Class picard.illumina.CheckIlluminaDirectoryTest

all > picard.illumina > CheckIlluminaDirectoryTest
12

tests
0

failures
0

ignored
2.357s

duration
100%

successful

Tests

Test Duration Result
basedirDoesntExistTest 0.046s passed
differentSizedBclTest 0.106s passed
negativeTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@1f890b10, [Lpicard.illumina.parser.IlluminaDataType;@4f2c1a5d, [], [], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@71bf26a9, 68T8B68T, 2, [], true) 0.570s passed
negativeTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@484385d6, [Lpicard.illumina.parser.IlluminaDataType;@4252d0a9, [BaseCalls/L002/C13.1/s_2_1201.bcl, BaseCalls/L002/C13.1/s_2_2101.bcl], [BaseCalls/L002/s_2_2101.filter], 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@54f1d28e, 13T, 3, [], true) 0.130s passed
negativeTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@1a589672, [Lpicard.illumina.parser.IlluminaDataType;@308f04d2, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@4782dd0, 250T, 98, [], true) 0.333s passed
negativeTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@2da824c2, [Lpicard.illumina.parser.IlluminaDataType;@29c9bdca, [], [], 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@5cf9ee95, 250T, 98, [1301, 2201], true) 0.279s passed
positiveTests[0]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@731ca326, [Lpicard.illumina.parser.IlluminaDataType;@3829ab4, 3, [1101, 1201, 1301, 2101, 2201, 2301], [I@ab85760, 25T25T, []) 0.369s passed
positiveTests[1]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@30f68dd7, [Lpicard.illumina.parser.IlluminaDataType;@38e85218, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@3aa30a85, 8S15T8S, []) 0.071s passed
positiveTests[2]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@70f4e140, [Lpicard.illumina.parser.IlluminaDataType;@27d6b33f, 2, [1101, 1201, 1301, 2101, 2201, 2301], [I@114aa451, 68T8B68T, []) 0.098s passed
positiveTests[3]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@4b1d1056, [Lpicard.illumina.parser.IlluminaDataType;@2b1fc774, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@541c5c71, 25T25T, []) 0.091s passed
positiveTests[4]([Lpicard.illumina.parser.IlluminaFileUtil$SupportedIlluminaFormat;@1102a3dc, [Lpicard.illumina.parser.IlluminaDataType;@7742730a, 5, [1101, 1201, 1301, 2101, 2201, 2301], [I@53d2b847, 25T25T, [1301, 2101]) 0.088s passed
symlinkLocsTest 0.176s passed

Standard error

[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5805242452604474613IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores] READ_STRUCTURE=50T 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
[Tue Aug 16 04:11:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test5805242452604474613IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:15	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
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected tiles: 1, 2, 3, 4
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	File type .bcl has cycles files of different length.  Current cycle (9) Length of first non-empty file (14) length of current cycle (56618) File(/tmp/ift_test5805242452604474613IlluminaDir/Data/Intensities/BaseCalls/L005/C9.1/s_5_3.bcl)
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 1
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	FAILED! There were 1 in the following lanes: 5
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1773142016
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6962765640530519323IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] 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
[Tue Aug 16 04:11:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test6962765640530519323IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:15	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
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Could not find a format with available files for the following data types: Barcodes, Position
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Lane 2 FAILED  Total Errors: 2
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	FAILED! There were 2 in the following lanes: 2
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1829765120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test6962765640530519323IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[Position, BaseCalls, QualityScores, PF, Barcodes] READ_STRUCTURE=68T8B68T LANES=[2] 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
[Tue Aug 16 04:11:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test6962765640530519323IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:15	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
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3663723363433876314IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] 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
[Tue Aug 16 04:11:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test3663723363433876314IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	File type .bcl is missing a file for cycle 13 and tile 1201
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	File type .bcl is missing a file for cycle 13 and tile 2101
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Missing tile [2101] for file type .filter.
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Lane 2 FAILED  Total Errors: 3
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	FAILED! There were 3 in the following lanes: 2
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3663723363433876314IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=13T LANES=[2] 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
[Tue Aug 16 04:11:15 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test3663723363433876314IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected cycles: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
INFO	2016-08-16 04:11:15	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:15 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] 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
[Tue Aug 16 04:11:16 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:16	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
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 153 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 154 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 155 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 156 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 157 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 158 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 159 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 160 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 161 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 162 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 163 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 164 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 165 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 166 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 167 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 168 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 169 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 170 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 171 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 172 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 173 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 174 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 175 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 176 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 177 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 178 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 179 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 180 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 181 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 182 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 183 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 184 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 185 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 186 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 187 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 188 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 189 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 190 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 191 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 192 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 193 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 194 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 195 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 196 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 197 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 198 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 199 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 200 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 201 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 202 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 203 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 204 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 205 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 206 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 207 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 208 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 209 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 210 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 211 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 212 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 213 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 214 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 215 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 216 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 217 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 218 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 219 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 220 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 221 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 222 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 223 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 224 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 225 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 226 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 227 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 228 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 229 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 230 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 231 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 232 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 233 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 234 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 235 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 236 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 237 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 238 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 239 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 240 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 241 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 242 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 243 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 244 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 245 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 246 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 247 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 248 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 249 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 250 in directory /tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 98
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	FAILED! There were 98 in the following lanes: 5
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls DATA_TYPES=[BaseCalls, QualityScores, PF] READ_STRUCTURE=250T LANES=[5] 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
[Tue Aug 16 04:11:16 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test2653505677882076930IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:16	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
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7421678242311894230IlluminaDir/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
[Tue Aug 16 04:11:16 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:16	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
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Expected tiles: 1301, 2201
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 153 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 154 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 155 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 156 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 157 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 158 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 159 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 160 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 161 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 162 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 163 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 164 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 165 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 166 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 167 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 168 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 169 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 170 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 171 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 172 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 173 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 174 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 175 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 176 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 177 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 178 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 179 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 180 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 181 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 182 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 183 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 184 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 185 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 186 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 187 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 188 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 189 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 190 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 191 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 192 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 193 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 194 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 195 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 196 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 197 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 198 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 199 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 200 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 201 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 202 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 203 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 204 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 205 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 206 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 207 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 208 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 209 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 210 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 211 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 212 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 213 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 214 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 215 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 216 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 217 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 218 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 219 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 220 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 221 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 222 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 223 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 224 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 225 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 226 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 227 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 228 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 229 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 230 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 231 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 232 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 233 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 234 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 235 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 236 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 237 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 238 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 239 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 240 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 241 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 242 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 243 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 244 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 245 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 246 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 247 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 248 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 249 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Missing file for cycle 250 in directory /tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls/L005 for file type .bcl
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Lane 5 FAILED  Total Errors: 98
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	FAILED! There were 98 in the following lanes: 5
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test7421678242311894230IlluminaDir/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
[Tue Aug 16 04:11:16 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test7421678242311894230IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:16	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
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Expected tiles: 1301, 2201
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:16	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:16 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4615820073816204852IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(3 in basecalls directory (/tmp/ift_test4615820073816204852IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 3
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 3 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test5341242897720937133IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test5341242897720937133IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected cycles: 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test8771661236326136907IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(2 in basecalls directory (/tmp/ift_test8771661236326136907IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 2
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 2 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test1164832603629085634IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test1164832603629085634IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1201, 1301, 2101, 2201, 2301
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test3207803744177626178IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test3207803744177626178IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1301, 2101
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4867179165316022404IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test4867179165316022404IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory BASECALLS_DIR=/tmp/ift_test4867179165316022404IlluminaDir/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
[Tue Aug 16 04:11:17 CDT 2016] Executing as jli@corona on Linux 3.19.0-61-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_91-b14; Picard version: null
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lanes(5 in basecalls directory (/tmp/ift_test4867179165316022404IlluminaDir/Data/Intensities/BaseCalls)

INFO	2016-08-16 04:11:17	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
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Checking lane 5
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Expected tiles: 1101, 1102, 1103, 2101, 2102, 2103
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	Lane 5 SUCCEEDED 
INFO	2016-08-16 04:11:17	CheckIlluminaDirectory	SUCCEEDED!  All required files are present and non-empty.
[Tue Aug 16 04:11:17 CDT 2016] picard.illumina.CheckIlluminaDirectory done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1829765120