## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G389_20/G389_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G389_20/G389_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G389_20/G389_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 15:41:01 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	23777	26742772	30933957	41373	1981	663619	0	0.024841	529893600

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25440569	25440569
2.0	1.950784	616018	616018
3.0	2.854775	21259	21259
4.0	3.714275	1032	1032
5.0	4.531473	126	126
6.0	5.308453	31	31
7.0	6.047193	20	20
8.0	6.749576	15	15
9.0	7.41739	10	10
10.0	8.052337	7	7
11.0	8.656034	12	12
12.0	9.23002	9	9
13.0	9.775757	7	7
14.0	10.294635	6	6
15.0	10.787976	7	7
16.0	11.257037	2	2
17.0	11.703013	4	4
18.0	12.127039	2	2
19.0	12.530197	5	5
20.0	12.913513	2	2
21.0	13.277964	2	2
22.0	13.624478	3	3
23.0	13.953938	1	1
24.0	14.267183	0	0
25.0	14.565012	1	1
26.0	14.848183	2	2
27.0	15.117417	1	1
28.0	15.373401	0	0
29.0	15.616786	0	0
30.0	15.848193	0	0
31.0	16.068211	0	0
32.0	16.277401	0	0
33.0	16.476295	0	0
34.0	16.6654	0	0
35.0	16.845199	0	0
36.0	17.016149	0	0
37.0	17.178685	0	0
38.0	17.333221	0	0
39.0	17.480153	0	0
40.0	17.619852	0	0
41.0	17.752677	0	0
42.0	17.878964	0	0
43.0	17.999036	0	0
44.0	18.113198	0	0
45.0	18.221742	0	0
46.0	18.324944	0	0
47.0	18.423067	0	0
48.0	18.51636	0	0
49.0	18.605062	0	0
50.0	18.689399	0	0
51.0	18.769585	0	0
52.0	18.845824	0	0
53.0	18.918311	0	0
54.0	18.987231	0	0
55.0	19.052758	0	0
56.0	19.115061	0	0
57.0	19.174297	0	0
58.0	19.230618	0	0
59.0	19.284168	0	0
60.0	19.335081	0	0
61.0	19.383489	0	0
62.0	19.429515	0	0
63.0	19.473275	0	0
64.0	19.514882	0	0
65.0	19.554441	0	0
66.0	19.592053	0	0
67.0	19.627813	0	0
68.0	19.661814	0	0
69.0	19.694142	0	0
70.0	19.724878	0	0
71.0	19.754102	0	0
72.0	19.781888	0	0
73.0	19.808306	0	0
74.0	19.833423	0	0
75.0	19.857305	0	0
76.0	19.880011	0	0
77.0	19.9016	0	0
78.0	19.922126	0	0
79.0	19.941642	0	0
80.0	19.960198	0	0
81.0	19.97784	0	0
82.0	19.994614	0	0
83.0	20.010563	0	0
84.0	20.025726	0	0
85.0	20.040144	0	0
86.0	20.053851	0	0
87.0	20.066884	0	0
88.0	20.079276	0	0
89.0	20.091058	0	0
90.0	20.10226	0	0
91.0	20.11291	0	0
92.0	20.123037	0	0
93.0	20.132665	0	0
94.0	20.141819	0	0
95.0	20.150523	0	0
96.0	20.158798	0	0
97.0	20.166666	0	0
98.0	20.174147	0	0
99.0	20.181259	0	0
100.0	20.188022	0	0