Class picard.sam.ReorderSamTest
|
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