## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G509_20/G509_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G509_20/G509_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G509_20/G509_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	24443	37297223	33435606	42159	2065	475980	0	0.012785	1448823840

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	36354580	36354580
2.0	1.974585	458201	458201
3.0	2.924402	7977	7977
4.0	3.85008	375	375
5.0	4.752232	56	56
6.0	5.631456	14	14
7.0	6.488335	11	11
8.0	7.323436	8	8
9.0	8.137314	4	4
10.0	8.930508	2	2
11.0	9.703543	1	1
12.0	10.456931	2	2
13.0	11.191173	1	1
14.0	11.906754	1	1
15.0	12.604149	2	2
16.0	13.28382	0	0
17.0	13.946217	2	2
18.0	14.59178	2	2
19.0	15.220936	1	1
20.0	15.834102	1	1
21.0	16.431685	1	1
22.0	17.014081	0	0
23.0	17.581676	0	0
24.0	18.134845	0	0
25.0	18.673955	0	0
26.0	19.199365	0	0
27.0	19.711421	1	1
28.0	20.210464	0	0
29.0	20.696823	0	0
30.0	21.170822	0	0
31.0	21.632775	0	0
32.0	22.082987	0	0
33.0	22.521757	0	0
34.0	22.949376	0	0
35.0	23.366128	0	0
36.0	23.772287	0	0
37.0	24.168125	0	0
38.0	24.553902	0	0
39.0	24.929875	0	0
40.0	25.296293	0	0
41.0	25.653398	0	0
42.0	26.001428	0	0
43.0	26.340613	0	0
44.0	26.671177	0	0
45.0	26.993341	0	0
46.0	27.307317	0	0
47.0	27.613313	0	0
48.0	27.911532	0	0
49.0	28.202172	0	0
50.0	28.485426	0	0
51.0	28.761481	0	0
52.0	29.03052	0	0
53.0	29.292722	0	0
54.0	29.54826	0	0
55.0	29.797303	0	0
56.0	30.040017	0	0
57.0	30.276563	0	0
58.0	30.507097	0	0
59.0	30.731772	0	0
60.0	30.950737	0	0
61.0	31.164137	0	0
62.0	31.372114	0	0
63.0	31.574805	0	0
64.0	31.772345	0	0
65.0	31.964864	0	0
66.0	32.152491	0	0
67.0	32.335349	0	0
68.0	32.51356	0	0
69.0	32.687241	0	0
70.0	32.856509	0	0
71.0	33.021475	0	0
72.0	33.182248	0	0
73.0	33.338935	0	0
74.0	33.49164	0	0
75.0	33.640465	0	0
76.0	33.785506	0	0
77.0	33.926862	0	0
78.0	34.064625	0	0
79.0	34.198887	0	0
80.0	34.329737	0	0
81.0	34.457261	0	0
82.0	34.581545	0	0
83.0	34.702669	0	0
84.0	34.820716	0	0
85.0	34.935762	0	0
86.0	35.047885	0	0
87.0	35.157157	0	0
88.0	35.263653	0	0
89.0	35.367442	0	0
90.0	35.468594	0	0
91.0	35.567175	0	0
92.0	35.66325	0	0
93.0	35.756884	0	0
94.0	35.848138	0	0
95.0	35.937072	0	0
96.0	36.023747	0	0
97.0	36.108219	0	0
98.0	36.190544	0	0
99.0	36.270776	0	0
100.0	36.34897	0	0