## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G2061_20/G2061_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G2061_20/G2061_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G2061_20/G2061_20_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	31212	46530172	37333109	52946	3222	1607405	0	0.034568	657862368

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	43378566	43378566
2.0	1.931714	1483945	1483945
3.0	2.799805	57553	57553
4.0	3.608618	2522	2522
5.0	4.3622	137	137
6.0	5.064323	30	30
7.0	5.718501	10	10
8.0	6.328007	2	2
9.0	6.895893	2	2
10.0	7.425	0	0
11.0	7.917977	0	0
12.0	8.37729	0	0
13.0	8.805239	0	0
14.0	9.203965	0	0
15.0	9.575463	0	0
16.0	9.921593	0	0
17.0	10.244088	0	0
18.0	10.54456	0	0
19.0	10.824515	0	0
20.0	11.085352	0	0
21.0	11.328378	0	0
22.0	11.554809	0	0
23.0	11.765778	0	0
24.0	11.96234	0	0
25.0	12.14548	0	0
26.0	12.316115	0	0
27.0	12.475097	0	0
28.0	12.623223	0	0
29.0	12.761234	0	0
30.0	12.889821	0	0
31.0	13.009627	0	0
32.0	13.121252	0	0
33.0	13.225255	0	0
34.0	13.322155	0	0
35.0	13.412439	0	0
36.0	13.496558	0	0
37.0	13.574932	0	0
38.0	13.647955	0	0
39.0	13.715991	0	0
40.0	13.779381	0	0
41.0	13.838443	0	0
42.0	13.893472	0	0
43.0	13.944742	0	0
44.0	13.992512	0	0
45.0	14.03702	0	0
46.0	14.078489	0	0
47.0	14.117125	0	0
48.0	14.153124	0	0
49.0	14.186664	0	0
50.0	14.217914	0	0
51.0	14.24703	0	0
52.0	14.274158	0	0
53.0	14.299433	0	0
54.0	14.322983	0	0
55.0	14.344924	0	0
56.0	14.365367	0	0
57.0	14.384414	0	0
58.0	14.40216	0	0
59.0	14.418695	0	0
60.0	14.4341	0	0
61.0	14.448454	0	0
62.0	14.461827	0	0
63.0	14.474287	0	0
64.0	14.485897	0	0
65.0	14.496713	0	0
66.0	14.506791	0	0
67.0	14.516181	0	0
68.0	14.52493	0	0
69.0	14.533081	0	0
70.0	14.540675	0	0
71.0	14.547751	0	0
72.0	14.554344	0	0
73.0	14.560487	0	0
74.0	14.56621	0	0
75.0	14.571542	0	0
76.0	14.57651	0	0
77.0	14.581139	0	0
78.0	14.585452	0	0
79.0	14.58947	0	0
80.0	14.593214	0	0
81.0	14.596702	0	0
82.0	14.599953	0	0
83.0	14.602981	0	0
84.0	14.605802	0	0
85.0	14.608431	0	0
86.0	14.61088	0	0
87.0	14.613162	0	0
88.0	14.615288	0	0
89.0	14.617269	0	0
90.0	14.619115	0	0
91.0	14.620834	0	0
92.0	14.622437	0	0
93.0	14.623929	0	0
94.0	14.62532	0	0
95.0	14.626616	0	0
96.0	14.627823	0	0
97.0	14.628948	0	0
98.0	14.629997	0	0
99.0	14.630973	0	0
100.0	14.631883	0	0