## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G716_22/G716_22_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G716_22/G716_22_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G716_22/G716_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 15:41:00 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	222446	159995801	116991652	572942	39022	6593297	0	0.041302	1887557199

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	147213136	147213136
2.0	1.91873	5866012	5866012
3.0	2.762794	283132	283132
4.0	3.53826	25275	25275
5.0	4.250705	6678	6678
6.0	4.905248	3198	3198
7.0	5.506597	1656	1656
8.0	6.059074	1064	1064
9.0	6.56665	673	673
10.0	7.032976	472	472
11.0	7.461403	344	344
12.0	7.855012	261	261
13.0	8.216632	170	170
14.0	8.548863	125	125
15.0	8.854094	83	83
16.0	9.134518	48	48
17.0	9.392153	39	39
18.0	9.628849	29	29
19.0	9.846308	21	21
20.0	10.046095	16	16
21.0	10.229645	18	18
22.0	10.398278	12	12
23.0	10.553206	7	7
24.0	10.695543	6	6
25.0	10.826312	5	5
26.0	10.946453	2	2
27.0	11.056831	2	2
28.0	11.158238	3	3
29.0	11.251404	1	1
30.0	11.336998	3	3
31.0	11.415635	0	0
32.0	11.487882	2	2
33.0	11.554258	1	1
34.0	11.615239	0	0
35.0	11.671264	1	1
36.0	11.722736	3	3
37.0	11.770024	1	1
38.0	11.81347	1	1
39.0	11.853385	0	0
40.0	11.890055	0	0
41.0	11.923746	1	1
42.0	11.954699	0	0
43.0	11.983136	0	0
44.0	12.009262	1	1
45.0	12.033264	0	0
46.0	12.055316	0	0
47.0	12.075576	0	0
48.0	12.094189	0	0
49.0	12.11129	0	0
50.0	12.127001	0	0
51.0	12.141435	0	0
52.0	12.154695	0	0
53.0	12.166879	0	0
54.0	12.178072	0	0
55.0	12.188355	0	0
56.0	12.197803	2	2
57.0	12.206483	0	0
58.0	12.214457	0	0
59.0	12.221783	0	0
60.0	12.228514	0	0
61.0	12.234698	0	0
62.0	12.24038	0	0
63.0	12.245599	0	0
64.0	12.250395	0	0
65.0	12.2548	0	0
66.0	12.258848	0	0
67.0	12.262567	0	0
68.0	12.265983	0	0
69.0	12.269122	0	0
70.0	12.272006	0	0
71.0	12.274655	0	0
72.0	12.277089	0	0
73.0	12.279325	0	0
74.0	12.28138	0	0
75.0	12.283267	0	0
76.0	12.285001	0	0
77.0	12.286595	0	0
78.0	12.288058	0	0
79.0	12.289403	0	0
80.0	12.290638	0	0
81.0	12.291774	0	0
82.0	12.292816	0	0
83.0	12.293774	0	0
84.0	12.294655	0	0
85.0	12.295463	0	0
86.0	12.296206	0	0
87.0	12.296889	0	0
88.0	12.297516	0	0
89.0	12.298092	0	0
90.0	12.298621	0	0
91.0	12.299108	0	0
92.0	12.299554	0	0
93.0	12.299965	0	0
94.0	12.300342	0	0
95.0	12.300688	0	0
96.0	12.301007	0	0
97.0	12.301299	0	0
98.0	12.301568	0	0
99.0	12.301815	0	0
100.0	12.302041	0	0