## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G118_22/G118_22_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G118_22/G118_22_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G118_22/G118_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 15:41:05 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	28178	49277594	35288727	40916	2418	680984	0	0.01384	1766456964

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	47928190	47928190
2.0	1.972489	656696	656696
3.0	2.918225	11110	11110
4.0	3.837942	480	480
5.0	4.732357	89	89
6.0	5.602166	23	23
7.0	6.448046	11	11
8.0	7.270655	6	6
9.0	8.070634	1	1
10.0	8.848605	2	2
11.0	9.605173	0	0
12.0	10.340927	1	1
13.0	11.05644	1	1
14.0	11.752269	0	0
15.0	12.428954	0	0
16.0	13.087024	0	0
17.0	13.72699	0	0
18.0	14.34935	0	0
19.0	14.954588	0	0
20.0	15.543176	0	0
21.0	16.115571	0	0
22.0	16.672219	0	0
23.0	17.213553	0	0
24.0	17.739995	0	0
25.0	18.251954	0	0
26.0	18.749828	0	0
27.0	19.234006	0	0
28.0	19.704863	0	0
29.0	20.162767	0	0
30.0	20.608074	0	0
31.0	21.041129	0	0
32.0	21.462271	0	0
33.0	21.871828	0	0
34.0	22.270117	0	0
35.0	22.657448	0	0
36.0	23.034124	0	0
37.0	23.400437	0	0
38.0	23.756673	0	0
39.0	24.103109	0	0
40.0	24.440013	0	0
41.0	24.767649	0	0
42.0	25.086272	0	0
43.0	25.396129	0	0
44.0	25.697462	0	0
45.0	25.990505	0	0
46.0	26.275485	0	0
47.0	26.552626	0	0
48.0	26.822143	0	0
49.0	27.084245	0	0
50.0	27.339136	0	0
51.0	27.587015	0	0
52.0	27.828075	0	0
53.0	28.062503	0	0
54.0	28.290481	0	0
55.0	28.512188	0	0
56.0	28.727796	0	0
57.0	28.937471	0	0
58.0	29.141379	0	0
59.0	29.339677	0	0
60.0	29.53252	0	0
61.0	29.720057	0	0
62.0	29.902435	0	0
63.0	30.079796	0	0
64.0	30.252277	0	0
65.0	30.420013	0	0
66.0	30.583135	0	0
67.0	30.741769	0	0
68.0	30.896039	0	0
69.0	31.046065	0	0
70.0	31.191963	0	0
71.0	31.333848	0	0
72.0	31.471829	0	0
73.0	31.606015	0	0
74.0	31.736509	0	0
75.0	31.863413	0	0
76.0	31.986825	0	0
77.0	32.106843	0	0
78.0	32.223558	0	0
79.0	32.337063	0	0
80.0	32.447445	0	0
81.0	32.554791	0	0
82.0	32.659183	0	0
83.0	32.760703	0	0
84.0	32.859431	0	0
85.0	32.955442	0	0
86.0	33.048812	0	0
87.0	33.139614	0	0
88.0	33.227917	0	0
89.0	33.313791	0	0
90.0	33.397303	0	0
91.0	33.478517	0	0
92.0	33.557497	0	0
93.0	33.634304	0	0
94.0	33.708998	0	0
95.0	33.781637	0	0
96.0	33.852278	0	0
97.0	33.920975	0	0
98.0	33.987783	0	0
99.0	34.052752	0	0
100.0	34.115934	0	0