Class picard.illumina.ExtractIlluminaBarcodesTest

all > picard.illumina > ExtractIlluminaBarcodesTest

tests

failures

ignored

1.189s

duration

94%

successful

Failed tests
Tests
Standard error

Failed tests

testNonWritableOutputFile

java.lang.AssertionError: expected [4] but found [0]
	at org.testng.Assert.fail(Assert.java:110)
	at org.testng.Assert.failNotEquals(Assert.java:1413)
	at org.testng.Assert.assertEqualsImpl(Assert.java:149)
	at org.testng.Assert.assertEquals(Assert.java:131)
	at org.testng.Assert.assertEquals(Assert.java:1240)
	at org.testng.Assert.assertEquals(Assert.java:1274)
	at picard.illumina.ExtractIlluminaBarcodesTest.testNonWritableOutputFile(ExtractIlluminaBarcodesTest.java:179)
	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)

Tests

Test	Duration	Result
testBarcodeMatching	0.061s	passed
testCbclDualBarcodes	0.856s	passed
testDelta[0]([Ljava.lang.String;@13dfaaf, [Ljava.lang.String;@1ffd3bbc, 2, 5)	0.001s	passed
testDelta[1]([Ljava.lang.String;@316129ae, [Ljava.lang.String;@496bd320, 5, 5)	0s	passed
testDelta[2]([Ljava.lang.String;@14488e0b, [Ljava.lang.String;@2cdcf975, 0, 5)	0s	passed
testDualBarcodes	0.020s	passed
testNoLocsSymlink	0.025s	passed
testNonWritableOutputFile	0.030s	failed
testPairedEndWithBarcodeAndMolecularIndicies	0.024s	passed
testPairedEndWithBarcodeOnFirstEnd	0.024s	passed
testPairedEndWithBarcodeOnSecondEnd	0.026s	passed
testQualityBarcodes[0](16, 0, 1, 0, Barcode has good quality, 1 match)	0.017s	passed
testQualityBarcodes[1](25, 0, 0, 0, Barcode has quality failures, no matches)	0.016s	passed
testSingleEndWithBarcodeAtEnd	0.023s	passed
testSingleEndWithBarcodeAtEndAndMolecularIndicies	0.023s	passed
testSingleEndWithBarcodeAtStart	0.021s	passed
testSingleEndWithBarcodeAtStartAndMolecularIndicies	0.022s	passed

Standard error

[Thu Apr 24 13:00:36 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.843718652466710239.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:36 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 13:00:36	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:36 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:00:36 EDT 2025] ExtractIlluminaBarcodes --BARCODE CACCTAGTACTCGAGT --LANE 1 --READ_STRUCTURE 151T8B8B151T --BASECALLS_DIR /tmp/eib_cbcl.tmp3542259375178543973/BaseCalls --METRICS_FILE /tmp/cbcl.11343781699555511957.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:36 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 13:00:36	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:36	CbclReader	Processing tile 1101
INFO	2025-04-24 13:00:36	ExtractIlluminaBarcodes	Extracting barcodes for tile 1102
INFO	2025-04-24 13:00:36	CbclReader	Processing tile 1102
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 2 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAATAGTCCGACTCTC --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR /tmp/eib_dual.tmp11299550619645856493 --METRICS_FILE /tmp/dual.13323874671546733187.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 1 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAATAGTCCGACTCTC --LANE 1 --READ_STRUCTURE 25T8B8B25T --BASECALLS_DIR /tmp/eib_nosymlink.tmp3765957520206187837 --METRICS_FILE /tmp/dual.10077972897297955885.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1102
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 2 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 25T8B25T --COMPRESS_OUTPUTS true --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.13231278878436116162.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 4M21T8B21T4M --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.15233097613888050810.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.1843039810365151272.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 25T25T8B --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.534105400102674002.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAATAGTC --MAX_MISMATCHES 0 --MINIMUM_BASE_QUALITY 16 --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR /tmp/eib_qual.tmp10599875682250997987 --METRICS_FILE /tmp/qual.3962665308148372122.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 1 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAATAGTC --MAX_MISMATCHES 0 --MINIMUM_BASE_QUALITY 25 --LANE 1 --READ_STRUCTURE 25T8B25T --BASECALLS_DIR /tmp/eib_qual.tmp10599875682250997987 --METRICS_FILE /tmp/qual.4661234059682871542.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 1 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 25T8B --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.2808715320116757623.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 4M21T8B --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.12713211706034411110.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 8B25T --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.11170431670021966915.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072
[Thu Apr 24 13:00:37 EDT 2025] ExtractIlluminaBarcodes --BARCODE CAACTCTC --BARCODE CAACTCTG --BARCODE ACAGGTAT --BARCODE GACCGTTG --BARCODE ATTATCAA --BARCODE TGCTGCTG --BARCODE AACAATGG --BARCODE TGTAATCA --BARCODE GCCGTCGA --BARCODE GTCCACAG --BARCODE TTGTCTAT --BARCODE GTGGAGAC --BARCODE TTGCAAAT --LANE 1 --READ_STRUCTURE 8B4M21T --BASECALLS_DIR /tmp/eib.tmp4960968998720288374 --METRICS_FILE /tmp/eib.9210056685746892657.metrics --NUM_PROCESSORS 1 --DISTANCE_MODE HAMMING --MAX_MISMATCHES 1 --MIN_MISMATCH_DELTA 1 --MAX_NO_CALLS 2 --MINIMUM_BASE_QUALITY 0 --MINIMUM_QUALITY 2 --COMPRESS_OUTPUTS false --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 13:00:37 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 13:00:37	ExtractIlluminaBarcodes	Processing with 1 PerTileBarcodeExtractor(s).
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 1201
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Extracting barcodes for tile 2101
INFO	2025-04-24 13:00:37	ExtractIlluminaBarcodes	Processed 3 tiles.
[Thu Apr 24 13:00:37 EDT 2025] picard.illumina.ExtractIlluminaBarcodes done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1097859072