## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F648_22/F648_22_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F648_22/F648_22_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/F648_22/F648_22_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 15:41:01 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	44643	72872076	64956201	57949	4791	1259814	0	0.017316	2083227349

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	70379330	70379330
2.0	1.965624	1207505	1207505
3.0	2.898055	24250	24250
4.0	3.798432	990	990
5.0	4.667859	136	136
6.0	5.507398	30	30
7.0	6.318078	12	12
8.0	7.10089	5	5
9.0	7.856792	1	1
10.0	8.58671	1	1
11.0	9.291537	1	1
12.0	9.972134	1	1
13.0	10.629336	0	0
14.0	11.263945	0	0
15.0	11.87674	0	0
16.0	12.46847	0	0
17.0	13.039858	0	0
18.0	13.591605	0	0
19.0	14.124385	0	0
20.0	14.63885	0	0
21.0	15.13563	0	0
22.0	15.615333	0	0
23.0	16.078546	0	0
24.0	16.525836	0	0
25.0	16.95775	0	0
26.0	17.374817	0	0
27.0	17.777546	0	0
28.0	18.166432	0	0
29.0	18.541949	0	0
30.0	18.904558	0	0
31.0	19.254702	0	0
32.0	19.592809	0	0
33.0	19.919294	0	0
34.0	20.234556	0	0
35.0	20.53898	0	0
36.0	20.832939	0	0
37.0	21.116794	0	0
38.0	21.390891	0	0
39.0	21.655565	0	0
40.0	21.911141	0	0
41.0	22.157932	0	0
42.0	22.396239	0	0
43.0	22.626354	0	0
44.0	22.848559	0	0
45.0	23.063125	0	0
46.0	23.270316	0	0
47.0	23.470384	0	0
48.0	23.663574	0	0
49.0	23.850124	0	0
50.0	24.030261	0	0
51.0	24.204205	0	0
52.0	24.372171	0	0
53.0	24.534362	0	0
54.0	24.690977	0	0
55.0	24.842209	0	0
56.0	24.988243	0	0
57.0	25.129256	0	0
58.0	25.265422	0	0
59.0	25.396907	0	0
60.0	25.523872	0	0
61.0	25.646473	0	0
62.0	25.764859	0	0
63.0	25.879176	0	0
64.0	25.989563	0	0
65.0	26.096155	0	0
66.0	26.199083	0	0
67.0	26.298473	0	0
68.0	26.394446	0	0
69.0	26.48712	0	0
70.0	26.576609	0	0
71.0	26.663021	0	0
72.0	26.746463	0	0
73.0	26.827036	0	0
74.0	26.90484	0	0
75.0	26.979969	0	0
76.0	27.052515	0	0
77.0	27.122568	0	0
78.0	27.190212	0	0
79.0	27.255532	0	0
80.0	27.318605	0	0
81.0	27.379511	0	0
82.0	27.438323	0	0
83.0	27.495113	0	0
84.0	27.549951	0	0
85.0	27.602904	0	0
86.0	27.654037	0	0
87.0	27.703412	0	0
88.0	27.751089	0	0
89.0	27.797128	0	0
90.0	27.841584	0	0
91.0	27.884512	0	0
92.0	27.925964	0	0
93.0	27.965992	0	0
94.0	28.004643	0	0
95.0	28.041965	0	0
96.0	28.078005	0	0
97.0	28.112806	0	0
98.0	28.14641	0	0
99.0	28.17886	0	0
100.0	28.210193	0	0