Class picard.sam.SamToFastqTest

all > picard.sam > SamToFastqTest
17

tests
0

failures
0

ignored
0.504s

duration
100%

successful

Tests

Test Duration Result
testBadFile[0](bad/unpaired-mate.sam) 0.031s passed
testBadGroupedFile[0](bad/grouped-unpaired-mate.sam, null, null, [Ljava.lang.String;@2e7eeb91) 0.026s passed
testClipping[0](null, AAAAAAAAAA, 1111111111, AAAAAAAAAA, 1111111111, CCCCCCCCCC, 2222222222, GGGGGGGGGG, 2222222222, No clipping test) 0.041s passed
testClipping[1](X, AAAAAAA, 1111111, AAAAAA, 111111, CCCCCCCC, 22222222, GGGGGG, 222222, Cut clipped bases test) 0.028s passed
testClipping[2](N, AAAAAAANNN, 1111111111, AAAAAANNNN, 1111111111, CCCCCCCCNN, 2222222222, GGGGGGNNNN, 2222222222, Mask clipped bases test) 0.028s passed
testClipping[3](2, AAAAAAAAAA, 1111111###, AAAAAAAAAA, 111111####, CCCCCCCCCC, 22222222##, GGGGGGGGGG, 222222####, Change clipped qualities test) 0.036s passed
testOkFile[0](ok/sorted-pair.sam) 0.031s passed
testOkFile[1](ok/sorted-pair-no-rg.sam) 0.029s passed
testOkFile[2](ok/last-pair-mates-flipped.sam) 0.027s passed
testOkFile[3](ok/first-mate-bof-last-mate-eof.sam) 0.028s passed
testOkGroupedFiles[0](ok/grouped-last-pair-mates-flipped.sam, null, null, [Ljava.lang.String;@109a029b) 0.029s passed
testOkInterleavedFile[0](ok/sorted-pair.sam) 0.025s passed
testOkInterleavedFile[1](ok/sorted-pair-no-rg.sam) 0.032s passed
testOkInterleavedFile[2](ok/last-pair-mates-flipped.sam) 0.034s passed
testOkInterleavedFile[3](ok/first-mate-bof-last-mate-eof.sam) 0.025s passed
testTrimming[0](ok/sorted-pair.sam, 6, 7, 7, 5, 8, 8) 0.028s passed
testTrimming[1](ok/sorted-pair.sam, 7, 7, 6, 3, 8, 8) 0.026s passed

Standard error

[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/bad/unpaired-mate.sam FASTQ=/tmp/tt-pair1.9045718794897728350.fastq SECOND_END_FASTQ=/tmp/tt-pair2.4897223450227398215.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/bad/grouped-unpaired-mate.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/jli    RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest1842694525063721218fastq SECOND_END_FASTQ=/tmp/clippingtest2674160855482270362fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest12519148276845597434fastq SECOND_END_FASTQ=/tmp/clippingtest28116587866909060577fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=X    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest1814962802480148336fastq SECOND_END_FASTQ=/tmp/clippingtest27300743092972951632fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=N    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/clipping_test.sam FASTQ=/tmp/clippingtest19175910766136107101fastq SECOND_END_FASTQ=/tmp/clippingtest21001671932383679580fastq CLIPPING_ATTRIBUTE=XT CLIPPING_ACTION=2    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair12168924938639869751.fastq SECOND_END_FASTQ=/tmp/pair24919526699995888485.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair18841812860384410974.fastq SECOND_END_FASTQ=/tmp/pair26597990232138194526.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair12230326387262324270.fastq SECOND_END_FASTQ=/tmp/pair27135146644715173759.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair11851059417854050197.fastq SECOND_END_FASTQ=/tmp/pair23209925740917511353.fastq    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/grouped-last-pair-mates-flipped.sam OUTPUT_PER_RG=true OUTPUT_DIR=/tmp/jli    RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair1944823934299111525.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair-no-rg.sam FASTQ=/tmp/pair8596036194056190908.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/last-pair-mates-flipped.sam FASTQ=/tmp/pair5051487160282261049.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/first-mate-bof-last-mate-eof.sam FASTQ=/tmp/pair1395688057019130326.fastq INTERLEAVE=true    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair17332218035270974933.fastq SECOND_END_FASTQ=/tmp/pair25224431419412860386.fastq READ1_TRIM=6 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=5 READ2_MAX_BASES_TO_WRITE=8    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq INPUT=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/bam2fastq/paired/ok/sorted-pair.sam FASTQ=/tmp/pair18692658891963105381.fastq SECOND_END_FASTQ=/tmp/pair22956491778129263358.fastq READ1_TRIM=7 READ1_MAX_BASES_TO_WRITE=7 READ2_TRIM=3 READ2_MAX_BASES_TO_WRITE=8    OUTPUT_PER_RG=false RG_TAG=PU RE_REVERSE=true INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=3098916 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json
[Tue Aug 16 04:12:05 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
[Tue Aug 16 04:12:05 CDT 2016] picard.sam.SamToFastq done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762131968