Class picard.sam.ReorderSamTest

24

tests

0

failures

0

ignored

0.598s

duration

100%

successful

Tests

Test Duration Result
TestsWithIndex[0](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[])], true, 0) 0.058s passed
TestsWithIndex[10](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[])], true, 0) 0.034s passed
TestsWithIndex[11](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[])], false, 1) 0.021s passed
TestsWithIndex[1](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[])], false, 0) 0.038s passed
TestsWithIndex[2](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null,alternate_names=[])], false, 1) 0.021s passed
TestsWithIndex[3](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null,alternate_names=[])], true, 1) 0.022s passed
TestsWithIndex[4](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[])], true, 0) 0.034s passed
TestsWithIndex[5](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[])], false, 1) 0.021s passed
TestsWithIndex[6](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[])], true, 0) 0.033s passed
TestsWithIndex[7](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[])], false, 1) 0.024s passed
TestsWithIndex[8](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[])], true, 0) 0.035s passed
TestsWithIndex[9](htsjdk.samtools.SAMRecordSetBuilder@5ba4a00d, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[])], false, 0) 0.034s passed
TestsWithoutIndex[0](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[])], true, 0) 0.023s passed
TestsWithoutIndex[10](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[])], true, 0) 0.022s passed
TestsWithoutIndex[11](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[])], false, 1) 0.013s passed
TestsWithoutIndex[1](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[])], false, 0) 0.022s passed
TestsWithoutIndex[2](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null,alternate_names=[])], false, 1) 0.014s passed
TestsWithoutIndex[3](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr1,length=200000001,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000001,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000001,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000001,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000001,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000001,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000001,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000001,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000001,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000001,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000001,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000001,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000001,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000001,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000001,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000001,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000001,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000001,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000001,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000001,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000001,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000001,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000001,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000001,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000001,dict_index=24,assembly=null,alternate_names=[])], true, 1) 0.014s passed
TestsWithoutIndex[4](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[])], true, 0) 0.022s passed
TestsWithoutIndex[5](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[])], false, 1) 0.013s passed
TestsWithoutIndex[6](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[])], true, 0) 0.022s passed
TestsWithoutIndex[7](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[])], false, 1) 0.014s passed
TestsWithoutIndex[8](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[])], true, 0) 0.022s passed
TestsWithoutIndex[9](htsjdk.samtools.SAMRecordSetBuilder@6f09180, [SAMSequenceRecord(name=test3,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr22,length=200000000,dict_index=21,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr15,length=200000000,dict_index=14,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr19,length=200000000,dict_index=18,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr17,length=200000000,dict_index=16,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr4,length=200000000,dict_index=3,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr8,length=200000000,dict_index=7,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr2,length=200000000,dict_index=1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrX,length=200000000,dict_index=22,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test1,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr1,length=200000000,dict_index=0,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test4,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=test2,length=100,dict_index=-1,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr11,length=200000000,dict_index=10,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr12,length=200000000,dict_index=11,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr7,length=200000000,dict_index=6,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr18,length=200000000,dict_index=17,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr9,length=200000000,dict_index=8,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr5,length=200000000,dict_index=4,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrM,length=200000000,dict_index=24,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chrY,length=200000000,dict_index=23,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr3,length=200000000,dict_index=2,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr6,length=200000000,dict_index=5,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr14,length=200000000,dict_index=13,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr21,length=200000000,dict_index=20,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr13,length=200000000,dict_index=12,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr10,length=200000000,dict_index=9,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr20,length=200000000,dict_index=19,assembly=null,alternate_names=[]), SAMSequenceRecord(name=chr16,length=200000000,dict_index=15,assembly=null,alternate_names=[])], false, 0) 0.022s 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
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 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN5819461147017982727.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN5819461147017982727.bam --OUTPUT /tmp/reorderOUT8482799999298608090.bam --SEQUENCE_DICTIONARY /tmp/reorder16227399313852320036.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT8482799999298608090.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN8226940562067052051.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN8226940562067052051.bam --OUTPUT /tmp/reorderOUT5178214279019896142.bam --SEQUENCE_DICTIONARY /tmp/reorder17255923966721093082.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT5178214279019896142.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN16713715467295841471.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN16713715467295841471.bam --OUTPUT /tmp/reorderOUT1321591120285947977.bam --SEQUENCE_DICTIONARY /tmp/reorder5417430136211471969.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN5958709717155278355.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN5958709717155278355.bam --OUTPUT /tmp/reorderOUT8097419867473927703.bam --SEQUENCE_DICTIONARY /tmp/reorder12229654030353176265.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN17013104219886864255.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN17013104219886864255.bam --OUTPUT /tmp/reorderOUT2885748754670891719.bam --SEQUENCE_DICTIONARY /tmp/reorder11896018796441753415.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT2885748754670891719.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN13060207383284690056.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN13060207383284690056.bam --OUTPUT /tmp/reorderOUT4249103108527856062.bam --SEQUENCE_DICTIONARY /tmp/reorder7280909970428459125.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr6
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN683037488632459807.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN683037488632459807.bam --OUTPUT /tmp/reorderOUT17393261292853363643.bam --SEQUENCE_DICTIONARY /tmp/reorder5744006933435459134.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT17393261292853363643.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN2375280450217745887.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN2375280450217745887.bam --OUTPUT /tmp/reorderOUT15163851587734142492.bam --SEQUENCE_DICTIONARY /tmp/reorder279802377229935062.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr7
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN2090180368105140902.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN2090180368105140902.bam --OUTPUT /tmp/reorderOUT15859035618457669129.bam --SEQUENCE_DICTIONARY /tmp/reorder183351185898931692.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=test3 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test1 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test4 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test2 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT15859035618457669129.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN15706690522305863637.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN15706690522305863637.bam --OUTPUT /tmp/reorderOUT9360055678761274098.bam --SEQUENCE_DICTIONARY /tmp/reorder9184120318109632371.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=test3 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test1 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test4 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test2 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT9360055678761274098.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN16090812195430311111.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN16090812195430311111.bam --OUTPUT /tmp/reorderOUT5640565060557736843.bam --SEQUENCE_DICTIONARY /tmp/reorder14455434194666011859.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr1
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr1
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 5 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr2
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr2
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr3
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr3
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr4
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr4
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr5
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr5
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 2 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr6
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr6
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 1 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr7
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr7
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr8
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr8
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr9
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr9
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr10
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr10
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr11
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr11
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr12
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr12
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr13
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr13
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr14
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr14
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr15
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr15
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr16
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr16
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr17
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr17
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr18
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr18
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr19
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr19
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr20
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr20
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr21
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr21
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chr22
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chr22
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrX
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrX
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrY
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrY
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	writing the reads from chrM
INFO	2025-04-24 13:04:13	ReorderSam	  Processing chrM
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 0 reads
INFO	2025-04-24 13:04:13	ReorderSam	  Processing unmapped
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 3 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderOUT5640565060557736843.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorderIN17825228590216331030.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorderIN17825228590216331030.bam --OUTPUT /tmp/reorderOUT11804635981887749874.bam --SEQUENCE_DICTIONARY /tmp/reorder11150436487759460589.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=22]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr1
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithIndex(ReorderSamTest.java:142)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder6949291189513250007.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder6949291189513250007.sam --OUTPUT /tmp/reorder4292546831215632392.bam --SEQUENCE_DICTIONARY /tmp/reorder1815435026363836294.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder4292546831215632392.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder5125412390183257903.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder5125412390183257903.sam --OUTPUT /tmp/reorder13806438179055541486.bam --SEQUENCE_DICTIONARY /tmp/reorder10610293032133093475.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder13806438179055541486.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder15640369442409227992.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder15640369442409227992.sam --OUTPUT /tmp/reorder3976074541614576337.bam --SEQUENCE_DICTIONARY /tmp/reorder1399911734020406048.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder8216388324870686087.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder8216388324870686087.sam --OUTPUT /tmp/reorder6048345125732792660.bam --SEQUENCE_DICTIONARY /tmp/reorder5392906804222885938.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000001

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: Discordant contig lengths: read chr1 LN=200000000, ref chr1 LN=200000001
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:257)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder1167460271212024913.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder1167460271212024913.sam --OUTPUT /tmp/reorder4698000014892149161.bam --SEQUENCE_DICTIONARY /tmp/reorder11891374493242108940.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder4698000014892149161.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder6433285775620051524.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder6433285775620051524.sam --OUTPUT /tmp/reorder7482173819613559885.bam --SEQUENCE_DICTIONARY /tmp/reorder17817173069868784719.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=20]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr6
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder15862086393879593722.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder15862086393879593722.sam --OUTPUT /tmp/reorder14732410008364178890.bam --SEQUENCE_DICTIONARY /tmp/reorder6898157195783827554.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder14732410008364178890.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder18303498559603145706.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder18303498559603145706.sam --OUTPUT /tmp/reorder17067569600873269678.bam --SEQUENCE_DICTIONARY /tmp/reorder3877975676313785188.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=21]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr7
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder8086403817112082269.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder8086403817112082269.sam --OUTPUT /tmp/reorder5900943133407911910.bam --SEQUENCE_DICTIONARY /tmp/reorder6429402549468137132.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=test3 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test1 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test4 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test2 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder5900943133407911910.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder18422764492991773688.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder18422764492991773688.sam --OUTPUT /tmp/reorder6106480467100398188.bam --SEQUENCE_DICTIONARY /tmp/reorder6809441865935800929.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=test3 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test1 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test4 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=test2 LN=100

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr2 [index=1] to => ref contig chr2 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr1 [index=0] to => ref contig chr1 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=23]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=24]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=25]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=26]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=27]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=28]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder6106480467100398188.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder3567153548122310156.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder3567153548122310156.sam --OUTPUT /tmp/reorder8693667832855932454.bam --SEQUENCE_DICTIONARY /tmp/reorder3905684752931746925.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE true --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=22]

INFO	2025-04-24 13:04:13	ReorderSam	Writing reads...
INFO	2025-04-24 13:04:13	ReorderSam	  Processing All reads
INFO	2025-04-24 13:04:13	ReorderSam	Wrote 17 reads
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder8693667832855932454.bam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ValidateSamFile --INPUT /tmp/reorder4835366899508326543.sam --IGNORE MISSING_TAG_NM --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 13:04:13 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 13:04:13	ValidateSamFile	NM validation cannot be performed without the reference. All other validations will still occur.
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ValidateSamFile done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
[Thu Apr 24 13:04:13 EDT 2025] ReorderSam --INPUT /tmp/reorder4835366899508326543.sam --OUTPUT /tmp/reorder17951184562140053943.bam --SEQUENCE_DICTIONARY /tmp/reorder10033264371001871491.dict --ALLOW_INCOMPLETE_DICT_CONCORDANCE false --ALLOW_CONTIG_LENGTH_DISCORDANCE 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 13:04:13 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 13:04:13	ReorderSam	SAM/BAM/CRAM file
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr1 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr2 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reference
INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr3 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr4 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr5 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr6 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr7 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr8 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr9 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr10 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr11 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr12 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr13 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr14 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr15 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr16 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr17 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr18 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr19 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr20 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr21 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chr22 LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrX LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrY LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	   SN=chrM LN=200000000

INFO	2025-04-24 13:04:13	ReorderSam	Reordering SAM/BAM/CRAM file:
INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr3 [index=2] to => ref contig chr3 [index=0]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr4 [index=3] to => ref contig chr4 [index=1]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr5 [index=4] to => ref contig chr5 [index=2]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr6 [index=5] to => ref contig chr6 [index=3]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr7 [index=6] to => ref contig chr7 [index=4]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr8 [index=7] to => ref contig chr8 [index=5]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr9 [index=8] to => ref contig chr9 [index=6]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr10 [index=9] to => ref contig chr10 [index=7]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr11 [index=10] to => ref contig chr11 [index=8]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr12 [index=11] to => ref contig chr12 [index=9]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr13 [index=12] to => ref contig chr13 [index=10]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr14 [index=13] to => ref contig chr14 [index=11]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr15 [index=14] to => ref contig chr15 [index=12]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr16 [index=15] to => ref contig chr16 [index=13]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr17 [index=16] to => ref contig chr17 [index=14]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr18 [index=17] to => ref contig chr18 [index=15]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr19 [index=18] to => ref contig chr19 [index=16]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr20 [index=19] to => ref contig chr20 [index=17]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr21 [index=20] to => ref contig chr21 [index=18]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chr22 [index=21] to => ref contig chr22 [index=19]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrX [index=22] to => ref contig chrX [index=20]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrY [index=23] to => ref contig chrY [index=21]

INFO	2025-04-24 13:04:13	ReorderSam	  Reordering read contig chrM [index=24] to => ref contig chrM [index=22]

ERROR	2025-04-24 13:04:13	ReorderSam	
picard.PicardException: New reference sequence does not contain a matching contig for chr1
	at picard.sam.ReorderSam.buildSequenceDictionaryMap(ReorderSam.java:273)
	at picard.sam.ReorderSam.doWork(ReorderSam.java:137)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:281)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:105)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:110)
	at picard.cmdline.CommandLineProgramTest.runPicardCommandLine(CommandLineProgramTest.java:109)
	at picard.sam.ReorderSamTest.tester(ReorderSamTest.java:183)
	at picard.sam.ReorderSamTest.TestsWithoutIndex(ReorderSamTest.java:159)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.testng.internal.invokers.MethodInvocationHelper.invokeMethod(MethodInvocationHelper.java:139)
	at org.testng.internal.invokers.TestInvoker.invokeMethod(TestInvoker.java:677)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethod(TestInvoker.java:221)
	at org.testng.internal.invokers.MethodRunner.runInSequence(MethodRunner.java:50)
	at org.testng.internal.invokers.TestInvoker$MethodInvocationAgent.invoke(TestInvoker.java:969)
	at org.testng.internal.invokers.TestInvoker.invokeTestMethods(TestInvoker.java:194)
	at org.testng.internal.invokers.TestMethodWorker.invokeTestMethods(TestMethodWorker.java:148)
	at org.testng.internal.invokers.TestMethodWorker.run(TestMethodWorker.java:128)
	at java.base/java.util.ArrayList.forEach(ArrayList.java:1511)
	at org.testng.TestRunner.privateRun(TestRunner.java:829)
	at org.testng.TestRunner.run(TestRunner.java:602)
	at org.testng.SuiteRunner.runTest(SuiteRunner.java:437)
	at org.testng.SuiteRunner.runSequentially(SuiteRunner.java:431)
	at org.testng.SuiteRunner.privateRun(SuiteRunner.java:391)
	at org.testng.SuiteRunner.run(SuiteRunner.java:330)
	at org.testng.SuiteRunnerWorker.runSuite(SuiteRunnerWorker.java:52)
	at org.testng.SuiteRunnerWorker.run(SuiteRunnerWorker.java:95)
	at org.testng.TestNG.runSuitesSequentially(TestNG.java:1256)
	at org.testng.TestNG.runSuitesLocally(TestNG.java:1176)
	at org.testng.TestNG.runSuites(TestNG.java:1099)
	at org.testng.TestNG.run(TestNG.java:1067)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.runTests(TestNGTestClassProcessor.java:148)
	at org.gradle.api.internal.tasks.testing.testng.TestNGTestClassProcessor.stop(TestNGTestClassProcessor.java:95)
	at org.gradle.api.internal.tasks.testing.SuiteTestClassProcessor.stop(SuiteTestClassProcessor.java:62)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
	at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.base/java.lang.reflect.Method.invoke(Method.java:569)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:36)
	at org.gradle.internal.dispatch.ReflectionDispatch.dispatch(ReflectionDispatch.java:24)
	at org.gradle.internal.dispatch.ContextClassLoaderDispatch.dispatch(ContextClassLoaderDispatch.java:33)
	at org.gradle.internal.dispatch.ProxyDispatchAdapter$DispatchingInvocationHandler.invoke(ProxyDispatchAdapter.java:94)
	at jdk.proxy2/jdk.proxy2.$Proxy5.stop(Unknown Source)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker$3.run(TestWorker.java:193)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.executeAndMaintainThreadName(TestWorker.java:129)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:100)
	at org.gradle.api.internal.tasks.testing.worker.TestWorker.execute(TestWorker.java:60)
	at org.gradle.process.internal.worker.child.ActionExecutionWorker.execute(ActionExecutionWorker.java:56)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:113)
	at org.gradle.process.internal.worker.child.SystemApplicationClassLoaderWorker.call(SystemApplicationClassLoaderWorker.java:65)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.run(GradleWorkerMain.java:69)
	at worker.org.gradle.process.internal.worker.GradleWorkerMain.main(GradleWorkerMain.java:74)
[Thu Apr 24 13:04:13 EDT 2025] picard.sam.ReorderSam done. Elapsed time: 0.00 minutes.
Runtime.totalMemory()=1073741824
To get help, see http://broadinstitute.github.io/picard/index.html#GettingHelp