## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_95/LuC_95_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_95/LuC_95_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/LuC_95/LuC_95_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 17:00:17 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	71483	17285053	5086741	75631	40164	5346667	180931	0.309844	22269870

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.007002	8328966	0	8381989
2.0	1.470393	2468876	100115	2462661
3.0	1.683631	765686	15270	749835
4.0	1.781756	244948	6150	232864
5.0	1.82691	81668	2792	74222
6.0	1.847688	28548	1352	24043
7.0	1.85725	10652	719	7998
8.0	1.86165	4424	395	2791
9.0	1.863674	1981	223	1056
10.0	1.864606	950	168	395
11.0	1.865035	562	80	176
12.0	1.865232	290	55	86
13.0	1.865323	212	35	45
14.0	1.865365	138	28	36
15.0	1.865384	99	16	30
16.0	1.865393	64	18	19
17.0	1.865397	55	11	11
18.0	1.865399	43	9	13
19.0	1.8654	34	7	9
20.0	1.8654	27	3	9
21.0	1.8654	27	1	10
22.0	1.8654	19	0	7
23.0	1.8654	11	2	5
24.0	1.8654	15	4	11
25.0	1.8654	10	1	5
26.0	1.8654	7	1	5
27.0	1.8654	9	0	5
28.0	1.8654	8	1	5
29.0	1.8654	4	1	3
30.0	1.8654	6	0	2
31.0	1.8654	3	1	3
32.0	1.8654	4	0	2
33.0	1.8654	1	0	2
34.0	1.8654	4	0	3
35.0	1.8654	2	0	1
36.0	1.8654	3	0	3
37.0	1.8654	0	0	0
38.0	1.8654	2	0	0
39.0	1.8654	4	1	5
40.0	1.8654	4	0	3
41.0	1.8654	2	0	1
42.0	1.8654	0	0	0
43.0	1.8654	1	0	2
44.0	1.8654	2	0	1
45.0	1.8654	2	0	1
46.0	1.8654	0	0	0
47.0	1.8654	0	0	0
48.0	1.8654	0	0	0
49.0	1.8654	0	0	1
50.0	1.8654	3	0	2
51.0	1.8654	0	0	0
52.0	1.8654	1	0	1
53.0	1.8654	1	0	1
54.0	1.8654	2	0	2
55.0	1.8654	0	0	2
56.0	1.8654	0	0	0
57.0	1.8654	1	0	1
58.0	1.8654	1	0	1
59.0	1.8654	1	0	0
60.0	1.8654	0	0	1
61.0	1.8654	2	0	0
62.0	1.8654	0	0	0
63.0	1.8654	0	0	0
64.0	1.8654	0	0	0
65.0	1.8654	0	0	1
66.0	1.8654	0	0	0
67.0	1.8654	0	0	0
68.0	1.8654	0	0	0
69.0	1.8654	0	0	0
70.0	1.8654	0	0	0
71.0	1.8654	0	0	0
72.0	1.8654	0	0	0
73.0	1.8654	0	0	0
74.0	1.8654	0	0	0
75.0	1.8654	0	0	0
76.0	1.8654	0	0	0
77.0	1.8654	0	0	0
78.0	1.8654	0	0	0
79.0	1.8654	0	0	0
80.0	1.8654	0	0	0
81.0	1.8654	0	0	0
82.0	1.8654	0	0	0
83.0	1.8654	0	0	0
84.0	1.8654	0	0	0
85.0	1.8654	0	0	0
86.0	1.8654	0	0	0
87.0	1.8654	0	0	0
88.0	1.8654	0	0	0
89.0	1.8654	0	0	0
90.0	1.8654	0	0	0
91.0	1.8654	0	0	0
92.0	1.8654	0	0	0
93.0	1.8654	0	0	0
94.0	1.8654	0	0	0
95.0	1.8654	0	0	0
96.0	1.8654	0	0	0
97.0	1.8654	0	0	0
98.0	1.8654	0	0	0
99.0	1.8654	0	0	0
100.0	1.8654	0	0	0
103.0	0	1	0	0