## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates TAG_DUPLICATE_SET_MEMBERS=true TAGGING_POLICY=All INPUT=[four.sorted.bam] OUTPUT=four.markdup.bam METRICS_FILE=four.markdup_metrics.txt REMOVE_DUPLICATES=false OPTICAL_DUPLICATE_PIXEL_DISTANCE=2500 TMP_DIR=[/tmp/nxf.ei2XOLkBkk] 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 19:30:54 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
four 16 874761 0 2404 16 696440 4515 0.796151 179739
## HISTOGRAM java.lang.Double
BIN CoverageMult all_sets optical_sets non_optical_sets
1.0 1.000193 48949 0 49178
2.0 1.007892 45804 4056 46003
3.0 1.007951 23047 200 22989
4.0 1.007952 14087 17 13996
5.0 1.007952 9238 2 9201
6.0 1.007952 6625 0 6607
7.0 1.007952 4840 0 4794
8.0 1.007952 3813 0 3793
9.0 1.007952 2913 0 2879
10.0 1.007952 2301 0 2283
11.0 1.007952 1978 0 1974
12.0 1.007952 1473 0 1465
13.0 1.007952 1206 0 1196
14.0 1.007952 1082 0 1087
15.0 1.007952 973 0 968
16.0 1.007952 798 0 788
17.0 1.007952 797 0 775
18.0 1.007952 654 0 653
19.0 1.007952 564 0 580
20.0 1.007952 510 0 493
21.0 1.007952 454 0 451
22.0 1.007952 430 0 420
23.0 1.007952 348 0 341
24.0 1.007952 282 0 298
25.0 1.007952 344 0 343
26.0 1.007952 289 0 282
27.0 1.007952 241 0 228
28.0 1.007952 193 0 202
29.0 1.007952 214 0 217
30.0 1.007952 198 0 194
31.0 1.007952 205 0 203
32.0 1.007952 168 0 162
33.0 1.007952 133 0 123
34.0 1.007952 166 0 182
35.0 1.007952 175 0 165
36.0 1.007952 120 0 127
37.0 1.007952 109 0 108
38.0 1.007952 95 0 83
39.0 1.007952 120 0 123
40.0 1.007952 119 0 124
41.0 1.007952 63 0 58
42.0 1.007952 83 0 86
43.0 1.007952 94 0 89
44.0 1.007952 102 0 102
45.0 1.007952 78 0 76
46.0 1.007952 48 0 58
47.0 1.007952 54 0 45
48.0 1.007952 65 0 62
49.0 1.007952 53 0 55
50.0 1.007952 60 0 51
51.0 1.007952 33 0 36
52.0 1.007952 38 0 45
53.0 1.007952 48 0 52
54.0 1.007952 58 0 66
55.0 1.007952 63 0 57
56.0 1.007952 54 0 46
57.0 1.007952 22 0 17
58.0 1.007952 52 0 66
59.0 1.007952 73 0 67
60.0 1.007952 40 0 43
61.0 1.007952 47 0 40
62.0 1.007952 38 0 40
63.0 1.007952 43 0 44
64.0 1.007952 41 0 44
65.0 1.007952 47 0 42
66.0 1.007952 32 0 34
67.0 1.007952 31 0 36
68.0 1.007952 45 0 46
69.0 1.007952 40 0 34
70.0 1.007952 45 0 49
71.0 1.007952 44 0 48
72.0 1.007952 33 0 27
73.0 1.007952 27 0 21
74.0 1.007952 41 0 41
75.0 1.007952 20 0 17
76.0 1.007952 20 0 20
77.0 1.007952 24 0 27
78.0 1.007952 19 0 18
79.0 1.007952 22 0 19
80.0 1.007952 18 0 21
81.0 1.007952 17 0 19
82.0 1.007952 17 0 13
83.0 1.007952 21 0 23
84.0 1.007952 18 0 29
85.0 1.007952 31 0 22
86.0 1.007952 21 0 22
87.0 1.007952 26 0 28
88.0 1.007952 26 0 23
89.0 1.007952 20 0 30
90.0 1.007952 33 0 28
91.0 1.007952 24 0 17
92.0 1.007952 23 0 17
93.0 1.007952 14 0 19
94.0 1.007952 14 0 12
95.0 1.007952 19 0 20
96.0 1.007952 10 0 11
97.0 1.007952 12 0 10
98.0 1.007952 14 0 12
99.0 1.007952 7 0 9
100.0 1.007952 17 0 19
101.0 0 11 0 5
102.0 0 3 0 1
103.0 0 2 0 1
105.0 0 1 0 1
107.0 0 2 0 2
109.0 0 1 0 1
114.0 0 0 0 1
115.0 0 2 0 1
117.0 0 1 0 1
121.0 0 0 0 1
122.0 0 1 0 0