## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/OPO_227/OPO_227_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/OPO_227/OPO_227_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2024-11-13_ENC/OPO_227/OPO_227_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	516992	59724118	24433401	530788	285724	11650391	593094	0.196611	137712493

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.008013	38885606	0	39133220
2.0	1.661322	7339115	348395	7245932
3.0	2.084741	1436521	48029	1362906
4.0	2.359165	301236	18609	263320
5.0	2.537024	71824	8287	52838
6.0	2.652296	20937	3894	11365
7.0	2.727006	8068	2114	2730
8.0	2.775427	4059	1169	841
9.0	2.806809	2240	642	322
10.0	2.827149	1323	398	130
11.0	2.840331	844	278	59
12.0	2.848874	547	175	26
13.0	2.854412	379	117	19
14.0	2.858	266	67	3
15.0	2.860326	193	39	7
16.0	2.861834	126	39	3
17.0	2.862811	116	31	0
18.0	2.863444	65	17	2
19.0	2.863854	40	15	0
20.0	2.86412	49	12	1
21.0	2.864293	38	18	1
22.0	2.864405	24	6	1
23.0	2.864477	17	4	0
24.0	2.864524	22	5	1
25.0	2.864554	10	3	0
26.0	2.864574	12	2	0
27.0	2.864587	9	4	0
28.0	2.864595	4	5	0
29.0	2.8646	6	0	0
30.0	2.864604	5	1	0
31.0	2.864606	6	0	0
32.0	2.864608	3	0	0
33.0	2.864609	1	3	0
34.0	2.864609	4	0	0
35.0	2.86461	4	0	0
36.0	2.86461	2	0	0
37.0	2.86461	1	0	0
38.0	2.86461	0	0	0
39.0	2.86461	0	0	0
40.0	2.86461	1	0	0
41.0	2.86461	0	0	0
42.0	2.86461	1	0	0
43.0	2.86461	1	1	0
44.0	2.86461	1	0	0
45.0	2.86461	0	0	0
46.0	2.86461	0	0	0
47.0	2.86461	0	0	0
48.0	2.86461	1	0	0
49.0	2.86461	0	0	0
50.0	2.86461	0	0	0
51.0	2.86461	0	0	0
52.0	2.86461	0	0	0
53.0	2.86461	0	0	0
54.0	2.86461	0	0	0
55.0	2.86461	0	0	0
56.0	2.86461	0	0	0
57.0	2.86461	0	0	0
58.0	2.86461	0	0	0
59.0	2.86461	0	0	0
60.0	2.86461	0	0	0
61.0	2.86461	0	0	0
62.0	2.86461	0	0	0
63.0	2.86461	0	0	0
64.0	2.86461	0	0	0
65.0	2.86461	0	0	0
66.0	2.86461	0	0	0
67.0	2.86461	0	0	0
68.0	2.86461	0	0	0
69.0	2.86461	0	0	0
70.0	2.86461	0	0	0
71.0	2.86461	0	0	0
72.0	2.86461	0	0	0
73.0	2.86461	0	0	0
74.0	2.86461	0	0	0
75.0	2.86461	0	0	0
76.0	2.86461	0	0	0
77.0	2.86461	0	0	0
78.0	2.86461	0	0	0
79.0	2.86461	0	0	0
80.0	2.86461	0	0	0
81.0	2.86461	0	0	0
82.0	2.86461	0	0	0
83.0	2.86461	0	0	0
84.0	2.86461	0	0	0
85.0	2.86461	0	0	0
86.0	2.86461	0	0	0
87.0	2.86461	0	0	0
88.0	2.86461	0	0	0
89.0	2.86461	0	0	0
90.0	2.86461	0	0	0
91.0	2.86461	0	0	0
92.0	2.86461	0	0	0
93.0	2.86461	0	0	0
94.0	2.86461	0	0	0
95.0	2.86461	0	0	0
96.0	2.86461	0	0	0
97.0	2.86461	0	0	0
98.0	2.86461	0	0	0
99.0	2.86461	0	0	0
100.0	2.86461	0	0	0