## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Was_Tac_1_2014-07-15/US_Was_Tac_1_2014-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Was_Tac_1_2014-07-15/US_Was_Tac_1_2014-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Was_Tac_1_2014-07-15/US_Was_Tac_1_2014-07-15.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 20 19:41:19 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	1314401	71123938	0	0	706695	18560	0	0.005181	136253622790

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	70831109	70831109
2.0	1.999478	14433	14433
3.0	2.998435	665	665
4.0	3.99687	145	145
5.0	4.994784	72	72
6.0	5.992178	46	46
7.0	6.98905	36	36
8.0	7.985403	23	23
9.0	8.981236	19	19
10.0	9.976549	20	20
11.0	10.971343	9	9
12.0	11.965617	8	8
13.0	12.959373	6	6
14.0	13.95261	7	7
15.0	14.945328	2	2
16.0	15.937529	2	2
17.0	16.929212	1	1
18.0	17.920377	1	1
19.0	18.911025	1	1
20.0	19.901156	1	1
21.0	20.890771	0	0
22.0	21.879869	2	2
23.0	22.86845	0	0
24.0	23.856516	0	0
25.0	24.844066	1	1
26.0	25.831101	1	1
27.0	26.817621	0	0
28.0	27.803626	1	1
29.0	28.789116	0	0
30.0	29.774093	0	0
31.0	30.758555	1	1
32.0	31.742503	0	0
33.0	32.725938	0	0
34.0	33.708859	0	0
35.0	34.691268	0	0
36.0	35.673164	0	0
37.0	36.654548	1	1
38.0	37.635419	1	1
39.0	38.615779	2	2
40.0	39.595627	0	0
41.0	40.574963	0	0
42.0	41.553789	0	0
43.0	42.532103	0	0
44.0	43.509908	1	1
45.0	44.487202	0	0
46.0	45.463985	0	0
47.0	46.44026	0	0
48.0	47.416024	2	2
49.0	48.39128	0	0
50.0	49.366026	1	1
51.0	50.340264	0	0
52.0	51.313993	0	0
53.0	52.287215	0	0
54.0	53.259928	0	0
55.0	54.232134	0	0
56.0	55.203832	1	1
57.0	56.175023	0	0
58.0	57.145708	0	0
59.0	58.115886	0	0
60.0	59.085558	1	1
61.0	60.054723	0	0
62.0	61.023383	0	0
63.0	61.991537	0	0
64.0	62.959186	0	0
65.0	63.92633	0	0
66.0	64.89297	0	0
67.0	65.859105	0	0
68.0	66.824735	0	0
69.0	67.789862	0	0
70.0	68.754485	1	1
71.0	69.718605	0	0
72.0	70.682222	0	0
73.0	71.645335	0	0
74.0	72.607947	0	0
75.0	73.570055	0	0
76.0	74.531662	0	0
77.0	75.492767	0	0
78.0	76.45337	0	0
79.0	77.413472	0	0
80.0	78.373073	0	0
81.0	79.332173	0	0
82.0	80.290773	0	0
83.0	81.248873	0	0
84.0	82.206472	0	0
85.0	83.163572	0	0
86.0	84.120172	0	0
87.0	85.076273	0	0
88.0	86.031875	0	0
89.0	86.986978	0	0
90.0	87.941583	0	0
91.0	88.89569	0	0
92.0	89.849299	0	0
93.0	90.80241	0	0
94.0	91.755024	0	0
95.0	92.707141	0	0
96.0	93.65876	0	0
97.0	94.609884	0	0
98.0	95.56051	0	0
99.0	96.510641	0	0
100.0	97.460276	0	0