## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F2255_23/F2255_23_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F2255_23/F2255_23_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F2255_23/F2255_23_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: Fri Aug 29 15:41:00 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	41579	71028036	61220260	53475	5860	2077153	0	0.029277	1190604995

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	66940831	66940831
2.0	1.942088	1945631	1945631
3.0	2.829616	61992	61992
4.0	3.665746	2229	2229
5.0	4.453454	167	167
6.0	5.195543	23	23
7.0	5.894657	5	5
8.0	6.553282	3	3
9.0	7.173766	1	1
10.0	7.758315	1	1
11.0	8.309012	0	0
12.0	8.827816	0	0
13.0	9.316576	0	0
14.0	9.77703	0	0
15.0	10.210818	0	0
16.0	10.619484	0	0
17.0	11.004483	0	0
18.0	11.367187	0	0
19.0	11.708885	0	0
20.0	12.030794	0	0
21.0	12.334061	0	0
22.0	12.619765	0	0
23.0	12.888923	0	0
24.0	13.142494	0	0
25.0	13.381379	0	0
26.0	13.606431	0	0
27.0	13.818448	0	0
28.0	14.018188	0	0
29.0	14.20636	0	0
30.0	14.383634	0	0
31.0	14.550643	0	0
32.0	14.707979	0	0
33.0	14.856203	0	0
34.0	14.995844	0	0
35.0	15.127397	0	0
36.0	15.251332	0	0
37.0	15.36809	0	0
38.0	15.478086	0	0
39.0	15.581712	0	0
40.0	15.679336	0	0
41.0	15.771307	0	0
42.0	15.857951	0	0
43.0	15.939578	0	0
44.0	16.016478	0	0
45.0	16.088924	0	0
46.0	16.157174	0	0
47.0	16.221473	0	0
48.0	16.282047	0	0
49.0	16.339113	0	0
50.0	16.392875	0	0
51.0	16.443523	0	0
52.0	16.491238	0	0
53.0	16.536189	0	0
54.0	16.578538	0	0
55.0	16.618433	0	0
56.0	16.656019	0	0
57.0	16.691428	0	0
58.0	16.724786	0	0
59.0	16.756212	0	0
60.0	16.785818	0	0
61.0	16.81371	0	0
62.0	16.839986	0	0
63.0	16.864741	0	0
64.0	16.888062	0	0
65.0	16.910033	0	0
66.0	16.930731	0	0
67.0	16.95023	0	0
68.0	16.9686	0	0
69.0	16.985907	0	0
70.0	17.002211	0	0
71.0	17.017571	0	0
72.0	17.032041	0	0
73.0	17.045673	0	0
74.0	17.058516	0	0
75.0	17.070615	0	0
76.0	17.082014	0	0
77.0	17.092752	0	0
78.0	17.102868	0	0
79.0	17.112399	0	0
80.0	17.121378	0	0
81.0	17.129836	0	0
82.0	17.137805	0	0
83.0	17.145312	0	0
84.0	17.152385	0	0
85.0	17.159048	0	0
86.0	17.165325	0	0
87.0	17.171238	0	0
88.0	17.176809	0	0
89.0	17.182058	0	0
90.0	17.187002	0	0
91.0	17.19166	0	0
92.0	17.196049	0	0
93.0	17.200183	0	0
94.0	17.204078	0	0
95.0	17.207747	0	0
96.0	17.211204	0	0
97.0	17.21446	0	0
98.0	17.217528	0	0
99.0	17.220419	0	0
100.0	17.223142	0	0