## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P14-female_bleached_44.sorted.bam] OUTPUT=P14-female_bleached_44.sorted.dedup.bam METRICS_FILE=P14-female_bleached_44-picard_metrics.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT    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: Thu Jul 18 19:33:32 PDT 2019

## 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	1307608	29718261	0	2569598	712426	7235381	1215530	0.249953	57597911

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.032616	17731188	0	18342662
2.0	1.649012	3379780	941696	3086576
3.0	2.016955	878500	102453	703946
4.0	2.23659	280347	16335	200845
5.0	2.367696	104265	3338	70018
6.0	2.445957	45083	799	30062
7.0	2.492673	21975	223	15177
8.0	2.520559	12131	75	8839
9.0	2.537205	7331	22	5663
10.0	2.547141	4868	16	3891
11.0	2.553073	3366	5	2905
12.0	2.556613	2428	6	2098
13.0	2.558727	1938	5	1702
14.0	2.559988	1432	3	1266
15.0	2.560741	1216	0	1040
16.0	2.561191	1014	1	871
17.0	2.561459	753	3	674
18.0	2.561619	654	0	566
19.0	2.561715	526	1	457
20.0	2.561772	425	4	373
21.0	2.561806	402	0	358
22.0	2.561826	333	1	292
23.0	2.561838	289	0	233
24.0	2.561846	259	0	218
25.0	2.56185	205	0	215
26.0	2.561853	173	0	177
27.0	2.561854	175	0	149
28.0	2.561855	141	0	136
29.0	2.561856	131	0	106
30.0	2.561856	133	0	115
31.0	2.561856	102	0	88
32.0	2.561856	93	0	90
33.0	2.561856	92	0	83
34.0	2.561856	90	0	74
35.0	2.561856	86	0	58
36.0	2.561856	63	0	68
37.0	2.561856	67	0	56
38.0	2.561856	54	0	45
39.0	2.561856	43	0	45
40.0	2.561856	43	0	49
41.0	2.561856	47	0	39
42.0	2.561856	38	0	32
43.0	2.561856	39	0	32
44.0	2.561856	31	0	36
45.0	2.561856	32	0	30
46.0	2.561856	34	0	27
47.0	2.561856	30	0	32
48.0	2.561856	30	0	24
49.0	2.561856	27	0	17
50.0	2.561856	25	0	20
51.0	2.561856	15	0	16
52.0	2.561856	17	0	15
53.0	2.561856	15	0	23
54.0	2.561856	20	0	14
55.0	2.561856	12	0	5
56.0	2.561856	14	0	12
57.0	2.561856	16	0	9
58.0	2.561856	13	0	13
59.0	2.561856	13	0	7
60.0	2.561856	12	0	14
61.0	2.561856	13	0	9
62.0	2.561856	6	0	3
63.0	2.561856	6	0	5
64.0	2.561856	8	0	6
65.0	2.561856	8	0	6
66.0	2.561856	6	0	5
67.0	2.561856	2	0	6
68.0	2.561856	6	0	3
69.0	2.561856	2	0	2
70.0	2.561856	6	0	4
71.0	2.561856	4	0	7
72.0	2.561856	5	0	3
73.0	2.561856	3	0	4
74.0	2.561856	8	0	5
75.0	2.561856	7	0	3
76.0	2.561856	3	0	3
77.0	2.561856	6	0	5
78.0	2.561856	1	0	6
79.0	2.561856	7	0	2
80.0	2.561856	1	0	5
81.0	2.561856	1	0	4
82.0	2.561856	3	0	3
83.0	2.561856	5	0	0
84.0	2.561856	3	0	5
85.0	2.561856	4	0	3
86.0	2.561856	0	0	0
87.0	2.561856	3	0	2
88.0	2.561856	4	0	3
89.0	2.561856	1	0	1
90.0	2.561856	2	0	0
91.0	2.561856	2	0	2
92.0	2.561856	2	0	0
93.0	2.561856	1	0	1
94.0	2.561856	5	0	5
95.0	2.561856	2	0	1
96.0	2.561856	1	0	2
97.0	2.561856	1	0	2
98.0	2.561856	2	0	1
99.0	2.561856	1	0	0
100.0	2.561856	0	0	1
101.0	0	1	0	1
103.0	0	0	0	1
104.0	0	3	0	0
105.0	0	1	0	0
108.0	0	1	0	1
109.0	0	0	0	2
110.0	0	2	0	1
112.0	0	1	0	1
113.0	0	1	0	1
114.0	0	3	0	1
115.0	0	1	0	1
116.0	0	1	0	1
118.0	0	0	0	1
119.0	0	0	0	1
120.0	0	0	0	1
121.0	0	0	0	1
122.0	0	1	0	0
123.0	0	2	0	0
124.0	0	1	0	1
125.0	0	1	0	0
126.0	0	1	0	1
130.0	0	1	0	1
132.0	0	0	0	1
135.0	0	1	0	0
136.0	0	1	0	0
139.0	0	0	0	1
141.0	0	1	0	0
142.0	0	0	0	1
144.0	0	1	0	1
146.0	0	0	0	1
149.0	0	1	0	0
150.0	0	0	0	1
153.0	0	1	0	0
155.0	0	1	0	0
156.0	0	1	0	0
158.0	0	0	0	1
162.0	0	1	0	1
163.0	0	0	0	1
166.0	0	0	0	1
169.0	0	1	0	0
173.0	0	1	0	1
178.0	0	1	0	0
182.0	0	1	0	0
183.0	0	0	0	1
186.0	0	1	0	0
193.0	0	0	0	2
195.0	0	1	0	0
198.0	0	1	0	0
206.0	0	0	0	1
212.0	0	0	0	1
217.0	0	1	0	0
219.0	0	1	0	0
224.0	0	0	0	1
235.0	0	0	0	1
237.0	0	0	0	1
238.0	0	0	0	1
239.0	0	0	0	1
240.0	0	1	0	0
241.0	0	1	0	0
247.0	0	0	0	1
249.0	0	1	0	0
250.0	0	0	0	1
251.0	0	1	0	0
253.0	0	1	0	0
255.0	0	0	0	1
256.0	0	0	0	1
258.0	0	1	0	0
259.0	0	0	0	1
262.0	0	1	0	0
265.0	0	1	0	0
267.0	0	1	0	0
277.0	0	1	0	0
282.0	0	0	0	1
287.0	0	0	0	2
290.0	0	1	0	0
296.0	0	0	0	1
305.0	0	1	0	0
306.0	0	1	0	0
315.0	0	1	0	0
443.0	0	0	0	1
448.0	0	1	0	0