Class picard.arrays.illumina.VcfToAdpcTest
|
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