[Qa-jenkins-scm] Build failed in Jenkins: reproducible_builder_armhf_10 #6574
jenkins at jenkins.debian.net
jenkins at jenkins.debian.net
Sun Apr 24 16:56:29 UTC 2016
See <https://jenkins.debian.net/job/reproducible_builder_armhf_10/6574/>
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[...truncated 27872 lines...]
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 225 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 226 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 227 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 228 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 229 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 230 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 231 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 232 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 233 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 234 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 235 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 236 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 237 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 238 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 239 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 240 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 241 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 242 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 243 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 244 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 245 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 246 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 247 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 248 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 249 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Missing file for cycle 250 in directory /tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory Lane 5 FAILED Total Errors: 98
[testng] INFO 2016-04-25 06:26:12 CheckIlluminaDirectory FAILED! There were 98 in the following lanes: 5
[testng] [Mon Apr 25 06:26:12 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.11 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[testng] [Mon Apr 25 06:26:14 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] TILE_NUMBERS=[1301, 2201] FAKE_FILES=true LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:14 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:14 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test6777780590475177693IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:14 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250
[testng] INFO 2016-04-25 06:26:14 CheckIlluminaDirectory Checking lane 5
[testng] INFO 2016-04-25 06:26:14 CheckIlluminaDirectory Expected tiles: 1301, 2201
[testng] INFO 2016-04-25 06:26:18 CheckIlluminaDirectory Lane 5 SUCCEEDED
[testng] INFO 2016-04-25 06:26:18 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:18 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.08 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:22 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5321878471260251336IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[3] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:22 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:22 CheckIlluminaDirectory Checking lanes(3 in basecalls directory (/tmp/ift_test5321878471260251336IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:22 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
[testng] INFO 2016-04-25 06:26:22 CheckIlluminaDirectory Checking lane 3
[testng] INFO 2016-04-25 06:26:22 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
[testng] INFO 2016-04-25 06:26:24 CheckIlluminaDirectory Lane 3 SUCCEEDED
[testng] INFO 2016-04-25 06:26:24 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:24 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.03 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:27 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7699729953854912151IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=8S15T8S LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:27 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:27 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test7699729953854912151IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:27 CheckIlluminaDirectory Expected cycles: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
[testng] INFO 2016-04-25 06:26:27 CheckIlluminaDirectory Checking lane 2
[testng] INFO 2016-04-25 06:26:27 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
[testng] INFO 2016-04-25 06:26:28 CheckIlluminaDirectory Lane 2 SUCCEEDED
[testng] INFO 2016-04-25 06:26:28 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:28 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.02 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:32 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6737874159656805044IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=68T8B68T LANES=[2] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:32 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:32 CheckIlluminaDirectory Checking lanes(2 in basecalls directory (/tmp/ift_test6737874159656805044IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:32 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144
[testng] INFO 2016-04-25 06:26:32 CheckIlluminaDirectory Checking lane 2
[testng] INFO 2016-04-25 06:26:32 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
[testng] INFO 2016-04-25 06:26:36 CheckIlluminaDirectory Lane 2 SUCCEEDED
[testng] INFO 2016-04-25 06:26:36 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:36 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.06 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:39 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7622556628625783099IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:39 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:39 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test7622556628625783099IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:39 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
[testng] INFO 2016-04-25 06:26:39 CheckIlluminaDirectory Checking lane 5
[testng] INFO 2016-04-25 06:26:39 CheckIlluminaDirectory Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
[testng] INFO 2016-04-25 06:26:40 CheckIlluminaDirectory Lane 5 SUCCEEDED
[testng] INFO 2016-04-25 06:26:40 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:40 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.02 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:43 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1476806100741877115IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF] READ_STRUCTURE=25T25T LANES=[5] TILE_NUMBERS=[1301, 2101] FAKE_FILES=false LINK_LOCS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:43 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:43 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test1476806100741877115IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:43 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
[testng] INFO 2016-04-25 06:26:43 CheckIlluminaDirectory Checking lane 5
[testng] INFO 2016-04-25 06:26:43 CheckIlluminaDirectory Expected tiles: 1301, 2101
[testng] INFO 2016-04-25 06:26:44 CheckIlluminaDirectory Lane 5 SUCCEEDED
[testng] INFO 2016-04-25 06:26:44 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:44 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.02 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:46 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3329331238523666611IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:46 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:46 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test3329331238523666611IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:46 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
[testng] INFO 2016-04-25 06:26:47 CheckIlluminaDirectory Checking lane 5
[testng] INFO 2016-04-25 06:26:47 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
[testng] INFO 2016-04-25 06:26:47 CheckIlluminaDirectory Lane 5 SUCCEEDED
[testng] INFO 2016-04-25 06:26:47 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:47 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:48 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3329331238523666611IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position] READ_STRUCTURE=50T LANES=[5] FAKE_FILES=false LINK_LOCS=true VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:48 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory Checking lanes(5 in basecalls directory (/tmp/ift_test3329331238523666611IlluminaDir/Data/Intensities/BaseCalls)
[testng]
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory Checking lane 5
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory Lane 5 SUCCEEDED
[testng] INFO 2016-04-25 06:26:48 CheckIlluminaDirectory SUCCEEDED! All required files are present and non-empty.
[testng] [Mon Apr 25 06:26:48 GMT+14:00 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:50 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/simple_fits.sam OUTPUT=/tmp/simple_fits.sam.4598778752035573681.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:50 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:26:50 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:26:51 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/simple_overhang.sam OUTPUT=/tmp/simple_overhang.sam.8895856604048172192.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:51 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] Ignoring SAM validation error: ERROR: Read name simple_overhang, Read CIGAR M operator maps off end of reference
[testng] [Mon Apr 25 06:26:52 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:26:53 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/fits_with_deletion.sam OUTPUT=/tmp/fits_with_deletion.sam.1284271486456988995.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] No errors found
[testng] [Mon Apr 25 06:26:53 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:26:53 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:54 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/overhang_with_deletion.sam OUTPUT=/tmp/overhang_with_deletion.sam.2679051163384971048.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:54 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] Ignoring SAM validation error: ERROR: Read name overhang_with_deletion, Read CIGAR M operator maps off end of reference
[testng] [Mon Apr 25 06:26:54 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:26:55 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/trailing_insertion.sam OUTPUT=/tmp/trailing_insertion.sam.6633131387219792769.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:55 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] No errors found
[testng] [Mon Apr 25 06:26:55 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:57 GMT+14:00 2016] picard.sam.CleanSam INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CleanSam/long_trailing_insertion.sam OUTPUT=/tmp/long_trailing_insertion.sam.5795613761533639314.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:57 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] No errors found
[testng] [Mon Apr 25 06:26:57 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:26:58 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.9126075301628053172.tmp/input.sam OUTPUT=/tmp/CleanSamTester.9126075301628053172.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:58 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:26:58 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:26:59 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.5802838903787719404.tmp/input.sam OUTPUT=/tmp/CleanSamTester.5802838903787719404.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:26:59 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[testng] [Mon Apr 25 06:26:59 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:27:01 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.853086691414128359.tmp/input.sam OUTPUT=/tmp/CleanSamTester.853086691414128359.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:01 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:01 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:27:02 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.3160599039479841635.tmp/input.sam OUTPUT=/tmp/CleanSamTester.3160599039479841635.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:02 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[testng] Ignoring SAM validation error: ERROR: Read name READ0, Read CIGAR M operator maps off end of reference
[testng] [Mon Apr 25 06:27:02 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:27:03 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.9199948080569680229.tmp/input.sam OUTPUT=/tmp/CleanSamTester.9199948080569680229.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:03 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:04 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:27:05 GMT+14:00 2016] picard.sam.CleanSam INPUT=/tmp/CleanSamTester.5032377016281287077.tmp/input.sam OUTPUT=/tmp/CleanSamTester.5032377016281287077.tmp/output.sam VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:05 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:05 GMT+14:00 2016] picard.sam.CleanSam done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] No errors found
[testng] [Mon Apr 25 06:27:28 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics REFERENCE_SEQUENCE=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5952860683100620776.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:28 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:28 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:30 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics IS_BISULFITE_SEQUENCED=true REFERENCE_SEQUENCE=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_bisulfite_test.sam OUTPUT=/tmp/alignmentMetrics2501801879520776372.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:30 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:30 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:31 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics MAX_INSERT_SIZE=20 REFERENCE_SEQUENCE=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.fasta INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test_chimeras.sam OUTPUT=/tmp/alignmentMetrics1618537791431027805.txt EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:31 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:31 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:32 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics METRIC_ACCUMULATION_LEVEL=[READ_GROUP, LIBRARY, SAMPLE, ALL_READS] INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test_multiple.sam OUTPUT=/tmp/alignmentMetrics6858820566428774171.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:32 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:33 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.01 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:34 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test.sam OUTPUT=/tmp/alignmentMetrics5656893101159911787.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:34 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:35 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:36 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/summary_alignment_stats_test2.sam OUTPUT=/tmp/alignmentMetrics3031507458068991818.txt MAX_INSERT_SIZE=100000 EXPECTED_PAIR_ORIENTATIONS=[FR] ADAPTER_SEQUENCE=[AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCGGTTCAGCAGGAATGCCGAGACCGATCTCGTATGCCGTCTTCTGCTTG, AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT, AGATCGGAAGAGCACACGTCTGAACTCCAGTCACNNNNNNNNATCTCGTATGCCGTCTTCTGCTTG] METRIC_ACCUMULATION_LEVEL=[ALL_READS] IS_BISULFITE_SEQUENCED=false ASSUME_SORTED=true STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:36 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] [Mon Apr 25 06:27:36 GMT+14:00 2016] picard.analysis.CollectAlignmentSummaryMetrics done. Elapsed time: 0.00 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:37 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test8884098344861205287.pdf SUMMARY_OUTPUT=/tmp/test1821314906062290273.gc_bias.summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias1987896879073729809.bam OUTPUT=/tmp/test1107983352400607011.gc_bias.detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:37 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:27:42 RExecutor Executing R script via command: Rscript /tmp/script1676017274754787220.R /tmp/test1107983352400607011.gc_bias.detail_metrics /tmp/test1821314906062290273.gc_bias.summary_metrics /tmp/test8884098344861205287.pdf 100
[testng] INFO 2016-04-25 06:27:45 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200
[testng] [Mon Apr 25 06:27:45 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.13 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:46 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test570902936393160952.pdf SUMMARY_OUTPUT=/tmp/test3823625163799291454.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias1987896879073729809.bam OUTPUT=/tmp/test7882446594968412517.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:46 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:27:51 RExecutor Executing R script via command: Rscript /tmp/script7658134034085194147.R /tmp/test7882446594968412517.gc_bias_detail_metrics /tmp/test3823625163799291454.gc_bias_summary_metrics /tmp/test570902936393160952.pdf 100
[testng] INFO 2016-04-25 06:27:53 ProcessExecutor Total clusters: 300 , Aligned reads: 600Total clusters: 200 , Aligned reads: 400Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200
[testng] [Mon Apr 25 06:27:53 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.12 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:27:54 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics CHART_OUTPUT=/tmp/test8313837132835944099.pdf SUMMARY_OUTPUT=/tmp/testAllChr6594607492371983741.gc_bias_summary_metrics SCAN_WINDOW_SIZE=100 MINIMUM_GENOME_FRACTION=1.0E-5 IS_BISULFITE_SEQUENCED=false METRIC_ACCUMULATION_LEVEL=[READ_GROUP, SAMPLE, ALL_READS] INPUT=/build/picard-tools-2.1.1+dfsg/testdata/picard/sam/CollectGcBiasMetrics/CollectGcBias6408153398662953533.bam OUTPUT=/tmp/testAllChrDetails9032989683835757667.gc_bias_detail_metrics ASSUME_SORTED=false REFERENCE_SEQUENCE=testdata/picard/metrics/chrMNO.reference.fasta STOP_AFTER=0 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:27:54 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:27:56 RExecutor Executing R script via command: Rscript /tmp/script8667965979940838074.R /tmp/testAllChrDetails9032989683835757667.gc_bias_detail_metrics /tmp/testAllChr6594607492371983741.gc_bias_summary_metrics /tmp/test8313837132835944099.pdf 100
[testng] INFO 2016-04-25 06:27:58 ProcessExecutor Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200Total clusters: 100 , Aligned reads: 200
[testng] [Mon Apr 25 06:27:58 GMT+14:00 2016] picard.analysis.CollectGcBiasMetrics done. Elapsed time: 0.07 minutes.
[testng] Runtime.totalMemory()=1181159424
[testng] [Mon Apr 25 06:28:01 GMT+14:00 2016] picard.analysis.directed.CollectHsMetrics BAIT_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] MINIMUM_MAPPING_QUALITY=1 MINIMUM_BASE_QUALITY=1 CLIP_OVERLAPPING_READS=true TARGET_INTERVALS=[testdata/picard/analysis/directed/CollectHsMetrics/chrM.interval_list] INPUT=testdata/picard/analysis/directed/CollectHsMetrics/lowbaseq.sam OUTPUT=testdata/picard/analysis/directed/CollectHsMetrics/CollectHsMetrics4135557386442724417.hs_metrics SAMPLE_SIZE=1000 METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 COVERAGE_CAP=200 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=1000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[testng] [Mon Apr 25 06:28:01 GMT+14:00 2016] Executing as pbuilder2 at i-capture-the-hostname on Linux 4.5.0-trunk-armmp-lpae arm; OpenJDK Zero VM 1.8.0_77-Debian-8u77-b03-3+b1-b1; Picard version: null JdkDeflater
[testng] INFO 2016-04-25 06:28:02 TheoreticalSensitivity Creating Roulette Wheel
[testng] INFO 2016-04-25 06:28:02 TheoreticalSensitivity Calculating quality sums from quality sampler
[testng] INFO 2016-04-25 06:28:04 TheoreticalSensitivity 0 sampling iterations completed
/srv/reproducible-results/rbuild-debian-fmPTlP3c/tmp.cq3zJjk5kh: FATAL: null
java.lang.NullPointerException
at hudson.plugins.build_timeout.BuildTimeoutWrapper$EnvironmentImpl.tearDown(BuildTimeoutWrapper.java:199)
at hudson.model.Build$BuildExecution.doRun(Build.java:173)
at hudson.model.AbstractBuild$AbstractBuildExecution.run(AbstractBuild.java:534)
at hudson.model.Run.execute(Run.java:1738)
at hudson.model.FreeStyleBuild.run(FreeStyleBuild.java:43)
at hudson.model.ResourceController.execute(ResourceController.java:98)
at hudson.model.Executor.run(Executor.java:410)
93.3% -- replaced with /srv/reproducible-results/rbuild-debian-fmPTlP3c/tmp.cq3zJjk5kh.gz
INFO: Starting at 2016-04-24 16:56:27.317057
INFO: Finished at 2016-04-24 16:56:27.333578, took: 0:00:00.016534
INFO: Starting at 2016-04-24 16:56:27.807666
INFO: Finished at 2016-04-24 16:56:28.000929, took: 0:00:00.193273
rm: cannot remove ‘/srv/reproducible-results/rbuild-debian-fmPTlP3c’: No such file or directory
Sun Apr 24 16:56:28 UTC 2016 - https://jenkins.debian.net/job/reproducible_builder_armhf_10/6574/console got remote error with exit code 143 from rpi2b-armhf-rb.debian.net for build #2 for picard-tools on testing/armhf
Sleeping 5m before aborting the job.
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