Class picard.sam.FastqToSamTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| readPairNameBad[0](, ) | 0s | passed |
| readPairNameBad[1](aa/1, bb/2) | 0s | passed |
| readPairNameBad[2](aa, bb) | 0s | passed |
| readPairNameBad[3](aa/1, aa) | 0s | passed |
| readPairNameBad[4](aa, aa/2) | 0s | passed |
| readPairNameBad[5](aa/1, aa/1) | 0s | passed |
| readPairNameBad[6](aa/2, aa/2) | 0s | passed |
| readPairNameOk[0](aa/1, aa/2) | 0s | passed |
| readPairNameOk[10](aa/, aa/) | 0s | passed |
| readPairNameOk[11](ab/c, ab/c) | 0s | passed |
| readPairNameOk[1](aa, aa) | 0.001s | passed |
| readPairNameOk[2](aa/bb, aa/bb) | 0s | passed |
| readPairNameOk[3](aa/bb/, aa/bb/) | 0s | passed |
| readPairNameOk[4](aa/bb/1, aa/bb/2) | 0s | passed |
| readPairNameOk[5](aa/bb/cc/dd/ee/ff/1, aa/bb/cc/dd/ee/ff/2) | 0s | passed |
| readPairNameOk[6](////1, ////2) | 0s | passed |
| readPairNameOk[7](/, /) | 0s | passed |
| readPairNameOk[8](////, ////) | 0s | passed |
| readPairNameOk[9](/aa, /aa) | 0s | passed |
| testBadFile[0](bad-format/bad-qual-header.txt) | 0.027s | passed |
| testBadFile[1](bad-format/bad-seq-header.txt) | 0.027s | passed |
| testBadFile[2](bad-format/extra-line.txt) | 0.027s | passed |
| testBadFile[3](bad-format/too-many-quals.txt) | 0.024s | passed |
| testBadFile[4](bad-format/1lines.txt) | 0.028s | passed |
| testBadFile[5](bad-format/2lines.txt) | 0.026s | passed |
| testBadFile[6](bad-format/3lines.txt) | 0.024s | passed |
| testFastqVersionBad[0](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Illumina) | 0.029s | passed |
| testFastqVersionBad[1](fastq-solexa/s_1_sequence.txt, Illumina) | 0.038s | passed |
| testFastqVersionOk[0](fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq, Standard) | 0.137s | passed |
| testFastqVersionOk[1](fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq, Standard) | 0.113s | passed |
| testFastqVersionOk[2](fastq-sanger/sanger_full_range_as_sanger-63.fastq, Standard) | 0.038s | passed |
| testFastqVersionOk[3](fastq-solexa/s_1_sequence.txt, Solexa) | 0.038s | passed |
| testFastqVersionOk[4](fastq-solexa/solexa_full_range_as_solexa.fastq, Solexa) | 0.038s | passed |
| testFastqVersionOk[5](fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.039s | passed |
| testFastqVersionOk[6](fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.038s | passed |
| testFastqVersionOk[7](fastq-illumina/s_1_sequence.txt, Illumina) | 0.039s | passed |
| testPairedBad[0](ok-paired/pair1.txt, bad-paired/pair2-one-more-record.txt) | 0.039s | passed |
| testPairedBad[1](bad-paired/pair1-one-more-record.txt, ok-paired/pair2.txt) | 0.039s | passed |
| testPairedBad[2](ok-paired/pair1.txt, bad-paired/pair2-badnum.txt) | 0.040s | passed |
| testPairedBad[3](bad-paired/pair1-badnum.txt, ok-paired/pair2.txt) | 0.036s | passed |
| testPairedBad[4](bad-paired/pair1-nonum.txt, ok-paired/pair2.txt) | 0.038s | passed |
| testPairedBad[5](bad-paired/pair1-onetoken.txt, ok-paired/pair2.txt) | 0.038s | passed |
| testPairedOk[0](ok-paired/pair1.txt, ok-paired/pair2.txt, Standard) | 0.036s | passed |
| testPairedOk[1](fastq-illumina/s_1_1_sequence.txt, fastq-illumina/s_1_2_sequence.txt, Illumina) | 0.047s | passed |
| testPermissiveFail[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) | 0.037s | passed |
| testPermissiveFail[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) | 0.038s | passed |
| testPermissiveFail[2](permissive-format/pair1.txt, null, Standard) | 0.050s | passed |
| testPermissiveFail[3](permissive-format/pair2.txt, null, Standard) | 0.034s | passed |
| testPermissiveFail[4](permissive-format/s_1_1_sequence.txt, null, Illumina) | 0.035s | passed |
| testPermissiveFail[5](permissive-format/s_1_2_sequence.txt, null, Illumina) | 0.036s | passed |
| testPermissiveFail[6](permissive-format/s_1_sequence.txt, null, Illumina) | 0.036s | passed |
| testPermissiveOk[0](permissive-format/pair1.txt, permissive-format/pair2.txt, Standard) | 0.048s | passed |
| testPermissiveOk[1](permissive-format/s_1_1_sequence.txt, permissive-format/s_1_2_sequence.txt, Illumina) | 0.040s | passed |
| testPermissiveOk[2](permissive-format/pair1.txt, null, Standard) | 0.038s | passed |
| testPermissiveOk[3](permissive-format/pair2.txt, null, Standard) | 0.038s | passed |
| testPermissiveOk[4](permissive-format/s_1_1_sequence.txt, null, Illumina) | 0.034s | passed |
| testPermissiveOk[5](permissive-format/s_1_2_sequence.txt, null, Illumina) | 0.036s | passed |
| testPermissiveOk[6](permissive-format/s_1_sequence.txt, null, Illumina) | 0.037s | passed |
| testSequentialFiles | 0.165s | passed |
Standard error
[Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/bad-qual-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-qual-header.txt4667082356107230991.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/bad-seq-header.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/bad-seq-header.txt6143078680373885173.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/extra-line.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/extra-line.txt2744771620201865906.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/too-many-quals.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/too-many-quals.txt7672026758523070164.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/1lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/1lines.txt4600843814437060006.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/2lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/2lines.txt1629776516958595477.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-format/3lines.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/3lines.txt2332235265006227522.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq3831705369525302927.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt1164467886166419394.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-sanger/5k-v1-Rhodobacter_LW1.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-v1-Rhodobacter_LW1.sam.fastq7542187607992831189.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:38 FastqToSam Processed 5000 fastq reads [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-sanger/5k-30BB2AAXX.3.aligned.sam.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/5k-30BB2AAXX.3.aligned.sam.fastq7637257129964099341.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:38 FastqToSam Processed 4952 fastq reads [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-sanger/sanger_full_range_as_sanger-63.fastq QUALITY_FORMAT=Standard OUTPUT=/tmp/sanger_full_range_as_sanger-63.fastq1864171183563158281.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:38 FastqToSam Processed 1 fastq reads [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-solexa/s_1_sequence.txt QUALITY_FORMAT=Solexa OUTPUT=/tmp/s_1_sequence.txt1487768439662423828.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 FastqToSam Auto-detected quality format as: Solexa. INFO 2016-08-16 04:11:38 FastqToSam Processed 25 fastq reads [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:38 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-solexa/solexa_full_range_as_solexa.fastq QUALITY_FORMAT=Solexa OUTPUT=/tmp/solexa_full_range_as_solexa.fastq6108514961339835710.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:38 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 04:11:38 FastqToSam Auto-detected quality format as: Solexa. INFO 2016-08-16 04:11:39 FastqToSam Processed 2 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt403036417553425313.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt1756331522951872414.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt8892631635179453573.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair2-one-more-record.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt8138738368042900335.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-one-more-record.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-one-more-record.txt3658424602564226482.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair2-badnum.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt5186946079553074562.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-badnum.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-badnum.txt2778693447681424059.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-nonum.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-nonum.txt280597415491115497.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/bad-paired/pair1-onetoken.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1-onetoken.txt5758637706118955359.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair1.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/ok-paired/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt3557551981632509670.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:39 FastqToSam Processed 5 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1823997952 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_1_sequence.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/fastq-illumina/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt7695728491553794854.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt3734120478034544336.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt1124510145948859690.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt5685313884908592028.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt8523478134238237217.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt3056855153185253862.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt4374329233889714982.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt3617079351691232659.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=false ALLOW_AND_IGNORE_EMPTY_LINES=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 04:11:39 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 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt949252652288061040.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:39 FastqToSam Processed 5 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt6352819754773328251.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair1.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair1.txt164957457966349622.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:39 FastqToSam Processed 5 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/pair2.txt QUALITY_FORMAT=Standard OUTPUT=/tmp/pair2.txt5825738259896939752.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 04:11:39 FastqToSam Auto-detected quality format as: Standard. INFO 2016-08-16 04:11:39 FastqToSam Processed 5 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_1_sequence.txt8785857571860211400.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_2_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_2_sequence.txt4239126278268591530.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/permissive-format/s_1_sequence.txt QUALITY_FORMAT=Illumina OUTPUT=/tmp/s_1_sequence.txt595936507000103249.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:39 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 WARNING 2016-08-16 04:11:39 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:39 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:39 FastqToSam Processed 10 fastq reads [Tue Aug 16 04:11:39 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq3648303197182467553.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:40 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 WARNING 2016-08-16 04:11:40 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:40 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/single_end_R1_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/single_end_R1_001.fastq3239502777141665468.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:40 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 WARNING 2016-08-16 04:11:40 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:40 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq5682614217358162145.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true USE_SEQUENTIAL_FASTQS=false SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:40 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 WARNING 2016-08-16 04:11:40 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:40 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680 [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam FASTQ=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R1_001.fastq FASTQ2=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/fastq2bam/sequential-files/paired_end_R2_001.fastq USE_SEQUENTIAL_FASTQS=true QUALITY_FORMAT=Illumina OUTPUT=/tmp/paired_end_R1_001.fastq1277862264723350432.sam READ_GROUP_NAME=rg SAMPLE_NAME=s1 ALLOW_AND_IGNORE_EMPTY_LINES=true SORT_ORDER=queryname MIN_Q=0 MAX_Q=93 STRIP_UNPAIRED_MATE_NUMBER=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 04:11:40 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 WARNING 2016-08-16 04:11:40 FastqToSam Making ambiguous determination about fastq's quality encoding; more than one format possible based on observed qualities. INFO 2016-08-16 04:11:40 FastqToSam Auto-detected quality format as: Illumina. INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads INFO 2016-08-16 04:11:40 FastqToSam Processed 1 fastq reads [Tue Aug 16 04:11:40 CDT 2016] picard.sam.FastqToSam done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1827143680