## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_46/LuC_46_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_46/LuC_46_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_46/LuC_46_dedup_metrics.txt 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 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_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 REMOVE_DUPLICATES=false 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> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Aug 28 17:00:15 NOVT 2025

## 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
Unknown Library	335093	57034094	21244077	344691	221887	17395703	613655	0.306051	74916610

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00726	27835432	0	28021374
2.0	1.47771	8110795	346609	8083660
3.0	1.697437	2491619	51852	2437128
4.0	1.800063	789609	20567	748319
5.0	1.847995	260298	9013	234708
6.0	1.870382	89977	4432	74783
7.0	1.880838	33033	2274	24349
8.0	1.885721	13311	1296	8264
9.0	1.888002	5978	683	2941
10.0	1.889068	2901	412	1170
11.0	1.889565	1719	286	547
12.0	1.889798	985	176	259
13.0	1.889906	630	143	149
14.0	1.889957	441	70	92
15.0	1.889981	302	63	78
16.0	1.889992	257	39	57
17.0	1.889997	194	41	61
18.0	1.889999	146	23	53
19.0	1.89	126	12	39
20.0	1.890001	77	12	29
21.0	1.890001	72	10	21
22.0	1.890001	55	9	23
23.0	1.890001	50	9	22
24.0	1.890001	36	5	17
25.0	1.890001	34	8	13
26.0	1.890001	30	0	17
27.0	1.890001	23	2	11
28.0	1.890001	19	1	12
29.0	1.890001	22	0	11
30.0	1.890001	23	0	19
31.0	1.890001	20	0	13
32.0	1.890001	14	0	7
33.0	1.890001	8	1	10
34.0	1.890001	7	1	6
35.0	1.890001	14	0	8
36.0	1.890001	8	1	11
37.0	1.890001	9	0	6
38.0	1.890001	6	0	5
39.0	1.890001	8	0	4
40.0	1.890001	7	0	6
41.0	1.890001	6	0	4
42.0	1.890001	6	0	4
43.0	1.890001	0	0	1
44.0	1.890001	6	0	7
45.0	1.890001	4	2	3
46.0	1.890001	6	0	4
47.0	1.890001	4	0	4
48.0	1.890001	2	0	3
49.0	1.890001	2	0	1
50.0	1.890001	2	0	4
51.0	1.890001	2	0	2
52.0	1.890001	5	0	2
53.0	1.890001	2	0	1
54.0	1.890001	1	0	3
55.0	1.890001	3	0	2
56.0	1.890001	0	0	0
57.0	1.890001	1	0	2
58.0	1.890001	5	0	5
59.0	1.890001	0	0	0
60.0	1.890001	2	0	3
61.0	1.890001	1	0	2
62.0	1.890001	4	0	1
63.0	1.890001	2	0	1
64.0	1.890001	1	0	2
65.0	1.890001	2	0	2
66.0	1.890001	1	0	0
67.0	1.890001	0	0	1
68.0	1.890001	1	0	0
69.0	1.890001	0	0	0
70.0	1.890001	0	0	0
71.0	1.890001	0	0	0
72.0	1.890001	0	0	1
73.0	1.890001	0	0	0
74.0	1.890001	1	0	1
75.0	1.890001	1	0	1
76.0	1.890001	2	0	1
77.0	1.890001	1	0	1
78.0	1.890001	1	0	1
79.0	1.890001	0	0	0
80.0	1.890001	0	0	2
81.0	1.890001	1	0	0
82.0	1.890001	1	0	0
83.0	1.890001	0	0	1
84.0	1.890001	1	0	0
85.0	1.890001	1	0	1
86.0	1.890001	0	0	1
87.0	1.890001	0	0	0
88.0	1.890001	2	0	1
89.0	1.890001	0	0	2
90.0	1.890001	2	0	1
91.0	1.890001	2	0	1
92.0	1.890001	0	0	0
93.0	1.890001	0	0	0
94.0	1.890001	0	0	0
95.0	1.890001	1	0	1
96.0	1.890001	0	0	2
97.0	1.890001	1	0	0
98.0	1.890001	0	0	0
99.0	1.890001	0	0	0
100.0	1.890001	0	0	0
101.0	0	2	0	1
102.0	0	1	0	1
109.0	0	1	0	1
113.0	0	1	0	1
137.0	0	0	0	1
139.0	0	1	0	0
152.0	0	0	0	1
153.0	0	1	0	0