## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[two.sorted.bam] OUTPUT=two.markdup.bam METRICS_FILE=two.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.a1OFT5tvei] VALIDATION_STRINGENCY=SILENT MAX_RECORDS_IN_RAM=250000 CREATE_INDEX=true MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 SORTING_COLLECTION_SIZE_RATIO=0.25 REMOVE_SEQUENCING_DUPLICATES=false CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_DUP_STRATEGY=FLOW_QUALITY_SUM_STRATEGY FLOW_USE_END_IN_UNPAIRED_READS=false FLOW_USE_UNPAIRED_CLIPPED_END=false FLOW_UNPAIRED_END_UNCERTAINTY=0 FLOW_UNPAIRED_START_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 CREATE_MD5_FILE=false USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Mon Jun 08 19:34:50 UTC 2026
## METRICS CLASS picard.sam.DuplicationMetrics
LIBRARY UNPAIRED_READS_EXAMINED READ_PAIRS_EXAMINED SECONDARY_OR_SUPPLEMENTARY_RDS UNMAPPED_READS UNPAIRED_READ_DUPLICATES READ_PAIR_DUPLICATES READ_PAIR_OPTICAL_DUPLICATES PERCENT_DUPLICATION ESTIMATED_LIBRARY_SIZE
two 6 878864 0 2410 5 700137 4560 0.796639 180131
## HISTOGRAM java.lang.Double
BIN CoverageMult all_sets optical_sets non_optical_sets
1.0 1.000191 48752 0 48981
2.0 1.007797 45388 4132 45595
3.0 1.007855 23405 185 23321
4.0 1.007856 14500 18 14442
5.0 1.007856 9603 1 9557
6.0 1.007856 6620 0 6557
7.0 1.007856 4818 0 4788
8.0 1.007856 3577 0 3575
9.0 1.007856 2919 0 2904
10.0 1.007856 2430 0 2409
11.0 1.007856 1841 0 1836
12.0 1.007856 1499 0 1476
13.0 1.007856 1320 0 1331
14.0 1.007856 1097 0 1078
15.0 1.007856 903 0 894
16.0 1.007856 853 0 846
17.0 1.007856 786 0 773
18.0 1.007856 597 0 603
19.0 1.007856 576 0 577
20.0 1.007856 491 0 483
21.0 1.007856 431 0 443
22.0 1.007856 399 0 369
23.0 1.007856 325 0 336
24.0 1.007856 342 0 350
25.0 1.007856 286 0 281
26.0 1.007856 257 0 245
27.0 1.007856 270 0 280
28.0 1.007856 234 0 224
29.0 1.007856 204 0 199
30.0 1.007856 187 0 192
31.0 1.007856 212 0 210
32.0 1.007856 158 0 148
33.0 1.007856 184 0 189
34.0 1.007856 148 0 153
35.0 1.007856 135 0 120
36.0 1.007856 120 0 126
37.0 1.007856 149 0 149
38.0 1.007856 110 0 111
39.0 1.007856 122 0 120
40.0 1.007856 111 0 119
41.0 1.007856 142 0 134
42.0 1.007856 76 0 81
43.0 1.007856 116 0 120
44.0 1.007856 100 0 84
45.0 1.007856 88 0 95
46.0 1.007856 72 0 73
47.0 1.007856 69 0 67
48.0 1.007856 76 0 82
49.0 1.007856 85 0 85
50.0 1.007856 71 0 64
51.0 1.007856 53 0 47
52.0 1.007856 47 0 43
53.0 1.007856 35 0 39
54.0 1.007856 51 0 50
55.0 1.007856 41 0 47
56.0 1.007856 65 0 62
57.0 1.007856 35 0 31
58.0 1.007856 34 0 39
59.0 1.007856 37 0 34
60.0 1.007856 46 0 44
61.0 1.007856 37 0 37
62.0 1.007856 45 0 53
63.0 1.007856 47 0 41
64.0 1.007856 35 0 32
65.0 1.007856 42 0 41
66.0 1.007856 33 0 32
67.0 1.007856 25 0 24
68.0 1.007856 33 0 38
69.0 1.007856 27 0 32
70.0 1.007856 44 0 40
71.0 1.007856 35 0 29
72.0 1.007856 34 0 35
73.0 1.007856 31 0 31
74.0 1.007856 33 0 33
75.0 1.007856 26 0 19
76.0 1.007856 23 0 37
77.0 1.007856 31 0 30
78.0 1.007856 20 0 12
79.0 1.007856 15 0 21
80.0 1.007856 29 0 22
81.0 1.007856 19 0 16
82.0 1.007856 16 0 25
83.0 1.007856 29 0 27
84.0 1.007856 29 0 26
85.0 1.007856 18 0 21
86.0 1.007856 13 0 18
87.0 1.007856 29 0 28
88.0 1.007856 24 0 20
89.0 1.007856 22 0 21
90.0 1.007856 16 0 18
91.0 1.007856 26 0 22
92.0 1.007856 19 0 19
93.0 1.007856 13 0 11
94.0 1.007856 10 0 11
95.0 1.007856 12 0 14
96.0 1.007856 18 0 15
97.0 1.007856 17 0 20
98.0 1.007856 16 0 14
99.0 1.007856 15 0 13
100.0 1.007856 7 0 7
101.0 0 3 0 2
102.0 0 3 0 1
103.0 0 2 0 1
104.0 0 1 0 0
106.0 0 0 0 1
109.0 0 1 0 1
110.0 0 2 0 1
112.0 0 1 0 1
114.0 0 0 0 1
115.0 0 1 0 1
116.0 0 1 0 0
125.0 0 1 0 1