## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1767_23/G1767_23_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1767_23/G1767_23_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1767_23/G1767_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 15:41:05 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	33658	54395401	45902438	46242	4266	2743129	0	0.050453	521033564

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	49058957	49058957
2.0	1.900866	2452255	2452255
3.0	2.712425	132957	132957
4.0	3.443531	7572	7572
5.0	4.102159	466	466
6.0	4.695494	44	44
7.0	5.23001	9	9
8.0	5.711537	3	3
9.0	6.145328	3	3
10.0	6.536116	4	4
11.0	6.888163	0	0
12.0	7.20531	0	0
13.0	7.491017	1	1
14.0	7.7484	1	1
15.0	7.980269	0	0
16.0	8.189151	0	0
17.0	8.377325	0	0
18.0	8.546845	0	0
19.0	8.69956	0	0
20.0	8.837136	0	0
21.0	8.961073	0	0
22.0	9.072724	0	0
23.0	9.173306	0	0
24.0	9.263917	0	0
25.0	9.345546	0	0
26.0	9.419082	0	0
27.0	9.485328	0	0
28.0	9.545008	0	0
29.0	9.59877	0	0
30.0	9.647203	0	0
31.0	9.690835	0	0
32.0	9.730141	0	0
33.0	9.765551	0	0
34.0	9.797451	0	0
35.0	9.826188	0	0
36.0	9.852076	0	0
37.0	9.875398	0	0
38.0	9.896408	0	0
39.0	9.915335	0	0
40.0	9.932385	0	0
41.0	9.947746	0	0
42.0	9.961583	0	0
43.0	9.974049	0	0
44.0	9.985279	0	0
45.0	9.995396	0	0
46.0	10.00451	0	0
47.0	10.012721	0	0
48.0	10.020117	0	0
49.0	10.02678	0	0
50.0	10.032783	0	0
51.0	10.03819	0	0
52.0	10.043062	0	0
53.0	10.047451	0	0
54.0	10.051404	0	0
55.0	10.054966	0	0
56.0	10.058174	0	0
57.0	10.061065	0	0
58.0	10.063668	0	0
59.0	10.066014	0	0
60.0	10.068127	0	0
61.0	10.070031	0	0
62.0	10.071746	0	0
63.0	10.073291	0	0
64.0	10.074683	0	0
65.0	10.075937	0	0
66.0	10.077066	0	0
67.0	10.078084	0	0
68.0	10.079001	0	0
69.0	10.079826	0	0
70.0	10.08057	0	0
71.0	10.081241	0	0
72.0	10.081844	0	0
73.0	10.082388	0	0
74.0	10.082878	0	0
75.0	10.08332	0	0
76.0	10.083717	0	0
77.0	10.084076	0	0
78.0	10.084398	0	0
79.0	10.084689	0	0
80.0	10.084951	0	0
81.0	10.085187	0	0
82.0	10.085399	0	0
83.0	10.085591	0	0
84.0	10.085763	0	0
85.0	10.085919	0	0
86.0	10.086059	0	0
87.0	10.086185	0	0
88.0	10.086299	0	0
89.0	10.086401	0	0
90.0	10.086493	0	0
91.0	10.086576	0	0
92.0	10.086651	0	0
93.0	10.086718	0	0
94.0	10.086779	0	0
95.0	10.086834	0	0
96.0	10.086883	0	0
97.0	10.086928	0	0
98.0	10.086968	0	0
99.0	10.087004	0	0
100.0	10.087036	0	0