Class picard.util.LiftoverVcfTest

all > picard.util > LiftoverVcfTest
179

tests
1

failures
0

ignored
0.351s

duration
99%

successful

Failed tests

testUnreadableDictionary

org.testng.TestException: 
Method LiftoverVcfTest.testUnreadableDictionary()[pri:0, instance:picard.util.LiftoverVcfTest@13809363] should have thrown an exception of type class htsjdk.samtools.SAMException
	at app//org.testng.internal.invokers.ExpectedExceptionsHolder.noException(ExpectedExceptionsHolder.java:81)
	at app//org.testng.internal.invokers.TestInvoker.considerExceptions(TestInvoker.java:873)
	at app//org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:731)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at app//org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at app//org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at app//org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at app//org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at app//org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base@17.0.13/java.util.ArrayList.forEach(ArrayList.java:1511)
	at app//org.testng.TestRunner.privateRun(TestRunner.java:829)
	at app//org.testng.TestRunner.run(TestRunner.java:602)
	at app//org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at app//org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at app//org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at app//org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at app//org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at app//org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at app//org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at app//org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at app//org.testng.TestNG.runSuites(TestNG.java:1099)
	at app//org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base@17.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base@17.0.13/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base@17.0.13/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base@17.0.13/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at app//worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)

Tests

Test Duration Result
snpWithChangedRef[0]([VC test1 @ chr1:12 Q. of type=SNP alleles=[A*, C] attr={} GT=[[test1 A*/C AD 5,4 PL 40,0,60]] filters=, [VC test1 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={SwappedAlleles=true} GT=[[test1 C*/A AD 4,5 PL 60,0,40]] filters=) 0.001s passed
snpWithChangedRef[1]([VC test1 @ chr1:12 Q. of type=SNP alleles=[A*, C] attr={} GT=[[test1 C/C AD 0,10 PL 400,40,0]] filters=, [VC test1 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={SwappedAlleles=true} GT=[[test1 C*/C* AD 10,0 PL 0,40,400]] filters=) 0s passed
testChangingInfoFields 0.024s passed
testChangingTagArguments 0.014s passed
testFlipIndelWithOriginalAlleles[0]([VC test1 @ chr1:537-539 Q. of type=INDEL alleles=[TTT*, T] attr={END=539} GT=[[test1 TTT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-3 Q. of type=INDEL alleles=[CAA*, C] attr={END=3, OriginalAlleles=[TTT, T], ReverseComplementedAlleles=true} GT=[[test1 CAA*/C]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[10]([VC test11 @ chr1:540 Q. of type=INDEL alleles=[G*, GG] attr={} GT=[[test1 G*/GG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={OriginalAlleles=[G, GG], ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[11]([VC test12 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, TTTTG] attr={} GT=[[test1 TTTT*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={OriginalAlleles=[TTTT, TTTTG], ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=) 0.001s passed
testFlipIndelWithOriginalAlleles[12]([VC test13 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, *, TTTTG] attr={} GT=[[test1 TTTT*/*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=MIXED alleles=[C*, *, CC] attr={OriginalAlleles=[TTTT, TTTTG, *], ReverseComplementedAlleles=true} GT=[[test1 C*/*/CC]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[13]([VC test14 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, *, A] attr={} GT=[[test1 ACGT*/*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, *, A] attr={OriginalAlleles=[ACGT, A, *], ReverseComplementedAlleles=true} GT=[[test1 AACG*/*/A]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[14]([VC test14 @ chr1:527-528 Q. of type=INDEL alleles=[AC*, *] attr={} GT=[[test1 AC*/*]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13-14 Q. of type=INDEL alleles=[GT*, *] attr={OriginalAlleles=[AC, *], ReverseComplementedAlleles=true} GT=[[test1 GT*/*]] filters=) 0.001s passed
testFlipIndelWithOriginalAlleles[1]([VC test2 @ chr1:537 Q. of type=INDEL alleles=[T*, TTT] attr={} GT=[[test1 T*/TTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CAA] attr={OriginalAlleles=[T, TTT], ReverseComplementedAlleles=true} GT=[[test1 C*/CAA]] filters=) 0.001s passed
testFlipIndelWithOriginalAlleles[2]([VC test3 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, A] attr={} GT=[[test1 ACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, A] attr={OriginalAlleles=[ACGT, A], ReverseComplementedAlleles=true} GT=[[test1 AACG*/A]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[3]([VC test4 @ chr1:527 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10 Q. of type=INDEL alleles=[A*, AACG] attr={OriginalAlleles=[A, ACGT], ReverseComplementedAlleles=true} GT=[[test1 A*/AACG]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[4]([VC test5 @ chr1:540 Q. of type=INDEL alleles=[G*, GTT] attr={} GT=[[test1 G*/GTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, AAC] attr={OriginalAlleles=[G, GTT], ReverseComplementedAlleles=true} GT=[[test1 C*/AAC]] filters=) 0.001s passed
testFlipIndelWithOriginalAlleles[5]([VC test6 @ chr1:541 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, null) 0s passed
testFlipIndelWithOriginalAlleles[6]([VC test7 @ chr1:529-531 Q. of type=INDEL alleles=[GTT*, ACGT] attr={} GT=[[test1 GTT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:11-12 Q. of type=INDEL alleles=[AC*, CGT] attr={OriginalAlleles=[GTT, ACGT], ReverseComplementedAlleles=true} GT=[[test1 AC*/CGT]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[7]([VC test8 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, ATT] attr={} GT=[[test1 ACGT*/ATT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:12-13 Q. of type=INDEL alleles=[CG*, A] attr={OriginalAlleles=[ACGT, ATT], ReverseComplementedAlleles=true} GT=[[test1 CG*/A]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[8]([VC test9 @ chr1:511 Q. of type=INDEL alleles=[T*, TAG] attr={} GT=[[test1 T*/TAG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={OriginalAlleles=[T, TAG], ReverseComplementedAlleles=true} GT=[[test1 A*/ACT]] filters=) 0s passed
testFlipIndelWithOriginalAlleles[9]([VC test10 @ chr1:540 Q. of type=INDEL alleles=[G*, GA] attr={} GT=[[test1 G*/GA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, TC] attr={OriginalAlleles=[G, GA], ReverseComplementedAlleles=true} GT=[[test1 C*/TC]] filters=) 0.001s passed
testFlipIndel[0]([VC test1 @ chr1:537-539 Q. of type=INDEL alleles=[TTT*, T] attr={END=539} GT=[[test1 TTT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-3 Q. of type=INDEL alleles=[CAA*, C] attr={END=3, ReverseComplementedAlleles=true} GT=[[test1 CAA*/C]] filters=) 0.001s passed
testFlipIndel[10]([VC test11 @ chr1:540 Q. of type=INDEL alleles=[G*, GG] attr={} GT=[[test1 G*/GG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=) 0s passed
testFlipIndel[11]([VC test12 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, TTTTG] attr={} GT=[[test1 TTTT*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CC]] filters=) 0s passed
testFlipIndel[12]([VC test13 @ chr1:536-539 Q. of type=INDEL alleles=[TTTT*, *, TTTTG] attr={} GT=[[test1 TTTT*/*/TTTTG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=MIXED alleles=[C*, *, CC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/*/CC]] filters=) 0.001s passed
testFlipIndel[13]([VC test14 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, *, A] attr={} GT=[[test1 ACGT*/*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, *, A] attr={ReverseComplementedAlleles=true} GT=[[test1 AACG*/*/A]] filters=) 0s passed
testFlipIndel[14]([VC test14 @ chr1:527-528 Q. of type=INDEL alleles=[AC*, *] attr={} GT=[[test1 AC*/*]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13-14 Q. of type=INDEL alleles=[GT*, *] attr={ReverseComplementedAlleles=true} GT=[[test1 GT*/*]] filters=) 0.001s passed
testFlipIndel[1]([VC test2 @ chr1:537 Q. of type=INDEL alleles=[T*, TTT] attr={} GT=[[test1 T*/TTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CAA] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/CAA]] filters=) 0s passed
testFlipIndel[2]([VC test3 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, A] attr={} GT=[[test1 ACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-13 Q. of type=INDEL alleles=[AACG*, A] attr={ReverseComplementedAlleles=true} GT=[[test1 AACG*/A]] filters=) 0.001s passed
testFlipIndel[3]([VC test4 @ chr1:527 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10 Q. of type=INDEL alleles=[A*, AACG] attr={ReverseComplementedAlleles=true} GT=[[test1 A*/AACG]] filters=) 0s passed
testFlipIndel[4]([VC test5 @ chr1:540 Q. of type=INDEL alleles=[G*, GTT] attr={} GT=[[test1 G*/GTT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, AAC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/AAC]] filters=) 0s passed
testFlipIndel[5]([VC test6 @ chr1:541 Q. of type=INDEL alleles=[A*, ACGT] attr={} GT=[[test1 A*/ACGT]] filters=, ReferenceSequence chr1, null) 0s passed
testFlipIndel[6]([VC test7 @ chr1:529-531 Q. of type=INDEL alleles=[GTT*, ACGT] attr={} GT=[[test1 GTT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:11-12 Q. of type=INDEL alleles=[AC*, CGT] attr={ReverseComplementedAlleles=true} GT=[[test1 AC*/CGT]] filters=) 0.001s passed
testFlipIndel[7]([VC test8 @ chr1:527-530 Q. of type=INDEL alleles=[ACGT*, ATT] attr={} GT=[[test1 ACGT*/ATT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:12-13 Q. of type=INDEL alleles=[CG*, A] attr={ReverseComplementedAlleles=true} GT=[[test1 CG*/A]] filters=) 0s passed
testFlipIndel[8]([VC test9 @ chr1:511 Q. of type=INDEL alleles=[T*, TAG] attr={} GT=[[test1 T*/TAG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={ReverseComplementedAlleles=true} GT=[[test1 A*/ACT]] filters=) 0s passed
testFlipIndel[9]([VC test10 @ chr1:540 Q. of type=INDEL alleles=[G*, GA] attr={} GT=[[test1 G*/GA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, TC] attr={ReverseComplementedAlleles=true} GT=[[test1 C*/TC]] filters=) 0.001s passed
testLeftAlignInRepeatingStart 0s passed
testLeftAlignVariants[0]([VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CCAAA] attr={} GT=[[test1 CAAA*/CCAAA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CC] attr={} GT=[[test1 C*/CC]] filters=) 0s passed
testLeftAlignVariants[10]([VC test2-8 @ chr1:8 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-8 @ chr1:8 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0.001s passed
testLeftAlignVariants[11]([VC test2-9 @ chr1:9 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-9 @ chr1:9 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[12]([VC test2-10 @ chr1:10 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-10 @ chr1:10 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[13]([VC test2-11 @ chr1:11 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-11 @ chr1:11 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[14]([VC test2-12 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-12 @ chr1:12 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[15]([VC test2-13 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-13 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=) 0.001s passed
testLeftAlignVariants[16]([VC test2-14 @ chr1:14 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-14 @ chr1:14 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[17]([VC test2-15 @ chr1:15 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-15 @ chr1:15 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[18]([VC test2-16 @ chr1:16 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-16 @ chr1:16 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0.006s passed
testLeftAlignVariants[19]([VC test2-17 @ chr1:17 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-17 @ chr1:17 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=) 0s passed
testLeftAlignVariants[1]([VC test1_5 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=) 0s passed
testLeftAlignVariants[20]([VC test2-18 @ chr1:18 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-18 @ chr1:18 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[21]([VC test2-19 @ chr1:19 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-19 @ chr1:19 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0.001s passed
testLeftAlignVariants[22]([VC test2-20 @ chr1:20 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-20 @ chr1:20 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[23]([VC test2-21 @ chr1:21 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-21 @ chr1:21 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[24]([VC test2-22 @ chr1:22 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-22 @ chr1:22 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[25]([VC test2-23 @ chr1:23 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-23 @ chr1:23 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[26]([VC test2-24 @ chr1:24 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-24 @ chr1:24 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[27]([VC test2-25 @ chr1:25 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-25 @ chr1:25 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0.001s passed
testLeftAlignVariants[28]([VC test2-26 @ chr1:26 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-26 @ chr1:26 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[29]([VC test2-27 @ chr1:27 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-27 @ chr1:27 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[2]([VC test1_5 @ chr1:13 Q. of type=MIXED alleles=[G*, <*>, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:13 Q. of type=MIXED alleles=[G*, <*>, A] attr={} GT=[[test1 G*/A]] filters=) 0s passed
testLeftAlignVariants[30]([VC test2-28 @ chr1:28 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-28 @ chr1:28 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[31]([VC test2-29 @ chr1:29 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-29 @ chr1:29 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[32]([VC test2-30 @ chr1:30 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-30 @ chr1:30 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[33]([VC test2-31 @ chr1:31 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-31 @ chr1:31 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[34]([VC test2-32 @ chr1:32 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=, ReferenceSequence chr1, [VC test2-32 @ chr1:32 Q. of type=SNP alleles=[G*, A] attr={} GT=[[test1 G*/A]] filters=) 0s passed
testLeftAlignVariants[35]([VC test2-33 @ chr1:33 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=, ReferenceSequence chr1, [VC test2-33 @ chr1:33 Q. of type=SNP alleles=[T*, A] attr={} GT=[[test1 T*/A]] filters=) 0s passed
testLeftAlignVariants[36]([VC test3-2 @ chr1:2-3 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[37]([VC test3-3 @ chr1:3-4 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[38]([VC test3-4 @ chr1:4-5 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[39]([VC test3-5 @ chr1:5-6 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[3]([VC test2-1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, ReferenceSequence chr1, [VC test2-1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0s passed
testLeftAlignVariants[40]([VC test3-6 @ chr1:6-7 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0.001s passed
testLeftAlignVariants[41]([VC test3-7 @ chr1:7-8 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[42]([VC test3-8 @ chr1:8-9 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[43]([VC test3-9 @ chr1:9-10 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[44]([VC test3-10 @ chr1:10-11 Q. of type=INDEL alleles=[AA*, A] attr={} GT=[[test1 AA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1-2 Q. of type=INDEL alleles=[CA*, C] attr={} GT=[[test1 CA*/C]] filters=) 0s passed
testLeftAlignVariants[45]([VC test4-2 @ chr1:2 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0.001s passed
testLeftAlignVariants[46]([VC test4-3 @ chr1:3 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[47]([VC test4-4 @ chr1:4 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[48]([VC test4-5 @ chr1:5 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[49]([VC test4-6 @ chr1:6 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[4]([VC test2-2 @ chr1:2 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-2 @ chr1:2 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0.001s passed
testLeftAlignVariants[50]([VC test4-7 @ chr1:7 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0.001s passed
testLeftAlignVariants[51]([VC test4-8 @ chr1:8 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[52]([VC test4-9 @ chr1:9 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[53]([VC test4-10 @ chr1:10 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[54]([VC test4-11 @ chr1:11 Q. of type=INDEL alleles=[A*, AA] attr={} GT=[[test1 A*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:1 Q. of type=INDEL alleles=[C*, CA] attr={} GT=[[test1 C*/CA]] filters=) 0s passed
testLeftAlignVariants[55]([VC test5-20 @ chr1:20-21 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0.001s passed
testLeftAlignVariants[56]([VC test5-22 @ chr1:22-23 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[57]([VC test5-24 @ chr1:24-25 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[58]([VC test5-26 @ chr1:26-27 Q. of type=INDEL alleles=[CT*, CTCT] attr={} GT=[[test1 CT*/CTCT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[59]([VC test6-21 @ chr1:21-22 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[5]([VC test2-3 @ chr1:3 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-3 @ chr1:3 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[60]([VC test6-23 @ chr1:23-24 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0.001s passed
testLeftAlignVariants[61]([VC test6-25 @ chr1:25-26 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[62]([VC test6-27 @ chr1:27-28 Q. of type=INDEL alleles=[TC*, TCTC] attr={} GT=[[test1 TC*/TCTC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19 Q. of type=INDEL alleles=[A*, ACT] attr={} GT=[[test1 A*/ACT]] filters=) 0s passed
testLeftAlignVariants[63]([VC test7-20 @ chr1:20-23 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[64]([VC test7-22 @ chr1:22-25 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[65]([VC test7-24 @ chr1:24-27 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0.001s passed
testLeftAlignVariants[66]([VC test7-26 @ chr1:26-29 Q. of type=INDEL alleles=[CTCT*, CT] attr={} GT=[[test1 CTCT*/CT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[67]([VC test8-21 @ chr1:21-24 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[68]([VC test8-23 @ chr1:23-26 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[69]([VC test8-25 @ chr1:25-28 Q. of type=INDEL alleles=[TCTC*, TC] attr={} GT=[[test1 TCTC*/TC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:19-21 Q. of type=INDEL alleles=[ACT*, A] attr={} GT=[[test1 ACT*/A]] filters=) 0s passed
testLeftAlignVariants[6]([VC test2-4 @ chr1:4 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-4 @ chr1:4 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[70]([VC test9-10-14 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[71]([VC test9-10-15 @ chr1:10-15 Q. of type=INDEL alleles=[AACGTA*, AA] attr={} GT=[[test1 AACGTA*/AA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0.001s passed
testLeftAlignVariants[72]([VC test9-10-16 @ chr1:10-16 Q. of type=INDEL alleles=[AACGTAC*, AAC] attr={} GT=[[test1 AACGTAC*/AAC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[73]([VC test9-10-17 @ chr1:10-17 Q. of type=INDEL alleles=[AACGTACG*, AACG] attr={} GT=[[test1 AACGTACG*/AACG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[74]([VC test9-10-18 @ chr1:10-18 Q. of type=INDEL alleles=[AACGTACGT*, AACGT] attr={} GT=[[test1 AACGTACGT*/AACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[75]([VC test9-10-19 @ chr1:10-19 Q. of type=INDEL alleles=[AACGTACGTA*, AACGTA] attr={} GT=[[test1 AACGTACGTA*/AACGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[76]([VC test9-11-15 @ chr1:11-15 Q. of type=INDEL alleles=[ACGTA*, A] attr={} GT=[[test1 ACGTA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0.001s passed
testLeftAlignVariants[77]([VC test9-11-16 @ chr1:11-16 Q. of type=INDEL alleles=[ACGTAC*, AC] attr={} GT=[[test1 ACGTAC*/AC]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[78]([VC test9-11-17 @ chr1:11-17 Q. of type=INDEL alleles=[ACGTACG*, ACG] attr={} GT=[[test1 ACGTACG*/ACG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[79]([VC test9-11-18 @ chr1:11-18 Q. of type=INDEL alleles=[ACGTACGT*, ACGT] attr={} GT=[[test1 ACGTACGT*/ACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[7]([VC test2-5 @ chr1:5 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-5 @ chr1:5 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[80]([VC test9-11-19 @ chr1:11-19 Q. of type=INDEL alleles=[ACGTACGTA*, ACGTA] attr={} GT=[[test1 ACGTACGTA*/ACGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[81]([VC test9-12-16 @ chr1:12-16 Q. of type=INDEL alleles=[CGTAC*, C] attr={} GT=[[test1 CGTAC*/C]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[82]([VC test9-12-17 @ chr1:12-17 Q. of type=INDEL alleles=[CGTACG*, CG] attr={} GT=[[test1 CGTACG*/CG]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[83]([VC test9-12-18 @ chr1:12-18 Q. of type=INDEL alleles=[CGTACGT*, CGT] attr={} GT=[[test1 CGTACGT*/CGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[84]([VC test9-12-19 @ chr1:12-19 Q. of type=INDEL alleles=[CGTACGTA*, CGTA] attr={} GT=[[test1 CGTACGTA*/CGTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[85]([VC test9-13-17 @ chr1:13-17 Q. of type=INDEL alleles=[GTACG*, G] attr={} GT=[[test1 GTACG*/G]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[86]([VC test9-13-18 @ chr1:13-18 Q. of type=INDEL alleles=[GTACGT*, GT] attr={} GT=[[test1 GTACGT*/GT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[87]([VC test9-13-19 @ chr1:13-19 Q. of type=INDEL alleles=[GTACGTA*, GTA] attr={} GT=[[test1 GTACGTA*/GTA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[88]([VC test9-14-18 @ chr1:14-18 Q. of type=INDEL alleles=[TACGT*, T] attr={} GT=[[test1 TACGT*/T]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[89]([VC test9-14-19 @ chr1:14-19 Q. of type=INDEL alleles=[TACGTA*, TA] attr={} GT=[[test1 TACGTA*/TA]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[8]([VC test2-6 @ chr1:6 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-6 @ chr1:6 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLeftAlignVariants[90]([VC test9-15-19 @ chr1:15-19 Q. of type=INDEL alleles=[ACGTA*, A] attr={} GT=[[test1 ACGTA*/A]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A] attr={} GT=[[test1 AACGT*/A]] filters=) 0s passed
testLeftAlignVariants[91]([VC test12 @ chr1:9-18 Q. of type=INDEL alleles=[AAACGTACGT*, AAACGACGT, AAACGT, AAACGTACGTACGT] attr={} GT=[[sample1 AAACGTACGT*/AAACGT],[sample2 AAACGTACGT*/AAACGACGT],[sample3 AAACGTACGT*/AAACGTACGTACGT],[sample_non_ref_het AAACGACGT/AAACGT]] filters=, ReferenceSequence chr1, [VC test1 @ chr1:10-14 Q. of type=INDEL alleles=[AACGT*, A, AACG, AACGTACGT] attr={} GT=[[sample1 AACGT*/A],[sample2 AACGT*/AACG],[sample3 AACGT*/AACGTACGT],[sample_non_ref_het A/AACG]] filters=) 0.001s passed
testLeftAlignVariants[9]([VC test2-7 @ chr1:7 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, ReferenceSequence chr1, [VC test2-7 @ chr1:7 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverIndels[0](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0.001s passed
testLiftOverIndels[10](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) 0.003s passed
testLiftOverIndels[11](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) 0s passed
testLiftOverIndels[12](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test11 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, null) 0s passed
testLiftOverIndels[13](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test12 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0.001s passed
testLiftOverIndels[14](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test13 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverIndels[1](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC testWithEND @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={END=4} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={END=4} GT=[[test1 CAAA*/CAA]] filters=) 0s passed
testLiftOverIndels[2](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test2 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=) 0s passed
testLiftOverIndels[3](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test3 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0s passed
testLiftOverIndels[4](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test4 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverIndels[5](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test5_WITH_END @ chr1:538-541 Q. of type=INDEL alleles=[AAAA*, AAA] attr={END=541} GT=[[test1 AAAA*/AAA]] filters=, null) 0s passed
testLiftOverIndels[6](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test6_withEND @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={END=541} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={END=546} GT=[[test1 A*/T]] filters=) 0.001s passed
testLiftOverIndels[7](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test7 @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverIndels[8](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test8 @ chr1:1040 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverIndels[9](htsjdk.samtools.liftover.LiftOver@616a83e9, ReferenceSequence chr1 dna:chromosome chromosome:GRCh37:1:1:1085:1, [VC test9 @ chr1:1037-1040 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1042-1045 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0s passed
testLiftOverNoCallAndSymbolic[0](htsjdk.samtools.liftover.LiftOver@60f7c642, [VC test1 @ chr1:10 Q. of type=MIXED alleles=[C*, <*>, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@6a27f2a2} GT=[[test1 ./.]] filters=, [VC test1 @ chr1:10 Q. of type=MIXED alleles=[C*, <*>, T] attr={OriginalContig=chr1, OriginalStart=10, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@e38808c} GT=[[test1 ./.]] filters=, false) 0s passed
testLiftOverNoCallAndSymbolic[1](htsjdk.samtools.liftover.LiftOver@60f7c642, [VC test2 @ chr1:10 Q. of type=SNP alleles=[C*, *, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@6a27f2a2} GT=[[test1 */T]] filters=, [VC test1 @ chr1:10 Q. of type=SNP alleles=[C*, *, T] attr={OriginalContig=chr1, OriginalStart=10, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@e38808c} GT=[[test1 */T]] filters=, false) 0.001s passed
testLiftOverNoCallAndSymbolic[2](htsjdk.samtools.liftover.LiftOver@729859fd, [VC test3 @ chr1:537 Q. of type=MIXED alleles=[C*, *, <*>, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@6a27f2a2} GT=[[test1 */T]] filters=, [VC test1 @ chr1:4 Q. of type=MIXED alleles=[G*, *, <*>, A] attr={OriginalAlleles=[C, T, *, <*>], OriginalContig=chr1, OriginalStart=537, ReverseComplementedAlleles=true, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@e38808c} GT=[[test1 */A]] filters=, true) 0s passed
testLiftOverNoCallAndSymbolic[3](htsjdk.samtools.liftover.LiftOver@729859fd, [VC test4 @ chr1:536 Q. of type=MIXED alleles=[C*, <*>, T] attr={TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@6a27f2a2} GT=[[test1 ./T]] filters=, [VC test1 @ chr1:5 Q. of type=MIXED alleles=[G*, <*>, A] attr={OriginalAlleles=[C, T, <*>], OriginalContig=chr1, OriginalStart=536, ReverseComplementedAlleles=true, TEST_ATTRIBUTE=1, TEST_ATTRIBUTE2=Hi, TEST_ATTRIBUTE3=[D@e38808c} GT=[[test1 ./A]] filters=, true) 0.001s passed
testLiftOverSimpleIndels[0](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=, [VC test1 @ chr1:1 Q. of type=SNP alleles=[C*, A] attr={} GT=[[test1 C*/A]] filters=) 0.001s passed
testLiftOverSimpleIndels[10](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test9 @ chr1:1038-1041 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) 0s passed
testLiftOverSimpleIndels[11](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test10 @ chr1:1045-1048 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) 0s passed
testLiftOverSimpleIndels[12](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test11 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, null) 0s passed
testLiftOverSimpleIndels[13](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test12 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1046-1049 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0s passed
testLiftOverSimpleIndels[14](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test13 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1046 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverSimpleIndels[1](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC testWithEND @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=) 0s passed
testLiftOverSimpleIndels[2](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test2 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=, [VC test1 @ chr1:1-4 Q. of type=INDEL alleles=[CAAA*, CAA] attr={} GT=[[test1 CAAA*/CAA]] filters=) 0s passed
testLiftOverSimpleIndels[3](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test3 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:537-540 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0s passed
testLiftOverSimpleIndels[4](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test4 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:540 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverSimpleIndels[5](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test5_WITH_END @ chr1:538-541 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, null) 0s passed
testLiftOverSimpleIndels[6](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test6_withEND @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverSimpleIndels[7](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test7 @ chr1:541 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:546 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0s passed
testLiftOverSimpleIndels[8](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test8 @ chr1:1040 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=, [VC test1 @ chr1:1045 Q. of type=SNP alleles=[A*, T] attr={} GT=[[test1 A*/T]] filters=) 0.001s passed
testLiftOverSimpleIndels[9](htsjdk.samtools.liftover.LiftOver@7ebce2f2, [VC test9 @ chr1:1037-1040 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=, [VC test1 @ chr1:1042-1045 Q. of type=INDEL alleles=[AAAA*, AAA] attr={} GT=[[test1 AAAA*/AAA]] filters=) 0s passed
testMissingContigInReference[0](false, 1) 0.020s passed
testMissingContigInReference[1](true, 0) 0.014s passed
testNoDictionary 0.010s passed
testReverseComplementFailureDoesNotErrorOut 0s passed
testReverseComplementWithRepeats 0s passed
testReverseComplementedIndels[0](testLiftoverBiallelicIndels.vcf, 5, 0) 0.019s passed
testReverseComplementedIndels[1](testLiftoverMultiallelicIndels.vcf, 2, 0) 0.013s passed
testReverseComplementedIndels[2](testLiftoverFailingVariants.vcf, 3, 0) 0.019s passed
testReverseComplementedIndels[3](testLiftoverMixedVariants.vcf, 4, 0) 0.013s passed
testReverseComplementedIndels[4](testLiftoverMismatchingSnps.vcf, 3, 1) 0.014s passed
testUnreadableDictionary 0.018s failed
testVcfSorted[0](false) 0.020s passed
testVcfSorted[1](true) 0.011s passed
testWriteOriginalPosition[0](false) 0.012s passed
testWriteOriginalPosition[1](true) 0.018s passed
testWriteVcfWithFlippedAlleles[0](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAlleles.reject.vcf, testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta, testdata/picard/vcf/LiftOver/test.two.block.over.chain) 0.025s passed
testWriteVcfWithFlippedAlleles[1](testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithFlippedAllelesNegativeChain.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain) 0.025s passed
testWriteVcfWithFlippedAlleles[2](testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.lift.vcf, testdata/picard/vcf/LiftOver/vcfWithMixed.reject.vcf, testdata/picard/vcf/LiftOver/dummy.reference.fasta, testdata/picard/vcf/LiftOver/test.over.chain) 0.020s passed

Standard error

[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 3 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3 / 3 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3
INFO	2025-04-24 13:18:05	LiftoverVcf	2 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf   --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 3 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	2 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	66.6667% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 1 / 3 (33.3333%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 1
WARNING	2025-04-24 13:18:05	LiftoverVcf	2 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
INFO	2025-04-24 13:18:05	LiftOver	Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0)
INFO	2025-04-24 13:18:05	LiftOver	Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0)
INFO	2025-04-24 13:18:05	LiftOver	Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0)
INFO	2025-04-24 13:18:05	LiftOver	Interval null failed to match chain 2 because intersection length 3 < minMatchSize 4.0 (0.75 < 1.0)
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --WARN_ON_MISSING_CONTIG false --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
ERROR	2025-04-24 13:18:05	LiftoverVcf	Encountered a contig, missingContig that is not part of the target reference.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverUsingMissingContig.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.badContig.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --WARN_ON_MISSING_CONTIG true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
WARNING	2025-04-24 13:18:05	LiftoverVcf	Encountered a contig, missingContig that is not part of the target reference.
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 2 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	2 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	100.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 0 / 1 (0.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	missingContig: 0 / 1 (0.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	no successfully lifted variants
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/tmpoutput5696070785534845866.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/tmpreject13500105465573308044.vcf --REFERENCE_SEQUENCE /tmp/copy11788363408749746314/refCopy.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
ERROR	2025-04-24 13:18:05	LiftoverVcf	Reference /tmp/copy11788363408749746314/refCopy.fasta must have an associated Dictionary .dict file in the same directory.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMultiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 2 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 2 / 2 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 2
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverFailingVariants.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 3 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3 / 3 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3
INFO	2025-04-24 13:18:05	LiftoverVcf	2 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 4 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 4 / 4 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 4
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 4 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	1 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	25.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3 / 4 (75.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 3
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/tmpouput10624318668958246255.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/tmpreject13213611683770489919.vcf --REFERENCE_SEQUENCE /tmp/copy8669213791954570506/refCopy.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --DISABLE_SORT false --CREATE_INDEX true --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --DISABLE_SORT true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and writing the output file. Variants will not be sorted.
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --WRITE_ORIGINAL_POSITION false --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverBiallelicIndels.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --WRITE_ORIGINAL_POSITION true --CREATE_INDEX false --REFERENCE_SEQUENCE testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --RECOVER_SWAPPED_REF_ALT false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:05	LiftoverVcf	Processed 5 variants.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:05	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:05	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:05	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5 / 5 (100.0000%)
INFO	2025-04-24 13:18:05	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:05	LiftoverVcf	chr1: 5
WARNING	2025-04-24 13:18:05	LiftoverVcf	0 variants with a swapped REF/ALT were identified, but were not recovered.  See RECOVER_SWAPPED_REF_ALT and associated caveats.
INFO	2025-04-24 13:18:05	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:05 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:05 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/test.two.block.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/dummy.two.block.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:05 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:05	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:05	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:06	LiftoverVcf	Processed 4 variants.
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:06	LiftoverVcf	2 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:06	LiftoverVcf	50.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:06	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 2 / 4 (50.0000%)
INFO	2025-04-24 13:18:06	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 2
INFO	2025-04-24 13:18:06	LiftoverVcf	1 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:06	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:06 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:06 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMismatchingSnps.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:06	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:06	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:06	LiftoverVcf	Processed 4 variants.
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:06	LiftoverVcf	1 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:06	LiftoverVcf	25.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:06	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 3 / 4 (75.0000%)
INFO	2025-04-24 13:18:06	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 3
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:06	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:06 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:18:06 EDT 2025] LiftoverVcf --INPUT /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/testLiftoverMixedVariants.vcf --OUTPUT /tmp/LiftoverVcfsTest.tmp12726991319975677663/lift-delete-me.vcf --CHAIN /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/test.over.chain --REJECT /tmp/LiftoverVcfsTest.tmp12726991319975677663/reject-delete-me.vcf --RECOVER_SWAPPED_REF_ALT true --CREATE_INDEX false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/vcf/LiftOver/dummy.reference.fasta --WARN_ON_MISSING_CONTIG false --LOG_FAILED_INTERVALS true --WRITE_ORIGINAL_POSITION false --WRITE_ORIGINAL_ALLELES false --LIFTOVER_MIN_MATCH 1.0 --ALLOW_MISSING_FIELDS_IN_HEADER false --TAGS_TO_REVERSE AF --TAGS_TO_DROP MAX_AF --DISABLE_SORT false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 2279706 --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:18:06 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null
INFO	2025-04-24 13:18:06	LiftoverVcf	Loading up the target reference genome.
INFO	2025-04-24 13:18:06	LiftoverVcf	Lifting variants over and sorting (not yet writing the output file.)
INFO	2025-04-24 13:18:06	LiftoverVcf	Processed 4 variants.
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants failed to liftover.
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants lifted over but had mismatching reference alleles after lift over.
INFO	2025-04-24 13:18:06	LiftoverVcf	0.0000% of variants were not successfully lifted over and written to the output.
INFO	2025-04-24 13:18:06	LiftoverVcf	liftover success by source contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 4 / 4 (100.0000%)
INFO	2025-04-24 13:18:06	LiftoverVcf	lifted variants by target contig:
INFO	2025-04-24 13:18:06	LiftoverVcf	chr1: 4
INFO	2025-04-24 13:18:06	LiftoverVcf	0 variants were lifted by swapping REF/ALT alleles.
INFO	2025-04-24 13:18:06	LiftoverVcf	Writing out sorted records to final VCF.
[Thu Apr 24 13:18:06 EDT 2025] picard.vcf.LiftoverVcf done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824