## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Cal_And_15_2013-10-15/US_Cal_And_15_2013-10-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Cal_And_15_2013-10-15/US_Cal_And_15_2013-10-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Cal_And_15_2013-10-15/US_Cal_And_15_2013-10-15.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    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 ADD_PG_TAG_TO_READS=true 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 COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false 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 Jan 13 21:11:54 UTC 2023

## 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
lib1	394115	4526231	0	0	34104	38591	0	0.011781	263923621

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	4400779	4400779
2.0	1.982996	37070	37070
3.0	2.949278	384	384
4.0	3.89913	72	72
5.0	4.832831	37	37
6.0	5.750656	18	18
7.0	6.652874	11	11
8.0	7.539752	8	8
9.0	8.411549	3	3
10.0	9.268523	3	3
11.0	10.110925	4	4
12.0	10.939003	1	1
13.0	11.753001	1	1
14.0	12.553159	2	2
15.0	13.33971	0	0
16.0	14.112888	0	0
17.0	14.872918	0	0
18.0	15.620026	0	0
19.0	16.35443	1	1
20.0	17.076347	1	1
21.0	17.785988	0	0
22.0	18.483563	0	0
23.0	19.169277	0	0
24.0	19.843331	0	0
25.0	20.505924	0	0
26.0	21.15725	0	0
27.0	21.797501	0	0
28.0	22.426866	0	0
29.0	23.04553	0	0
30.0	23.653674	0	0
31.0	24.251477	0	0
32.0	24.839116	0	0
33.0	25.416763	0	0
34.0	25.984587	0	0
35.0	26.542757	0	0
36.0	27.091436	0	0
37.0	27.630785	0	0
38.0	28.160963	0	0
39.0	28.682127	0	0
40.0	29.194429	0	0
41.0	29.69802	0	0
42.0	30.193048	0	0
43.0	30.679659	0	0
44.0	31.157995	0	0
45.0	31.628199	0	0
46.0	32.090407	0	0
47.0	32.544756	0	0
48.0	32.991379	0	0
49.0	33.430408	0	0
50.0	33.861973	0	0
51.0	34.286199	0	0
52.0	34.703211	0	0
53.0	35.113133	0	0
54.0	35.516085	0	0
55.0	35.912186	0	0
56.0	36.301551	0	0
57.0	36.684295	0	0
58.0	37.060532	0	0
59.0	37.430371	0	0
60.0	37.793922	0	0
61.0	38.151291	0	0
62.0	38.502583	0	0
63.0	38.847902	0	0
64.0	39.18735	0	0
65.0	39.521025	0	0
66.0	39.849027	0	0
67.0	40.171452	0	0
68.0	40.488395	0	0
69.0	40.799948	0	0
70.0	41.106204	0	0
71.0	41.407252	0	0
72.0	41.703182	0	0
73.0	41.994079	0	0
74.0	42.280031	0	0
75.0	42.56112	0	0
76.0	42.837429	0	0
77.0	43.109041	0	0
78.0	43.376034	0	0
79.0	43.638487	0	0
80.0	43.896478	0	0
81.0	44.150081	0	0
82.0	44.399373	0	0
83.0	44.644426	0	0
84.0	44.885312	0	0
85.0	45.122102	0	0
86.0	45.354866	0	0
87.0	45.583672	0	0
88.0	45.808587	0	0
89.0	46.029678	0	0
90.0	46.24701	0	0
91.0	46.460647	0	0
92.0	46.67065	0	0
93.0	46.877083	0	0
94.0	47.080006	0	0
95.0	47.279479	0	0
96.0	47.47556	0	0
97.0	47.668306	0	0
98.0	47.857775	0	0
99.0	48.044023	0	0
100.0	48.227104	0	0