## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_104/LuC_104_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_104/LuC_104_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_104/LuC_104_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 17:00:13 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	183035	68243582	28320375	215711	128527	25736146	773567	0.377557	66936534

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.006603	27238957	0	27417130
2.0	1.369751	9285605	405501	9283783
3.0	1.500763	3511582	66107	3469736
4.0	1.548027	1406500	27228	1365676
5.0	1.565078	587299	12911	556255
6.0	1.57123	255167	6479	233559
7.0	1.573449	114148	3451	99917
8.0	1.57425	52938	1927	43944
9.0	1.574539	25556	1135	19698
10.0	1.574643	12767	714	8942
11.0	1.574681	6558	479	4080
12.0	1.574694	3738	308	2070
13.0	1.574699	2144	195	1037
14.0	1.574701	1248	144	534
15.0	1.574701	839	94	286
16.0	1.574702	538	63	156
17.0	1.574702	419	76	127
18.0	1.574702	262	47	63
19.0	1.574702	187	35	50
20.0	1.574702	154	32	45
21.0	1.574702	124	23	43
22.0	1.574702	106	19	38
23.0	1.574702	81	11	25
24.0	1.574702	94	14	39
25.0	1.574702	66	6	25
26.0	1.574702	58	2	16
27.0	1.574702	35	7	11
28.0	1.574702	31	6	11
29.0	1.574702	28	5	11
30.0	1.574702	21	0	12
31.0	1.574702	25	3	10
32.0	1.574702	14	1	8
33.0	1.574702	14	0	7
34.0	1.574702	14	1	5
35.0	1.574702	8	1	5
36.0	1.574702	12	0	7
37.0	1.574702	9	1	6
38.0	1.574702	10	1	5
39.0	1.574702	6	1	3
40.0	1.574702	4	1	8
41.0	1.574702	8	0	5
42.0	1.574702	5	0	2
43.0	1.574702	6	1	6
44.0	1.574702	7	1	4
45.0	1.574702	2	0	3
46.0	1.574702	5	0	3
47.0	1.574702	4	0	3
48.0	1.574702	2	0	3
49.0	1.574702	1	0	0
50.0	1.574702	2	0	3
51.0	1.574702	2	0	1
52.0	1.574702	2	0	2
53.0	1.574702	3	0	2
54.0	1.574702	1	0	1
55.0	1.574702	0	0	0
56.0	1.574702	7	0	4
57.0	1.574702	1	0	1
58.0	1.574702	0	0	0
59.0	1.574702	2	0	2
60.0	1.574702	2	0	1
61.0	1.574702	0	0	0
62.0	1.574702	0	0	0
63.0	1.574702	0	0	0
64.0	1.574702	2	0	2
65.0	1.574702	0	0	1
66.0	1.574702	3	0	1
67.0	1.574702	0	0	0
68.0	1.574702	0	0	0
69.0	1.574702	1	0	1
70.0	1.574702	0	0	0
71.0	1.574702	0	0	1
72.0	1.574702	1	0	0
73.0	1.574702	0	0	0
74.0	1.574702	0	0	0
75.0	1.574702	0	0	0
76.0	1.574702	0	0	0
77.0	1.574702	1	0	1
78.0	1.574702	0	0	0
79.0	1.574702	0	0	0
80.0	1.574702	0	0	0
81.0	1.574702	0	0	0
82.0	1.574702	0	0	0
83.0	1.574702	0	0	0
84.0	1.574702	0	0	0
85.0	1.574702	0	0	0
86.0	1.574702	0	0	0
87.0	1.574702	0	0	0
88.0	1.574702	0	0	0
89.0	1.574702	0	0	0
90.0	1.574702	0	0	0
91.0	1.574702	0	0	0
92.0	1.574702	0	0	0
93.0	1.574702	0	0	0
94.0	1.574702	0	0	0
95.0	1.574702	0	0	0
96.0	1.574702	0	0	0
97.0	1.574702	0	0	0
98.0	1.574702	0	0	0
99.0	1.574702	0	0	0
100.0	1.574702	0	0	0