Class picard.sam.MergeBamAlignmentTest
|
100%
successful |
Tests
| Test | Duration | Result |
|---|---|---|
| testBestFragmentMapqStrategy[0](singleAlignmentFirstEnd, [I@78208239, [I@12a55bb0, 12, -1) | 0.021s | passed |
| testBestFragmentMapqStrategy[1](singleAlignmentSecondEnd, [I@323bc94d, [I@36dbaaa4, -1, 12) | 0.018s | passed |
| testBestFragmentMapqStrategy[2](singleAlignmentBothEnd, [I@609c67de, [I@727400d3, 13, 12) | 0.018s | passed |
| testBestFragmentMapqStrategy[3](multipleBothEnds1, [I@6037db83, [I@19bf9cbc, 11, 14) | 0.019s | passed |
| testBestFragmentMapqStrategy[4](multipleBothEnds2, [I@56329b99, [I@68e5eff, 255, 255) | 0.018s | passed |
| testBestFragmentMapqStrategy[5](multipleFirstEnd, [I@305a321e, [I@69de2b67, 12, -1) | 0.019s | passed |
| testBestFragmentMapqStrategy[6](multipleSecondEnd, [I@64323453, [I@74ca1e7d, -1, 12) | 0.018s | passed |
| testBestFragmentMapqStrategy[7](multipleFirstEndSingleSecondEnd, [I@26b71857, [I@42d88d7f, 12, 255) | 0.019s | passed |
| testBestFragmentMapqStrategy[8](singleFirstEndMultipleSecondEnd, [I@59bddd49, [I@1d7625c, 0, 12) | 0.018s | passed |
| testContaminationDetection[0](DO_NOT_CHANGE, contam.expected.NO_CHANGE.sam) | 0.016s | passed |
| testContaminationDetection[1](DO_NOT_CHANGE_INVALID, contam.expected.NO_CHANGE_INVALID.sam) | 0.009s | passed |
| testContaminationDetection[2](null, contam.expected.NO_CHANGE.sam) | 0.015s | passed |
| testContaminationDetection[3](COPY_TO_TAG, contam.expected.COPY_TO_TAG.sam) | 0.014s | passed |
| testContaminationDetection[4](MOVE_TO_TAG, contam.expected.MOVE_TO_TAG.sam) | 0.014s | passed |
| testEarliestFragmentStrategyPaired | 0.008s | passed |
| testEarliestFragmentStrategy[0](simpleForward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@62935b84) | 0.008s | passed |
| testEarliestFragmentStrategy[10](one cigar with deletion and higher MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@1ac59294) | 0.008s | passed |
| testEarliestFragmentStrategy[11](one cigar with deletion and lower MAPQ -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@4ee686f7) | 0.008s | passed |
| testEarliestFragmentStrategy[12](Insertion makes alignment later -- reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@35e3b23b) | 0.008s | passed |
| testEarliestFragmentStrategy[1](simpleReverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@787aadb4) | 0.009s | passed |
| testEarliestFragmentStrategy[2](2 forward one earlier, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5ea46ceb) | 0.008s | passed |
| testEarliestFragmentStrategy[3](forward earlier than reverse, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@7b51f6eb) | 0.008s | passed |
| testEarliestFragmentStrategy[4](reverse earlier than forward, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@37aa7a2f) | 0.008s | passed |
| testEarliestFragmentStrategy[5](tie resolved via MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@7c3b3d15) | 0.008s | passed |
| testEarliestFragmentStrategy[6](tie with same MAPQ resolved arbitrarily, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@5206127e) | 0.009s | passed |
| testEarliestFragmentStrategy[7](one cigar with deletion and higher MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@7d6894c4) | 0.008s | passed |
| testEarliestFragmentStrategy[8](one cigar with deletion and lower MAPQ, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@46bd3c1d) | 0.008s | passed |
| testEarliestFragmentStrategy[9](Insertion makes alignment later, [Lpicard.sam.MergeBamAlignmentTest$MultipleAlignmentSpec;@31d1dee6) | 0.009s | passed |
| testFragmentMultiHitWithFiltering[0](One secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@1a02ae0b, picard.sam.MergeBamAlignmentTest$HitSpec@3ffaad6, picard.sam.MergeBamAlignmentTest$HitSpec@2483015a], -1, 2, 8) | 0.014s | passed |
| testFragmentMultiHitWithFiltering[1](Primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@5da886da, picard.sam.MergeBamAlignmentTest$HitSpec@7c5195f, picard.sam.MergeBamAlignmentTest$HitSpec@237c0d38], -1, 2, 11) | 0.014s | passed |
| testFragmentMultiHitWithFiltering[2](Primary filtered, two secondaries with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@b536e5d, picard.sam.MergeBamAlignmentTest$HitSpec@69fa24d7, picard.sam.MergeBamAlignmentTest$HitSpec@68553e26], -1, 2, 11) | 0.013s | passed |
| testFragmentMultiHitWithFiltering[3](Primary and one secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@455e3515, picard.sam.MergeBamAlignmentTest$HitSpec@34152006, picard.sam.MergeBamAlignmentTest$HitSpec@209a2edb], -1, 1, 9) | 0.014s | passed |
| testFragmentMultiHitWithFiltering[4](All filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@790dbe06, picard.sam.MergeBamAlignmentTest$HitSpec@7525e895, picard.sam.MergeBamAlignmentTest$HitSpec@111c79fa], null, 1, 0) | 0.013s | passed |
| testHeaderFromMappedBreaks[0](specialHeader.aligned.breaks.length.sam) | 0.007s | passed |
| testHeaderFromMappedBreaks[1](specialHeader.aligned.breaks.md5.sam) | 0.007s | passed |
| testMappedReadInUnmappedBam[0](false, false, false, true) | 0.008s | passed |
| testMappedReadInUnmappedBam[1](true, true, false, true) | 0.009s | passed |
| testMappedReadInUnmappedBam[2](true, false, true, true) | 0.007s | passed |
| testMappedReadInUnmappedBam[3](true, true, true, false) | 0.008s | passed |
| testMappedToMultipleStrands | 0.008s | passed |
| testMergeHeaderMappedAndReference | 0.014s | passed |
| testMergeHeaderMappedAndReferenceWithAlignedAsNamedStream | 0.014s | passed |
| testMergeHeaderMappedAndReferenceWithUnmappedAsNamedStream | 0.014s | passed |
| testMerger | 0.023s | passed |
| testMergerFromMultipleFiles | 0.012s | passed |
| testMergerWithSupplemental | 0.009s | 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) | 0.011s | 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) | 0.015s | passed |
| testMostDistantStrategy[0](multipleAlignmentsBothEnds, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@75c8b16f, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@598aa852) | 0.018s | passed |
| testMostDistantStrategy[1](multipleAlignmentsAllChimeric, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@21ec4de7, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3388e0e8) | 0.016s | passed |
| testMostDistantStrategy[2](multipleAlignmentsFirstEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@206083b7, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@34efbca0) | 0.017s | passed |
| testMostDistantStrategy[3](multipleAlignmentsSecondEnd, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@3b0f0fd9, [Lpicard.sam.MergeBamAlignmentTest$MostDistantStrategyAlignmentSpec;@58686389) | 0.016s | passed |
| testMultiHit | 0.015s | passed |
| testOldQuerynameSortFails | 0.007s | passed |
| testPairedMultiHitWithFiltering[0](Only 1st end has alignments, primary alignment is filtered, one 2ndary is filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@38157e38, picard.sam.MergeBamAlignmentTest$HitSpec@65b90fef, picard.sam.MergeBamAlignmentTest$HitSpec@49be9498], [], -1, 1, 1, 9) | 0.014s | passed |
| testPairedMultiHitWithFiltering[10](Both ends aligned, secondary filtered on second end, [picard.sam.MergeBamAlignmentTest$HitSpec@2cffd01d, picard.sam.MergeBamAlignmentTest$HitSpec@698d89b0, picard.sam.MergeBamAlignmentTest$HitSpec@394945b1], [picard.sam.MergeBamAlignmentTest$HitSpec@191a54d, picard.sam.MergeBamAlignmentTest$HitSpec@533ce25a, picard.sam.MergeBamAlignmentTest$HitSpec@56f93184], 2, 3, 2, 40) | 0.013s | passed |
| testPairedMultiHitWithFiltering[11](Both ends aligned, secondary filtered on first end, [picard.sam.MergeBamAlignmentTest$HitSpec@76d1f12, picard.sam.MergeBamAlignmentTest$HitSpec@60c52165, picard.sam.MergeBamAlignmentTest$HitSpec@bfc6f71], [picard.sam.MergeBamAlignmentTest$HitSpec@6cb294b2, picard.sam.MergeBamAlignmentTest$HitSpec@34883b9, picard.sam.MergeBamAlignmentTest$HitSpec@4a4f44bc], 2, 2, 3, 40) | 0.020s | passed |
| testPairedMultiHitWithFiltering[12](Both ends aligned, all filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@28cf09ed, picard.sam.MergeBamAlignmentTest$HitSpec@3e7306cb, picard.sam.MergeBamAlignmentTest$HitSpec@4189ed52], [picard.sam.MergeBamAlignmentTest$HitSpec@29e1eb0c, picard.sam.MergeBamAlignmentTest$HitSpec@79310fbc, picard.sam.MergeBamAlignmentTest$HitSpec@5f521b0f], null, 1, 1, 0) | 0.014s | passed |
| testPairedMultiHitWithFiltering[1](Only 2nd end has alignments, primary alignment is filtered, one 2ndary is filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@49f3ceda, picard.sam.MergeBamAlignmentTest$HitSpec@6d921de8, picard.sam.MergeBamAlignmentTest$HitSpec@73d0907d], -1, 1, 1, 11) | 0.013s | passed |
| testPairedMultiHitWithFiltering[2](Only 1st end has alignments, all are filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@48fb0a31, picard.sam.MergeBamAlignmentTest$HitSpec@53cee8f9, picard.sam.MergeBamAlignmentTest$HitSpec@21d729ec], [], null, 1, 1, 0) | 0.013s | passed |
| testPairedMultiHitWithFiltering[3](Only 2nd end has alignments, all are filtered, [], [picard.sam.MergeBamAlignmentTest$HitSpec@64df048, picard.sam.MergeBamAlignmentTest$HitSpec@5dcbbf91, picard.sam.MergeBamAlignmentTest$HitSpec@56462bde], null, 1, 1, 0) | 0.013s | passed |
| testPairedMultiHitWithFiltering[4](Both ends aligned, one end of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@352450b7, picard.sam.MergeBamAlignmentTest$HitSpec@3a3df7e0, picard.sam.MergeBamAlignmentTest$HitSpec@28f0792e], [picard.sam.MergeBamAlignmentTest$HitSpec@22cb472f, picard.sam.MergeBamAlignmentTest$HitSpec@35fd1a29, picard.sam.MergeBamAlignmentTest$HitSpec@602a6981], -1, 3, 3, 30) | 0.013s | passed |
| testPairedMultiHitWithFiltering[5](Both ends aligned, one end of primary filtered, one end of secondary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@48f9dae7, picard.sam.MergeBamAlignmentTest$HitSpec@2a20949a, picard.sam.MergeBamAlignmentTest$HitSpec@5fc6a2cb], [picard.sam.MergeBamAlignmentTest$HitSpec@13639868, picard.sam.MergeBamAlignmentTest$HitSpec@15cb5601, picard.sam.MergeBamAlignmentTest$HitSpec@3be18466], -1, 2, 3, 30) | 0.021s | passed |
| testPairedMultiHitWithFiltering[6](Both ends aligned, both ends of primary filtered, [picard.sam.MergeBamAlignmentTest$HitSpec@2196bbd5, picard.sam.MergeBamAlignmentTest$HitSpec@339f3520, picard.sam.MergeBamAlignmentTest$HitSpec@c07cabc], [picard.sam.MergeBamAlignmentTest$HitSpec@5800ece, picard.sam.MergeBamAlignmentTest$HitSpec@115c45b8, picard.sam.MergeBamAlignmentTest$HitSpec@5ba04486], 1, 2, 2, 21) | 0.014s | passed |
| testPairedMultiHitWithFiltering[7](Both ends aligned, both ends of primary filtered, two secondary alignments with identical mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@2ae2f027, picard.sam.MergeBamAlignmentTest$HitSpec@7dbf51cb, picard.sam.MergeBamAlignmentTest$HitSpec@4e1c3a92], [picard.sam.MergeBamAlignmentTest$HitSpec@61b53bcb, picard.sam.MergeBamAlignmentTest$HitSpec@5ceb9c12, picard.sam.MergeBamAlignmentTest$HitSpec@5b5daf4d], 1, 2, 2, 21) | 0.014s | passed |
| testPairedMultiHitWithFiltering[8](Both ends aligned, both ends of primary filtered, one end of secondary filtered, but with high mapq, [picard.sam.MergeBamAlignmentTest$HitSpec@5ab003b1, picard.sam.MergeBamAlignmentTest$HitSpec@b1eab76, picard.sam.MergeBamAlignmentTest$HitSpec@262b299c], [picard.sam.MergeBamAlignmentTest$HitSpec@9aab530, picard.sam.MergeBamAlignmentTest$HitSpec@535d923f, picard.sam.MergeBamAlignmentTest$HitSpec@2de6c639], -1, 2, 2, 30) | 0.013s | passed |
| testPairedMultiHitWithFiltering[9](Both ends aligned, secondary filtered on both ends, [picard.sam.MergeBamAlignmentTest$HitSpec@bc7a247, picard.sam.MergeBamAlignmentTest$HitSpec@292cf1fb, picard.sam.MergeBamAlignmentTest$HitSpec@45d700fd], [picard.sam.MergeBamAlignmentTest$HitSpec@3a9250e3, picard.sam.MergeBamAlignmentTest$HitSpec@cf1186c, picard.sam.MergeBamAlignmentTest$HitSpec@429c8320], 1, 2, 2, 40) | 0.013s | passed |
| testRemoveNmMdAndUqOnOverlappingReads | 0.008s | passed |
| testShortFragmentClipping | 0.009s | passed |
| testShortFragmentHardClipping | 0.008s | passed |
| testShortFragmentWithIndelsClipping[0](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected.sam, false) | 0.010s | passed |
| testShortFragmentWithIndelsClipping[1](indel_reads_aligned.sam, indel_reads_unmapped.sam, indel_reads_expected_with_hardclips.sam, true) | 0.009s | passed |
| testSortingOnSamAlignmentMerger[0](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, true, Basic test with pre-sorted alignment) | 0.003s | passed |
| testSortingOnSamAlignmentMerger[1](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, true, Basic test with unsorted alignment) | 0.005s | passed |
| testSortingOnSamAlignmentMerger[2](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned_queryname_sorted.sam, true, false, Basic test with pre-sorted alignment) | 0.002s | passed |
| testSortingOnSamAlignmentMerger[3](testdata/picard/sam/unmapped.sam, testdata/picard/sam/aligned.sam, false, false, Basic test with unsorted alignment) | 0.005s | 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 No errors found No errors found No errors found No errors found No errors found No errors found
Standard error
[Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.1465996826326505610.sam --ALIGNED_BAM /tmp/aligned.4716943363134864319.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndincludeSecondary9962894334592872772.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4716943363134864319.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.10130872271180869001.sam --ALIGNED_BAM /tmp/aligned.1870318670373363666.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentFirstEndexcludeSecondary5733927588096944801.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1870318670373363666.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.6553122999930289676.sam --ALIGNED_BAM /tmp/aligned.13854922593008241950.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndincludeSecondary5348771358618369871.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13854922593008241950.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.16784184458255106031.sam --ALIGNED_BAM /tmp/aligned.16374106162370520789.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentSecondEndexcludeSecondary15792088461236875249.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16374106162370520789.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.15742109920822908301.sam --ALIGNED_BAM /tmp/aligned.16490775971918284977.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndincludeSecondary12241491346854841092.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16490775971918284977.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.10249821173230312374.sam --ALIGNED_BAM /tmp/aligned.9693830279667908460.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleAlignmentBothEndexcludeSecondary13749048736395789000.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.9693830279667908460.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.8850594297202136990.sam --ALIGNED_BAM /tmp/aligned.7718361464912157715.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1includeSecondary16957305271075434389.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7718361464912157715.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.7673441616625552324.sam --ALIGNED_BAM /tmp/aligned.5129531775702310873.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds1excludeSecondary225311851283373799.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5129531775702310873.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.2893720932860346414.sam --ALIGNED_BAM /tmp/aligned.18263115339624400401.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2includeSecondary7285494283365351096.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18263115339624400401.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.12567877103186429040.sam --ALIGNED_BAM /tmp/aligned.3277779539699643319.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleBothEnds2excludeSecondary1793982934712503736.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3277779539699643319.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.415954015389512334.sam --ALIGNED_BAM /tmp/aligned.535011818449276570.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndincludeSecondary5208945392250993777.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.535011818449276570.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.3447832154821399653.sam --ALIGNED_BAM /tmp/aligned.10280088928348655863.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndexcludeSecondary5710201862585827243.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10280088928348655863.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.8663296037022746848.sam --ALIGNED_BAM /tmp/aligned.13477748727841028935.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndincludeSecondary8087587612984520677.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.13477748727841028935.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.10407650431983102856.sam --ALIGNED_BAM /tmp/aligned.3986557972860691350.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleSecondEndexcludeSecondary14493396102343943320.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3986557972860691350.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.13186866896992067948.sam --ALIGNED_BAM /tmp/aligned.8913204579362169718.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndincludeSecondary2224102542449339172.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8913204579362169718.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.166443565352155707.sam --ALIGNED_BAM /tmp/aligned.8857496536618380087.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.multipleFirstEndSingleSecondEndexcludeSecondary2412172921399139609.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8857496536618380087.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.8583230577177465322.sam --ALIGNED_BAM /tmp/aligned.8227147592440213019.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndincludeSecondary9887869715428415286.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8227147592440213019.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.15299882926295493291.sam --ALIGNED_BAM /tmp/aligned.14993019808787458623.sam --OUTPUT /tmp/testBestFragmentMapqStrategy.singleFirstEndMultipleSecondEndexcludeSecondary12589471912495281079.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY BestEndMapq --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14993019808787458623.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam --OUTPUT /tmp/merged482124387330040905.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --SORT_ORDER coordinate --UNMAP_CONTAMINANT_READS true --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged482124387330040905.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam --OUTPUT /tmp/merged18402018346409462747.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --SORT_ORDER coordinate --UNMAP_CONTAMINANT_READS true --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE_INVALID --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam --OUTPUT /tmp/merged9789048505064768877.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --SORT_ORDER coordinate --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged9789048505064768877.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam --OUTPUT /tmp/merged860215458301514525.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --SORT_ORDER coordinate --UNMAP_CONTAMINANT_READS true --UNMAPPED_READ_STRATEGY COPY_TO_TAG --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged860215458301514525.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam --OUTPUT /tmp/merged15962175598457178630.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --SORT_ORDER coordinate --UNMAP_CONTAMINANT_READS true --UNMAPPED_READ_STRATEGY MOVE_TO_TAG --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/contam.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged15962175598457178630.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.11151520580639830310.sam --ALIGNED_BAM /tmp/aligned.11549542088674022565.sam --OUTPUT /tmp/simpleForward16563351993886914362.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11549542088674022565.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.4465625895330546626.sam --ALIGNED_BAM /tmp/aligned.9619299120521285961.sam --OUTPUT /tmp/simpleReverse230532313537065415.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.9619299120521285961.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.5205374259967468016.sam --ALIGNED_BAM /tmp/aligned.11157752091300551000.sam --OUTPUT /tmp/2 forward one earlier2394090722983291282.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11157752091300551000.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.15127304744337411023.sam --ALIGNED_BAM /tmp/aligned.6546325879475622854.sam --OUTPUT /tmp/forward earlier than reverse14776214113267576258.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.6546325879475622854.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.7552630103983141078.sam --ALIGNED_BAM /tmp/aligned.17665709479372599475.sam --OUTPUT /tmp/reverse earlier than forward13475803267284891653.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17665709479372599475.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.7049672008552180056.sam --ALIGNED_BAM /tmp/aligned.11140236865175505446.sam --OUTPUT /tmp/tie resolved via MAPQ15297659037085677429.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11140236865175505446.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.3542555523268324786.sam --ALIGNED_BAM /tmp/aligned.8119284543315347157.sam --OUTPUT /tmp/tie with same MAPQ resolved arbitrarily1579116203998030178.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8119284543315347157.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.10097535395399910559.sam --ALIGNED_BAM /tmp/aligned.1111067925429150783.sam --OUTPUT /tmp/one cigar with deletion and higher MAPQ7363026307534361667.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.1111067925429150783.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.8381863390226407118.sam --ALIGNED_BAM /tmp/aligned.4498016042523518108.sam --OUTPUT /tmp/one cigar with deletion and lower MAPQ14665225777015809505.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4498016042523518108.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.2166782463083407800.sam --ALIGNED_BAM /tmp/aligned.17466661674231377730.sam --OUTPUT /tmp/Insertion makes alignment later3097175210309304764.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17466661674231377730.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.14974344289760706677.sam --ALIGNED_BAM /tmp/aligned.7871928288244065299.sam --OUTPUT /tmp/one cigar with deletion and higher MAPQ -- reverse2369452740929595864.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7871928288244065299.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.14429309418908665098.sam --ALIGNED_BAM /tmp/aligned.18052876012375946653.sam --OUTPUT /tmp/one cigar with deletion and lower MAPQ -- reverse14910935738097696459.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18052876012375946653.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.9323302331704537319.sam --ALIGNED_BAM /tmp/aligned.16600813522943116065.sam --OUTPUT /tmp/Insertion makes alignment later -- reverse543725068136441212.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --UNMAP_CONTAMINANT_READS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16600813522943116065.sam] WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr1 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr2 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr3 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr4 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr5 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr6 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr7 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta WARNING 2025-04-24 13:04:07 SAMSequenceDictionary Found sequence entry for which tags differ: chr8 and tag UR has the two values: merger.fasta and file:testdata/net/sf/picard/sam/merger.fasta. Using merger.fasta INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.3959002884991905983.sam --ALIGNED_BAM /tmp/aligned.5524832296986081124.sam --OUTPUT /tmp/mergeTest4354581012413423874.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY EarliestFragment --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.5524832296986081124.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam --ALIGNED_BAM /tmp/aligned.7035061497568470277.sam --OUTPUT /tmp/merged.11257895926778288982.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7035061497568470277.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.11257895926778288982.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam --ALIGNED_BAM /tmp/aligned.2858883373354282105.sam --OUTPUT /tmp/merged.7416274166262051778.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2858883373354282105.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.7416274166262051778.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam --ALIGNED_BAM /tmp/aligned.11307585667041800354.sam --OUTPUT /tmp/merged.14395771192167564486.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11307585667041800354.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.14395771192167564486.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam --ALIGNED_BAM /tmp/aligned.17533742700669343974.sam --OUTPUT /tmp/merged.12387707535145451231.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.17533742700669343974.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.12387707535145451231.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.fragment.unmapped.sam --ALIGNED_BAM /tmp/aligned.11840825428545676711.sam --OUTPUT /tmp/merged.4401926084595446955.sam --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 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11840825428545676711.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 0 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.4401926084595446955.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam --OUTPUT /tmp/merged12259276149077339969.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.length.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam --OUTPUT /tmp/merged3568868667327046727.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.breaks.md5.sam] ERROR 2025-04-24 13:04:07 SAMSequenceDictionary Cannot merge dictionaries. Found sequence entry for which tags differ: chr1_alt and tag M5 has the two values: dummy! and 8e0c728a0fb8a73feb55f9a447f4b144. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /tmp/unmapped.4747038929155842521.sam --ALIGNED_BAM /tmp/aligned.7170971308007053744.sam --OUTPUT /tmp/output10490775155587226902.sam --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.7170971308007053744.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /tmp/unmapped.2350578658408635756.sam --ALIGNED_BAM /tmp/aligned.10853552008035058768.sam --OUTPUT /tmp/output5000389160909266628.sam --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10853552008035058768.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /tmp/unmapped.17963532778653149834.sam --ALIGNED_BAM /tmp/aligned.10741833251865858896.sam --OUTPUT /tmp/output2622786552481243490.sam --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.10741833251865858896.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /tmp/unmapped.4504548969860107885.sam --ALIGNED_BAM /tmp/aligned.14728161449001049215.sam --OUTPUT /tmp/output5776309919408422700.sam --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14728161449001049215.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 2 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam --OUTPUT /tmp/mappedToMultipleStrands11413885784024135733.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.both.strands.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 9 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam --OUTPUT /tmp/merged13290123585590506798.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged13290123585590506798.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.unmapped.sam --ALIGNED_BAM /dev/fd/5453 --OUTPUT /tmp/merged18101891609163167224.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/dev/fd/5453] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged18101891609163167224.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /dev/fd/5457 --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam --OUTPUT /tmp/merged1790979107358966405.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --UNMAP_CONTAMINANT_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/specialHeader.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 11 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged1790979107358966405.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/aligned.sam --OUTPUT /tmp/mergeTest13430629287034125635.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/aligned.sam] WARNING 2025-04-24 13:04:07 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 to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. INFO 2025-04-24 13:04:07 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/aligned.sam --OUTPUT /tmp/mergeTest13430629287034125635.sam --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/aligned.sam] WARNING 2025-04-24 13:04:07 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 to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. INFO 2025-04-24 13:04:07 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/onehalfaligned.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/otherhalfaligned.sam --OUTPUT /tmp/mergeTest5385289480053970790.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/onehalfaligned.sam, /mounts/lovelace/software/picard/picard/testdata/picard/sam/otherhalfaligned.sam] WARNING 2025-04-24 13:04:07 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 to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. INFO 2025-04-24 13:04:07 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam --OUTPUT /tmp/mergeWithSupplementalTest2587596004328624566.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.supplement.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/unmapped.sam --READ1_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/allread1.trimmed.aligned.sam --READ2_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/allread2.trimmed.aligned.sam --OUTPUT /tmp/mergeMultipleAlignmentsTest12406129451038619023.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --READ1_TRIM 17 --READ2_TRIM 20 --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/unmapped.sam --READ1_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/firsthalf.read1.trimmed.aligned.sam --READ1_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/secondhalf.read1.trimmed.aligned.sam --READ2_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/firsthalf.read2.trimmed.aligned.sam --READ2_ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/secondhalf.read2.trimmed.aligned.sam --OUTPUT /tmp/mergeMultipleAlignmentsTest619581634078902981.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --READ1_TRIM 17 --READ2_TRIM 20 --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [] WARNING 2025-04-24 13:04:07 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 to chr1:15-50. > test:2 1/2 36b aligned to chr7:50-85. INFO 2025-04-24 13:04:07 SamAlignmentMerger Finished reading 12 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 4 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.14915097951041372966.sam --ALIGNED_BAM /tmp/aligned.3773823876033143911.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.includeSecondary3662562856522883309.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3773823876033143911.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.3868227136413726684.sam --ALIGNED_BAM /tmp/aligned.4776493302304462185.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsBothEnds.excludeSecondary162847863676580940.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.4776493302304462185.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.7351300518664607223.sam --ALIGNED_BAM /tmp/aligned.9322546528949864191.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.includeSecondary1359902875551804676.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.9322546528949864191.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.3574272980381187423.sam --ALIGNED_BAM /tmp/aligned.12521727496315108906.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsAllChimeric.excludeSecondary2374835408525168296.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.12521727496315108906.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 14 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.871164770270651354.sam --ALIGNED_BAM /tmp/aligned.8798108780434689854.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.includeSecondary16091326284775879993.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8798108780434689854.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.5385168828030437896.sam --ALIGNED_BAM /tmp/aligned.2610067332180365641.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsFirstEnd.excludeSecondary10301978240871964972.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2610067332180365641.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.17199732355250355169.sam --ALIGNED_BAM /tmp/aligned.8777470597112692325.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.includeSecondary10632496187349839899.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8777470597112692325.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /tmp/unmapped.1632752903902663716.sam --ALIGNED_BAM /tmp/aligned.204982650377474644.sam --OUTPUT /tmp/testMostDistantStrategy.multipleAlignmentsSecondEnd.excludeSecondary3059366972840394826.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --PRIMARY_ALIGNMENT_STRATEGY MostDistant --INCLUDE_SECONDARY_ALIGNMENTS false --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.204982650377474644.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam --OUTPUT /tmp/merged11862845764764058962.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 20 alignment records and 7 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged11862845764764058962.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/unmapped.badorder.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam --OUTPUT /tmp/merged12595180727433781438.bam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/aligned.badorder.sam] [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.14630954389887397763.sam --OUTPUT /tmp/merged.16707438581584347685.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14630954389887397763.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.16707438581584347685.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.628837817444079364.sam --OUTPUT /tmp/merged.11090578444113271058.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.628837817444079364.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 1 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.11090578444113271058.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.3403484546405967744.sam --OUTPUT /tmp/merged.7942721151144941380.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3403484546405967744.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.7942721151144941380.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.2529949460475231218.sam --OUTPUT /tmp/merged.7843647138556746527.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.2529949460475231218.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.7843647138556746527.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.14418104972426641439.sam --OUTPUT /tmp/merged.2395860405492133773.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.14418104972426641439.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.2395860405492133773.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.16480995393435355277.sam --OUTPUT /tmp/merged.8769106051016521495.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16480995393435355277.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.8769106051016521495.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.3879515607479028377.sam --OUTPUT /tmp/merged.8211968842763354839.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.3879515607479028377.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.8211968842763354839.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.12977464226116979966.sam --OUTPUT /tmp/merged.3807026412608787051.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.12977464226116979966.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.3807026412608787051.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.16545960271977462133.sam --OUTPUT /tmp/merged.15720234540719727440.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.16545960271977462133.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 3 alignment records and 1 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.15720234540719727440.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.8727874394870855330.sam --OUTPUT /tmp/merged.12025847795934068790.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8727874394870855330.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 4 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.12025847795934068790.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.11804643755587898545.sam --OUTPUT /tmp/merged.4632427439667698414.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.11804643755587898545.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.4632427439667698414.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.8623030808786182725.sam --OUTPUT /tmp/merged.6191520089226701007.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.8623030808786182725.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 5 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.6191520089226701007.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/multihit.filter.unmapped.sam --ALIGNED_BAM /tmp/aligned.18445171430134126590.sam --OUTPUT /tmp/merged.17360074795165876465.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/merger.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/tmp/aligned.18445171430134126590.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 0 alignment records and 2 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] ValidateSamFile --INPUT /tmp/merged.17360074795165876465.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 --SKIP_MATE_VALIDATION false --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null WARNING 2025-04-24 13:04:07 ValidateSamFile NM validation cannot be performed without the reference. All other validations will still occur. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/removetags.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam --OUTPUT /tmp/testRemoveNmMdAndUqOnOverlappingReads12604263280019023199.sam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --SORT_ORDER queryname --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/removetags.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/removetags.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 8 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:07 EDT 2025] MergeBamAlignment --ADD_PG_TAG_TO_READS true --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam --OUTPUT /tmp/testShortFragmentClipping17309977025078219211.bam --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_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE aa --ATTRIBUTES_TO_REVERSE ac --ATTRIBUTES_TO_REVERSE af --ATTRIBUTES_TO_REVERSE ai --ATTRIBUTES_TO_REVERSE as --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --ATTRIBUTES_TO_REVERSE_COMPLEMENT ab --EXPECTED_ORIENTATIONS FR --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --SORT_ORDER coordinate --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --HARD_CLIP_OVERLAPPING_READS false --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:07 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:07 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.aligned.sam] INFO 2025-04-24 13:04:07 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:07 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:08 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam --OUTPUT /tmp/testShortFragmentClipping9511979777052659681.sam --HARD_CLIP_OVERLAPPING_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --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 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:08 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/hardclip.aligned.sam] INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 10 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:08 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:08 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam --OUTPUT /tmp/testShortFragmentClipping2994757982865890877.sam --SORT_ORDER queryname --HARD_CLIP_OVERLAPPING_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:08 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:08 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 [Thu Apr 24 13:04:08 EDT 2025] MergeBamAlignment --UNMAPPED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_unmapped.sam --ALIGNED_BAM /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam --OUTPUT /tmp/testShortFragmentClipping5964045365724846002.sam --SORT_ORDER queryname --HARD_CLIP_OVERLAPPING_READS true --REFERENCE_SEQUENCE /mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/cliptest.fasta --ADD_PG_TAG_TO_READS true --PAIRED_RUN true --CLIP_ADAPTERS true --IS_BISULFITE_SEQUENCE false --ALIGNED_READS_ONLY false --MAX_INSERTIONS_OR_DELETIONS 1 --ATTRIBUTES_TO_REVERSE OQ --ATTRIBUTES_TO_REVERSE U2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT E2 --ATTRIBUTES_TO_REVERSE_COMPLEMENT SQ --READ1_TRIM 0 --READ2_TRIM 0 --ALIGNER_PROPER_PAIR_FLAGS false --PRIMARY_ALIGNMENT_STRATEGY BestMapq --CLIP_OVERLAPPING_READS true --INCLUDE_SECONDARY_ALIGNMENTS true --ADD_MATE_CIGAR true --UNMAP_CONTAMINANT_READS false --MIN_UNCLIPPED_BASES 32 --MATCHING_DICTIONARY_TAGS M5 --MATCHING_DICTIONARY_TAGS LN --UNMAPPED_READ_STRATEGY DO_NOT_CHANGE --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 100 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false [Thu Apr 24 13:04:08 EDT 2025] Executing as root@lovelace on Linux 6.1.0-28-amd64 amd64; OpenJDK 64-Bit Server VM 17.0.13+11-Debian-2deb12u1; Deflater: Intel; Inflater: Intel; Provider GCS is available; Picard version: Version:null INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [/mounts/lovelace/software/picard/picard/testdata/picard/sam/MergeBamAlignment/indel_reads_aligned.sam] INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 26 alignment records and 0 unmapped reads. [Thu Apr 24 13:04:08 EDT 2025] picard.sam.MergeBamAlignment done. Elapsed time: 0.00 minutes. Runtime.totalMemory()=1073741824 INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] INFO 2025-04-24 13:04:08 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target11841078653754743807bam INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] WARNING 2025-04-24 13:04:08 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 to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. INFO 2025-04-24 13:04:08 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:08 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target10836826439952185524bam INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned_queryname_sorted.sam] INFO 2025-04-24 13:04:08 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target5550842573354005333bam INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads. INFO 2025-04-24 13:04:08 SamAlignmentMerger Processing SAM file(s): [testdata/picard/sam/aligned.sam] INFO 2025-04-24 13:04:08 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target7235917345676818734bam WARNING 2025-04-24 13:04:08 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 to chr7:1-101. > both_reads_align_clip_adapter 2/2 101b aligned to chr7:16-116. INFO 2025-04-24 13:04:08 SamAlignmentMerger Finished reading 8 total records from alignment SAM/BAM. INFO 2025-04-24 13:04:08 SAMFileWriterFactory Unknown file extension, assuming BAM format when writing file: file:///tmp/target7235917345676818734bam INFO 2025-04-24 13:04:08 AbstractAlignmentMerger Wrote 6 alignment records and 4 unmapped reads.