Class picard.sam.MergeBamAlignmentTest

all > picard.sam > MergeBamAlignmentTest

tests

failures

ignored

3.748s

duration

100%

successful

Tests
Standard output
Standard error

Tests

Test	Duration	Result
testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@795af3ab, [I@541bb317, 12, -1)	0.083s	passed
testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@5dae868d, [I@c28e4d8, -1, 12)	0.068s	passed
testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@11b5284e, [I@52c004e5, 13, 12)	0.092s	passed
testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@3af67ecd, [I@32c27a7a, 11, 14)	0.104s	passed
testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@158454c4, [I@214bff1f, 255, 255)	0.110s	passed
testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@4651ade, [I@37a8b5fb, 12, -1)	0.117s	passed
testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@7da6b66a, [I@35f35b39, -1, 12)	0.122s	passed
testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@2c1589f8, [I@123d1da7, 12, 255)	0.115s	passed
testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@2e3e266d, [I@493c746c, 0, 12)	0.121s	passed
testContaminationDetection	0.079s	passed
testEarliestFragmentStrategyPaired	0.045s	passed
testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@43026f98)	0.041s	passed
testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@576b2078)	0.055s	passed
testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@371abe6e)	0.052s	passed
testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@28221c9b)	0.052s	passed
testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@4ace9763)	0.038s	passed
testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@43667599)	0.050s	passed
testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@115aa581)	0.048s	passed
testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@759fd7ec)	0.048s	passed
testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@25be77ab)	0.047s	passed
testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@4a10ac7d)	0.048s	passed
testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@3135c5fc)	0.047s	passed
testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1e5ad3)	0.048s	passed
testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@29cd2784)	0.055s	passed
testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@33cccd6a, picard.sam.MergeBamAlignmentTest$HitSpec@ce0ce1, picard.sam.MergeBamAlignmentTest$HitSpec@5b716a6a], -1, 2, 8)	0.087s	passed
testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@67ed306e, picard.sam.MergeBamAlignmentTest$HitSpec@78ac4ac3, picard.sam.MergeBamAlignmentTest$HitSpec@2f14b2ec], -1, 2, 11)	0.074s	passed
testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@1cb73857, picard.sam.MergeBamAlignmentTest$HitSpec@77ad6f17, picard.sam.MergeBamAlignmentTest$HitSpec@5a8b6e42], -1, 2, 11)	0.071s	passed
testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@3328bde7, picard.sam.MergeBamAlignmentTest$HitSpec@21394f3d, picard.sam.MergeBamAlignmentTest$HitSpec@1805b175], -1, 1, 9)	0.080s	passed
testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@743f4fff, picard.sam.MergeBamAlignmentTest$HitSpec@4d5efa4f, picard.sam.MergeBamAlignmentTest$HitSpec@4687ab66], null, 1, 0)	0.080s	passed
testMerger	0.090s	passed
testMergerFromMultipleFiles	0.055s	passed
testMergerWithSupplemental	0.040s	passed
testMergingFromSeparatedReadTrimmedAlignments[0](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam], 17, 20, one file per read)	0.054s	passed
testMergingFromSeparatedReadTrimmedAlignments[1](testdata/picard/sam/MergeBamAlignment/unmapped.sam, [testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam], [testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam], 17, 20, two files per read)	0.113s	passed
testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2507b3d, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@f670760)	0.095s	passed
testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2cfa1b52, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2675d0ee)	0.104s	passed
testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@2af3dd33, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@65f95d25)	0.105s	passed
testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@423ad7c6, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3be8ce4b)	0.119s	passed
testMultiHit	0.085s	passed
testOldQuerynameSortFails	0.044s	passed
testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@297a20a8, picard.sam.MergeBamAlignmentTest$HitSpec@172a4e93, picard.sam.MergeBamAlignmentTest$HitSpec@5be99b30], [], -1, 1, 1, 9)	0.072s	passed
testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@35d0af71, picard.sam.MergeBamAlignmentTest$HitSpec@71f99324, picard.sam.MergeBamAlignmentTest$HitSpec@2ea99e37], [picard.sam.MergeBamAlignmentTest$HitSpec@10b5e13e, picard.sam.MergeBamAlignmentTest$HitSpec@20ae7f7e, picard.sam.MergeBamAlignmentTest$HitSpec@1df3a8fc], 2, 3, 2, 40)	0.053s	passed
testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@16aa1057, picard.sam.MergeBamAlignmentTest$HitSpec@63cbe93c, picard.sam.MergeBamAlignmentTest$HitSpec@2c1d56a1], [picard.sam.MergeBamAlignmentTest$HitSpec@18c1752b, picard.sam.MergeBamAlignmentTest$HitSpec@5eafe6cc, picard.sam.MergeBamAlignmentTest$HitSpec@6291762c], 2, 2, 3, 40)	0.051s	passed
testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1605397b, picard.sam.MergeBamAlignmentTest$HitSpec@2a2d8df, picard.sam.MergeBamAlignmentTest$HitSpec@6c298061], [picard.sam.MergeBamAlignmentTest$HitSpec@3cac5612, picard.sam.MergeBamAlignmentTest$HitSpec@35d7e1d, picard.sam.MergeBamAlignmentTest$HitSpec@17ad3a89], null, 1, 1, 0)	0.064s	passed
testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@450f1b1e, picard.sam.MergeBamAlignmentTest$HitSpec@4e224396, picard.sam.MergeBamAlignmentTest$HitSpec@3b40bbb3], -1, 1, 1, 11)	0.051s	passed
testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@35e54f10, picard.sam.MergeBamAlignmentTest$HitSpec@5ce604bc, picard.sam.MergeBamAlignmentTest$HitSpec@16c185f7], [], null, 1, 1, 0)	0.049s	passed
testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@1e0229f9, picard.sam.MergeBamAlignmentTest$HitSpec@173b5398, picard.sam.MergeBamAlignmentTest$HitSpec@3c49573f], null, 1, 1, 0)	0.052s	passed
testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@4ec58f6, picard.sam.MergeBamAlignmentTest$HitSpec@4fb89c4, picard.sam.MergeBamAlignmentTest$HitSpec@378a1c88], [picard.sam.MergeBamAlignmentTest$HitSpec@17966345, picard.sam.MergeBamAlignmentTest$HitSpec@715bb2a9, picard.sam.MergeBamAlignmentTest$HitSpec@2936a0ef], -1, 3, 3, 30)	0.049s	passed
testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@4b35d9c6, picard.sam.MergeBamAlignmentTest$HitSpec@48cbe76f, picard.sam.MergeBamAlignmentTest$HitSpec@52c88024], [picard.sam.MergeBamAlignmentTest$HitSpec@54293e8a, picard.sam.MergeBamAlignmentTest$HitSpec@31b72620, picard.sam.MergeBamAlignmentTest$HitSpec@26d04fe6], -1, 2, 3, 30)	0.049s	passed
testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@63ed7ee3, picard.sam.MergeBamAlignmentTest$HitSpec@670500a0, picard.sam.MergeBamAlignmentTest$HitSpec@12215844], [picard.sam.MergeBamAlignmentTest$HitSpec@1c3b043c, picard.sam.MergeBamAlignmentTest$HitSpec@14296b3e, picard.sam.MergeBamAlignmentTest$HitSpec@5b66791b], 1, 2, 2, 21)	0.047s	passed
testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@5bc9f865, picard.sam.MergeBamAlignmentTest$HitSpec@4b0f8d51, picard.sam.MergeBamAlignmentTest$HitSpec@59ef5610], [picard.sam.MergeBamAlignmentTest$HitSpec@42defa6f, picard.sam.MergeBamAlignmentTest$HitSpec@56c02881, picard.sam.MergeBamAlignmentTest$HitSpec@6192420d], 1, 2, 2, 21)	0.051s	passed
testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@5cee47d6, picard.sam.MergeBamAlignmentTest$HitSpec@3781b28c, picard.sam.MergeBamAlignmentTest$HitSpec@13b58650], [picard.sam.MergeBamAlignmentTest$HitSpec@6ddc4a59, picard.sam.MergeBamAlignmentTest$HitSpec@432270c3, picard.sam.MergeBamAlignmentTest$HitSpec@798daff9], -1, 2, 2, 30)	0.069s	passed
testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@4c9f5872, picard.sam.MergeBamAlignmentTest$HitSpec@4721cafc, picard.sam.MergeBamAlignmentTest$HitSpec@24a32c6a], [picard.sam.MergeBamAlignmentTest$HitSpec@14e35896, picard.sam.MergeBamAlignmentTest$HitSpec@2209ceb0, picard.sam.MergeBamAlignmentTest$HitSpec@6bb68627], 1, 2, 2, 40)	0.057s	passed
testShortFragmentClipping	0.028s	passed
testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, Basic test with pre-sorted alignment)	0.011s	passed
testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, Basic test with unsorted alignment)	0.014s	passed

Standard output

No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found
No errors found

Standard error

[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8308020900688176681.sam ALIGNED_BAM=[/tmp/aligned.4116099007356663233.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary4470006605862741174.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.4116099007356663233.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5547336296155264099.sam ALIGNED_BAM=[/tmp/aligned.394806908706393452.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary8050237968577445077.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.394806908706393452.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.731588744497544108.sam ALIGNED_BAM=[/tmp/aligned.2519176884035441087.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary958628788286122579.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.2519176884035441087.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7579025887919317022.sam ALIGNED_BAM=[/tmp/aligned.2504637004385388192.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary6035919463262610503.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.2504637004385388192.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3711375531432251301.sam ALIGNED_BAM=[/tmp/aligned.4820065579194757716.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary1390331305794397990.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.4820065579194757716.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1586756054021091398.sam ALIGNED_BAM=[/tmp/aligned.1203189100566210768.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary3243600245289660498.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.1203189100566210768.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6062962415549872936.sam ALIGNED_BAM=[/tmp/aligned.8751629118253341400.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary2406422989482376522.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.8751629118253341400.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6675315051206584949.sam ALIGNED_BAM=[/tmp/aligned.3100246363269302597.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary5726742311015319127.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.3100246363269302597.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6153371676043689830.sam ALIGNED_BAM=[/tmp/aligned.2080919421141693134.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary46429611297501561.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.2080919421141693134.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2921440749254313427.sam ALIGNED_BAM=[/tmp/aligned.6165150429432764346.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary7161234646720669692.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.6165150429432764346.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.645914904750235720.sam ALIGNED_BAM=[/tmp/aligned.5914128636687635061.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary1611823270847521117.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.5914128636687635061.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7943859509104145784.sam ALIGNED_BAM=[/tmp/aligned.239749465557906154.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary3079246463144212457.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:55 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 04:11:55	SamAlignmentMerger	[/tmp/aligned.239749465557906154.sam]
INFO	2016-08-16 04:11:55	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:55 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5064157878511146934.sam ALIGNED_BAM=[/tmp/aligned.7753932883418969496.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary3679571842535716942.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.7753932883418969496.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.746554391749719934.sam ALIGNED_BAM=[/tmp/aligned.5700492940348633869.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary6477578498175128575.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.5700492940348633869.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3530918522730329132.sam ALIGNED_BAM=[/tmp/aligned.1482978467118886340.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary3748349686472960435.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.1482978467118886340.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2023144002775881798.sam ALIGNED_BAM=[/tmp/aligned.6494797434560088405.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary4200373874867046304.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.6494797434560088405.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757937664
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3977420692369402431.sam ALIGNED_BAM=[/tmp/aligned.5483323283077327862.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary2441493277354349282.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.5483323283077327862.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4029292843396552304.sam ALIGNED_BAM=[/tmp/aligned.6646340188905520928.sam] OUTPUT=/tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary8052251163771314596.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=BestEndMapq INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.6646340188905520928.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 6 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] OUTPUT=/tmp/merged5560798288906688686.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 UNMAP_CONTAMINANT_READS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam]
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_multiple_primary_1 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_multiple_primary_1 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: frag_primary_clipped 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_clipped 1/2 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_clipped 2/2 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_perfect 1/2 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_perfect 2/2 50b aligned read.
WARNING	2016-08-16 04:11:56	AbstractAlignmentMerger	Record looks like foreign contamination; making unmapped: r1_clipped_r2_unmapped 1/2 50b aligned read.
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 4 alignment records and 11 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged5560798288906688686.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:56 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 04:11:56 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.8718730608688437795.sam ALIGNED_BAM=[/tmp/aligned.8249164866990270124.sam] OUTPUT=/tmp/simpleForward6257766511644012512.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.8249164866990270124.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.702180268385687350.sam ALIGNED_BAM=[/tmp/aligned.8302395450457866103.sam] OUTPUT=/tmp/simpleReverse3521162525031584346.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.8302395450457866103.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2448400122640139571.sam ALIGNED_BAM=[/tmp/aligned.5842800660117742339.sam] OUTPUT=/tmp/2 forward one earlier4785140863025811591.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.5842800660117742339.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3470896927230792805.sam ALIGNED_BAM=[/tmp/aligned.2065282348928171896.sam] OUTPUT=/tmp/forward earlier than reverse2037540485634600000.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.2065282348928171896.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3583260330204963153.sam ALIGNED_BAM=[/tmp/aligned.456431811335939957.sam] OUTPUT=/tmp/reverse earlier than forward4799587288019069327.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.456431811335939957.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4201191562398108469.sam ALIGNED_BAM=[/tmp/aligned.2795484779800564099.sam] OUTPUT=/tmp/tie resolved via MAPQ5871770542283080725.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.2795484779800564099.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2785488768725226133.sam ALIGNED_BAM=[/tmp/aligned.3878622910349451574.sam] OUTPUT=/tmp/tie with same MAPQ resolved arbitrarily23222188760546009.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.3878622910349451574.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2515950307770337116.sam ALIGNED_BAM=[/tmp/aligned.677873534749683384.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ598372575866020703.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.677873534749683384.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4408874091773353675.sam ALIGNED_BAM=[/tmp/aligned.2028329916292947148.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ4558813616787032249.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.2028329916292947148.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.379010154194280836.sam ALIGNED_BAM=[/tmp/aligned.2052938250947426648.sam] OUTPUT=/tmp/Insertion makes alignment later3232562543853379288.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.2052938250947426648.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.7990496941877503993.sam ALIGNED_BAM=[/tmp/aligned.3200792057656172557.sam] OUTPUT=/tmp/one cigar with deletion and higher MAPQ -- reverse4343553742473646284.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:56 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 04:11:56	SamAlignmentMerger	[/tmp/aligned.3200792057656172557.sam]
INFO	2016-08-16 04:11:56	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:56 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.4542208715952223104.sam ALIGNED_BAM=[/tmp/aligned.285230701781730550.sam] OUTPUT=/tmp/one cigar with deletion and lower MAPQ -- reverse4312410455110033492.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.285230701781730550.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5950331013205227970.sam ALIGNED_BAM=[/tmp/aligned.4221204509606191918.sam] OUTPUT=/tmp/Insertion makes alignment later -- reverse4918044297396297776.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 ATTRIBUTES_TO_RETAIN=[YB] EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment UNMAP_CONTAMINANT_READS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.4221204509606191918.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1086691658119367796.sam ALIGNED_BAM=[/tmp/aligned.9059507068253584146.sam] OUTPUT=/tmp/mergeTest2235094573464887687.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=EarliestFragment    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.9059507068253584146.sam]
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.225143882220786654.sam] OUTPUT=/tmp/merged.3962277066299275764.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.225143882220786654.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1762656256
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.3962277066299275764.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:57 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 04:11:57 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.3793387900525465918.sam] OUTPUT=/tmp/merged.6120700189941620186.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.3793387900525465918.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6120700189941620186.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:57 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 04:11:57 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8110530995124572244.sam] OUTPUT=/tmp/merged.4213339331497717253.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.8110530995124572244.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 2 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.4213339331497717253.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:57 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 04:11:57 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.227618970625354836.sam] OUTPUT=/tmp/merged.6157152816286411376.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.227618970625354836.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 1 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6157152816286411376.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:57 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 04:11:57 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam ALIGNED_BAM=[/tmp/aligned.5159773670586860728.sam] OUTPUT=/tmp/merged.2811032279254403319.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=false CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.5159773670586860728.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 0 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.2811032279254403319.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:57 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 04:11:57 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest9184569063966810006.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/aligned.sam]
WARNING	2016-08-16 04:11:57	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
INFO	2016-08-16 04:11:57	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/aligned.sam] OUTPUT=/tmp/mergeTest9184569063966810006.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/aligned.sam]
WARNING	2016-08-16 04:11:57	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
INFO	2016-08-16 04:11:57	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/onehalfaligned.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/otherhalfaligned.sam] OUTPUT=/tmp/mergeTest5469458980977312861.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/onehalfaligned.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/otherhalfaligned.sam]
WARNING	2016-08-16 04:11:57	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: both_reads_present_only_first_aligns 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
INFO	2016-08-16 04:11:57	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] OUTPUT=/tmp/mergeWithSupplementalTest4173862782230060436.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest337999499607702867.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR]    ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/unmapped.sam READ1_ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam] READ2_ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam, /bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam] OUTPUT=/tmp/mergeMultipleAlignmentsTest6351577054098560164.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 READ1_TRIM=17 READ2_TRIM=20 EXPECTED_ORIENTATIONS=[FR]    ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[]
WARNING	2016-08-16 04:11:57	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: test:6 1/2 36b aligned read. > test:2 1/2 36b aligned read.
INFO	2016-08-16 04:11:57	SamAlignmentMerger	Finished reading 12 total records from alignment SAM/BAM.
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 8 alignment records and 4 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.6444901536994647377.sam ALIGNED_BAM=[/tmp/aligned.2960708499730875478.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary9024983188011444870.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.2960708499730875478.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3072266904874681238.sam ALIGNED_BAM=[/tmp/aligned.3636736686767374587.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary3229102569144315286.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:57 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 04:11:57	SamAlignmentMerger	[/tmp/aligned.3636736686767374587.sam]
INFO	2016-08-16 04:11:57	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:57 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1302675247140343986.sam ALIGNED_BAM=[/tmp/aligned.2784391193656164823.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary627200285569610815.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.2784391193656164823.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.3695914373852990297.sam ALIGNED_BAM=[/tmp/aligned.3938751767808128393.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary9201200690721285728.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.3938751767808128393.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 14 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.5083037787128282106.sam ALIGNED_BAM=[/tmp/aligned.903547354373224313.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary5326058007049864977.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.903547354373224313.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1518005053567750647.sam ALIGNED_BAM=[/tmp/aligned.2535245838994241770.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary7071450611863707638.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.2535245838994241770.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.1401417629593284743.sam ALIGNED_BAM=[/tmp/aligned.4858389684172875190.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary6429108930023095927.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=true    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.4858389684172875190.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/tmp/unmapped.2738402361401972075.sam ALIGNED_BAM=[/tmp/aligned.1307376000322694095.sam] OUTPUT=/tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary6902908130799209644.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR] PRIMARY_ALIGNMENT_STRATEGY=MostDistant INCLUDE_SECONDARY_ALIGNMENTS=false    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate CLIP_OVERLAPPING_READS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.1307376000322694095.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 8 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] OUTPUT=/tmp/merged1943447101197001953.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 20 alignment records and 7 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged1943447101197001953.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] OUTPUT=/tmp/merged6227011914081526117.bam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam]
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7302468427913654424.sam] OUTPUT=/tmp/merged.8312193738117242994.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.7302468427913654424.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.8312193738117242994.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.6830605938925962865.sam] OUTPUT=/tmp/merged.6388150386410246627.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.6830605938925962865.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 1 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.6388150386410246627.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1395527318307212788.sam] OUTPUT=/tmp/merged.7002966967935671931.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.1395527318307212788.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.7002966967935671931.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.4761022421957960482.sam] OUTPUT=/tmp/merged.1162798060554523131.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.4761022421957960482.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.1162798060554523131.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7970467477375876177.sam] OUTPUT=/tmp/merged.1657277165718995751.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.7970467477375876177.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 5 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.1657277165718995751.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.1742770225057021583.sam] OUTPUT=/tmp/merged.1515502124233527511.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.1742770225057021583.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 4 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.1515502124233527511.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.7584884706745270201.sam] OUTPUT=/tmp/merged.2309919582876124530.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.7584884706745270201.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.2309919582876124530.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.8554902845135804316.sam] OUTPUT=/tmp/merged.144418233678419184.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.8554902845135804316.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.144418233678419184.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1757413376
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.3787279795302823020.sam] OUTPUT=/tmp/merged.5695401245913042357.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.3787279795302823020.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 3 alignment records and 1 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.5695401245913042357.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.2023701509722868457.sam] OUTPUT=/tmp/merged.3587651977533152905.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.2023701509722868457.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 4 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.3587651977533152905.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:58 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 04:11:58 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.9137052760779090925.sam] OUTPUT=/tmp/merged.687430152315981404.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:58 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 04:11:58	SamAlignmentMerger	[/tmp/aligned.9137052760779090925.sam]
INFO	2016-08-16 04:11:58	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:58 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.687430152315981404.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:59 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 04:11:59 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.475343617408929615.sam] OUTPUT=/tmp/merged.4563081225146581857.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:59 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 04:11:59	SamAlignmentMerger	[/tmp/aligned.475343617408929615.sam]
INFO	2016-08-16 04:11:59	AbstractAlignmentMerger	Wrote 5 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.4563081225146581857.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:59 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 04:11:59 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam ALIGNED_BAM=[/tmp/aligned.9167072798147434577.sam] OUTPUT=/tmp/merged.1470753523253609765.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/merger.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:59 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 04:11:59	SamAlignmentMerger	[/tmp/aligned.9167072798147434577.sam]
INFO	2016-08-16 04:11:59	AbstractAlignmentMerger	Wrote 0 alignment records and 2 unmapped reads.
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.ValidateSamFile INPUT=/tmp/merged.1470753523253609765.sam    MODE=VERBOSE MAX_OUTPUT=100 IGNORE_WARNINGS=false VALIDATE_INDEX=true INDEX_VALIDATION_STRINGENCY=EXHAUSTIVE IS_BISULFITE_SEQUENCED=false MAX_OPEN_TEMP_FILES=8000 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 04:11:59 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 04:11:59 CDT 2016] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment UNMAPPED_BAM=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam ALIGNED_BAM=[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] OUTPUT=/tmp/testShortFragmentClipping7628669862888509527.sam REFERENCE_SEQUENCE=/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta PROGRAM_RECORD_ID=0 PROGRAM_GROUP_VERSION=1.0 PROGRAM_GROUP_COMMAND_LINE=align! PROGRAM_GROUP_NAME=myAligner PAIRED_RUN=true CLIP_ADAPTERS=true IS_BISULFITE_SEQUENCE=false ALIGNED_READS_ONLY=false MAX_INSERTIONS_OR_DELETIONS=1 EXPECTED_ORIENTATIONS=[FR]    READ1_TRIM=0 READ2_TRIM=0 ALIGNER_PROPER_PAIR_FLAGS=false SORT_ORDER=coordinate PRIMARY_ALIGNMENT_STRATEGY=BestMapq CLIP_OVERLAPPING_READS=true INCLUDE_SECONDARY_ALIGNMENTS=true ADD_MATE_CIGAR=true UNMAP_CONTAMINANT_READS=false MIN_UNCLIPPED_BASES=32 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 04:11:59 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 04:11:59	SamAlignmentMerger	[/bar/jli/Chip-seq/script/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam]
INFO	2016-08-16 04:11:59	AbstractAlignmentMerger	Wrote 10 alignment records and 0 unmapped reads.
[Tue Aug 16 04:11:59 CDT 2016] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1760559104
INFO	2016-08-16 04:11:59	SamAlignmentMerger	[testdata/picard/sam/aligned_queryname_sorted.sam]
INFO	2016-08-16 04:11:59	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.
INFO	2016-08-16 04:11:59	SamAlignmentMerger	[testdata/picard/sam/aligned.sam]
WARNING	2016-08-16 04:11:59	SamAlignmentMerger	Exception merging bam alignment - attempting to sort aligned reads and try again: Underlying iterator is not queryname sorted: read_2_too_many_gaps 1/2 101b aligned read. > both_reads_align_clip_adapter 2/2 101b aligned read.
INFO	2016-08-16 04:11:59	SamAlignmentMerger	Finished reading 8 total records from alignment SAM/BAM.
INFO	2016-08-16 04:11:59	AbstractAlignmentMerger	Wrote 6 alignment records and 4 unmapped reads.