computing pedigree graph for family family
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family family
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:228)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUpCatalogManager(AbstractClinicalManagerTest.java:111)
	at org.opencb.opencga.catalog.managers.AbstractClinicalManagerTest.setUp(AbstractClinicalManagerTest.java:88)
	at org.opencb.opencga.analysis.clinical.ClinicalAnalysisUtilsTest.getClinicalTest(ClinicalAnalysisUtilsTest.java:52)
	at org.opencb.opencga.analysis.clinical.exomiser.ExomiserInterpretationAnalysisTest.setUp(ExomiserInterpretationAnalysisTest.java:51)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-12e31105-0192-0007-0001-1dacf5bffc94-8916669866425
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 46 more

Check failure on line 83 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/family/FamilyAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

FamilyAnalysisTest. 

Error computing pedigree graph for family Martinez-Martinez
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family Martinez-Martinez
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.family.FamilyAnalysisTest.createDummyFamily(FamilyAnalysisTest.java:337)
	at org.opencb.opencga.analysis.family.FamilyAnalysisTest.createDummyFamily(FamilyAnalysisTest.java:215)
	at org.opencb.opencga.analysis.family.FamilyAnalysisTest.setUpCatalogManager(FamilyAnalysisTest.java:102)
	at org.opencb.opencga.analysis.family.FamilyAnalysisTest.setUp(FamilyAnalysisTest.java:83)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExternalResource$1.evaluate(ExternalResource.java:54)
	at org.junit.rules.RunRules.evaluate(RunRules.java:20)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-130a8372-0192-0007-0001-0e9b0ba16aec-11501861852405
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 44 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testCohortStatsIndex[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-130c0268-0192-0007-0001-feb0033947d0-11599791120898
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testHRDetectParseResults[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-130d253f-0192-0007-0001-f491ee89b01e-11674230234239
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testVariantStatsTwoCohorts[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-130e3ebe-0192-0007-0001-1a27f1af8055-11746288255561
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testCellbaseConfigure[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-130f5549-0192-0007-0001-2dd47b1fee2c-11817591099782
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testPedigreeGraph[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131071f6-0192-0007-0001-b45d60ea34e7-11890470611544
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testVariantStats[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-13118628-0192-0007-0001-96e07d236979-11961172311582
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testGwas[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1312a30f-0192-0007-0001-29acb113cfe6-12034107287283
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testVariantStatsWithFilter[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1313b395-0192-0007-0001-ed8e51e54fd8-12103871328906
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testKnockoutGenesByBiotype[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1314c126-0192-0007-0001-339106363f2e-12172881379030
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testClinicalAnalysisLoading[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1315d7f1-0192-0007-0001-53a45ac5a152-12244252451692
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testHRDetect[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1316ef15-0192-0007-0001-f5f4cc141b5b-12315713415926
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testMalformedVcfFileIndex[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1317f24d-0192-0007-0001-6bcf3289da99-12382071723344
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testSampleStats[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1319050f-0192-0007-0001-0c437c4a2715-12452409558966
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testExportTped[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131a1731-0192-0007-0001-aa3704bd8634-12522589076677
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testGwasByPhenotype[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131b2397-0192-0007-0001-d82497e4b96c-12591296870450
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testMutationalSignatureFittingSNV[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131c377e-0192-0007-0001-ccde52c7fa4b-12661932817608
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 59 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testKnockoutGenesSpecificGenesAndBiotypeProteinCoding[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131d53b3-0192-0007-0001-3d506a856aec-12734686660946
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testCohortStats[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131e59a5-0192-0007-0001-e5c1bfbc9f7c-12801742325755
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testKnockoutGenesSpecificGenesAndBiotypeNMD[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-131f6543-0192-0007-0001-41c324300cb7-12870251602938
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testSampleStatsSampleFilter[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-132070a9-0192-0007-0001-f7eb82a38191-12938728460125
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testExportVep[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-1321830d-0192-0007-0001-2c4c940d331a-13008953853276
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more

Check failure on line 226 in opencga-analysis/src/test/java/org/opencb/opencga/analysis/variant/VariantAnalysisTest.java

See this annotation in the file changed.

@github-actions github-actions / Surefire tests report emr6.1 runShortTests,runMediumTests,runLongTests

VariantAnalysisTest.testExport[hadoop] 

Error computing pedigree graph for family f1
Raw output 
org.opencb.opencga.catalog.exceptions.CatalogDBException: Error computing pedigree graph for family f1
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:215)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.lambda$insert$0(FamilyMongoDBAdaptor.java:131)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.lambda$runTransaction$1(MongoDBAdaptor.java:126)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:211)
	at com.mongodb.client.internal.ClientSessionImpl.withTransaction(ClientSessionImpl.java:199)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:124)
	at org.opencb.opencga.catalog.db.mongodb.MongoDBAdaptor.runTransaction(MongoDBAdaptor.java:101)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:122)
	at org.opencb.opencga.catalog.managers.FamilyManager.create(FamilyManager.java:286)
	at org.opencb.opencga.analysis.variant.VariantAnalysisTest.setUp(VariantAnalysisTest.java:226)
	at sun.reflect.GeneratedMethodAccessor1801.invoke(Unknown Source)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at org.junit.runners.model.FrameworkMethod$1.runReflectiveCall(FrameworkMethod.java:59)
	at org.junit.internal.runners.model.ReflectiveCallable.run(ReflectiveCallable.java:12)
	at org.junit.runners.model.FrameworkMethod.invokeExplosively(FrameworkMethod.java:56)
	at org.junit.internal.runners.statements.RunBefores.invokeMethod(RunBefores.java:33)
	at org.junit.internal.runners.statements.RunBefores.evaluate(RunBefores.java:24)
	at org.junit.rules.ExpectedException$ExpectedExceptionStatement.evaluate(ExpectedException.java:258)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.BlockJUnit4ClassRunner$1.evaluate(BlockJUnit4ClassRunner.java:100)
	at org.junit.runners.ParentRunner.runLeaf(ParentRunner.java:366)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:103)
	at org.junit.runners.BlockJUnit4ClassRunner.runChild(BlockJUnit4ClassRunner.java:63)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.internal.runners.statements.RunAfters.evaluate(RunAfters.java:27)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.junit.runners.Suite.runChild(Suite.java:128)
	at org.junit.runners.Suite.runChild(Suite.java:27)
	at org.junit.runners.ParentRunner$4.run(ParentRunner.java:331)
	at org.junit.runners.ParentRunner$1.schedule(ParentRunner.java:79)
	at org.junit.runners.ParentRunner.runChildren(ParentRunner.java:329)
	at org.junit.runners.ParentRunner.access$100(ParentRunner.java:66)
	at org.junit.runners.ParentRunner$2.evaluate(ParentRunner.java:293)
	at org.junit.runners.ParentRunner$3.evaluate(ParentRunner.java:306)
	at org.junit.runners.ParentRunner.run(ParentRunner.java:413)
	at org.apache.maven.surefire.junitcore.JUnitCore.run(JUnitCore.java:49)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.createRequestAndRun(JUnitCoreWrapper.java:120)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.executeEager(JUnitCoreWrapper.java:95)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:75)
	at org.apache.maven.surefire.junitcore.JUnitCoreWrapper.execute(JUnitCoreWrapper.java:69)
	at org.apache.maven.surefire.junitcore.JUnitCoreProvider.invoke(JUnitCoreProvider.java:146)
	at org.apache.maven.surefire.booter.ForkedBooter.runSuitesInProcess(ForkedBooter.java:385)
	at org.apache.maven.surefire.booter.ForkedBooter.execute(ForkedBooter.java:162)
	at org.apache.maven.surefire.booter.ForkedBooter.run(ForkedBooter.java:507)
	at org.apache.maven.surefire.booter.ForkedBooter.main(ForkedBooter.java:495)
Caused by: java.io.IOException: Pedigree graph image file (pedigree.png) not found at /tmp/pedigree-graph-13229a55-0192-0007-0001-cbd0ac918f04-13080447513969
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getB64Image(PedigreeGraphUtils.java:90)
	at org.opencb.opencga.catalog.utils.PedigreeGraphUtils.getPedigreeGraph(PedigreeGraphUtils.java:47)
	at org.opencb.opencga.catalog.db.mongodb.FamilyMongoDBAdaptor.insert(FamilyMongoDBAdaptor.java:211)
	... 58 more
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