Class picard.arrays.illumina.VcfToAdpcTest

6

tests

0

failures

0

ignored

0.040s

duration

100%

successful

Tests

Test Duration Result
testVcfToAdpcFailOnDifferingNumberOfLoci 0.006s passed
testVcfToAdpc[0]([testdata/picard/arrays/illumina/TestVcfToAdpc.vcf], testdata/picard/arrays/illumina/TestVcfToAdpc.adpc.bin, testdata/picard/arrays/illumina/TestVcfToAdpc.samples.txt, testdata/picard/arrays/illumina/TestVcfToAdpc.num_markers.txt) 0.006s passed
testVcfToAdpc[1]([testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) 0.005s passed
testVcfToAdpc[2]([testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) 0.007s passed
testVcfToAdpc[3]([testdata/picard/arrays/illumina/TestAdpc1.vcf, testdata/picard/arrays/illumina/TestAdpc23.vcf], testdata/picard/arrays/illumina/TestAdpc1_23.adpc.bin, testdata/picard/arrays/illumina/TestAdpc1_23.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) 0.008s passed
testVcfToAdpc[4]([testdata/picard/arrays/illumina/TestAdpc23.vcf, testdata/picard/arrays/illumina/TestAdpc1.vcf], testdata/picard/arrays/illumina/TestAdpc23_1.adpc.bin, testdata/picard/arrays/illumina/TestAdpc23_1.samples.txt, testdata/picard/arrays/illumina/TestAdpc.num_markers.txt) 0.008s passed

Standard error

[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestVcfToAdpc.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.13768165160615896163.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.15906490546091938249.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.6838802112779390604.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203078500006_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestAdpc1.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.8478834811219456537.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.4172764240246669162.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.3562999884783895050.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203469020115_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc1.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestAdpc23.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.16156529383343529685.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.2233678418558235195.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.43496525376418736.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203469020115_R02C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R03C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestAdpc1.vcf --VCF testdata/picard/arrays/illumina/TestAdpc23.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.3106813480206651034.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.14073885051644458138.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.12905851531850802215.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203469020115_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc1.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R02C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R03C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestAdpc23.vcf --VCF testdata/picard/arrays/illumina/TestAdpc1.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.17861931738814903925.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.5514833843760643456.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.1674278409201104592.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203469020115_R02C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R03C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc23.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc1.vcf
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:14 EDT 2025] VcfToAdpc --VCF testdata/picard/arrays/illumina/TestVcfToAdpc.vcf --VCF testdata/picard/arrays/illumina/TestAdpc1.vcf --OUTPUT /tmp/testIlluminaAdpcFileWriter.13044423390383958288.adpc.bin --SAMPLES_FILE /tmp/testIlluminaAdpcFileWriter.8236603203505866310.samples.txt --NUM_MARKERS_FILE /tmp/testIlluminaAdpcFileWriter.1745804519596027961.num_markers.txt --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
[Thu Apr 24 13:00:14 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 13:00:14	VcfToAdpc	Processing sample: 203078500006_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestVcfToAdpc.vcf
INFO	2025-04-24 13:00:14	VcfToAdpc	Processing sample: 203469020115_R01C01 from VCF: /mounts/lovelace/software/picard/picard/testdata/picard/arrays/illumina/TestAdpc1.vcf
ERROR	2025-04-24 13:00:14	VcfToAdpc	
picard.PicardException: VCFs have differing number of loci
	at picard.arrays.VcfToAdpc.doWork(VcfToAdpc.java:144)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.arrays.illumina.VcfToAdpcTest.testVcfToAdpcFailOnDifferingNumberOfLoci(VcfToAdpcTest.java:92)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at 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/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/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 worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:00:14 EDT 2025] picard.arrays.VcfToAdpc done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp