## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[P03-female_bleached_44.sorted.bam] OUTPUT=P03-female_bleached_44.sorted.dedup.bam METRICS_FILE=P03-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 12:07:42 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	993262	21447569	0	2161572	528907	5837818	932064	0.278081	35744624

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.0332	11855052	0	12266898
2.0	1.60022	2581155	700870	2423313
3.0	1.9114	740196	83929	616547
4.0	2.082175	250999	14674	184798
5.0	2.175896	95540	3152	62754
6.0	2.227331	40070	782	24314
7.0	2.255558	18613	232	11063
8.0	2.271049	9467	76	5758
9.0	2.27955	5297	37	3449
10.0	2.284216	3156	15	2258
11.0	2.286776	2086	8	1571
12.0	2.288182	1483	3	1138
13.0	2.288953	1038	3	880
14.0	2.289376	794	3	715
15.0	2.289608	686	1	577
16.0	2.289736	502	2	427
17.0	2.289806	408	0	358
18.0	2.289844	348	0	337
19.0	2.289865	280	0	266
20.0	2.289877	273	1	250
21.0	2.289883	240	1	181
22.0	2.289886	190	1	162
23.0	2.289888	164	1	151
24.0	2.289889	127	1	127
25.0	2.28989	132	2	105
26.0	2.28989	101	0	99
27.0	2.289891	90	0	83
28.0	2.289891	86	1	79
29.0	2.289891	64	0	52
30.0	2.289891	60	1	67
31.0	2.289891	65	0	58
32.0	2.289891	52	0	42
33.0	2.289891	43	0	49
34.0	2.289891	45	0	41
35.0	2.289891	54	0	45
36.0	2.289891	44	0	40
37.0	2.289891	33	0	40
38.0	2.289891	39	0	34
39.0	2.289891	28	0	27
40.0	2.289891	25	0	30
41.0	2.289891	27	0	21
42.0	2.289891	38	0	28
43.0	2.289891	19	0	31
44.0	2.289891	29	0	19
45.0	2.289891	26	0	22
46.0	2.289891	23	0	19
47.0	2.289891	17	0	14
48.0	2.289891	13	0	14
49.0	2.289891	19	0	21
50.0	2.289891	17	0	10
51.0	2.289891	17	0	18
52.0	2.289891	15	0	14
53.0	2.289891	17	0	8
54.0	2.289891	9	0	8
55.0	2.289891	11	0	20
56.0	2.289891	15	0	10
57.0	2.289891	10	0	13
58.0	2.289891	9	0	9
59.0	2.289891	16	0	10
60.0	2.289891	4	0	7
61.0	2.289891	8	0	6
62.0	2.289891	8	0	2
63.0	2.289891	9	0	8
64.0	2.289891	3	0	3
65.0	2.289891	5	0	3
66.0	2.289891	3	0	4
67.0	2.289891	9	0	4
68.0	2.289891	2	0	5
69.0	2.289891	7	0	8
70.0	2.289891	1	0	5
71.0	2.289891	3	0	9
72.0	2.289891	10	0	6
73.0	2.289891	5	0	4
74.0	2.289891	11	0	7
75.0	2.289891	4	0	3
76.0	2.289891	4	0	2
77.0	2.289891	4	0	4
78.0	2.289891	5	0	4
79.0	2.289891	2	0	3
80.0	2.289891	0	0	4
81.0	2.289891	3	0	1
82.0	2.289891	3	0	3
83.0	2.289891	5	0	4
84.0	2.289891	4	0	4
85.0	2.289891	6	0	9
86.0	2.289891	3	0	6
87.0	2.289891	8	0	5
88.0	2.289891	8	0	3
89.0	2.289891	3	0	2
90.0	2.289891	3	0	0
91.0	2.289891	2	0	2
92.0	2.289891	2	0	2
93.0	2.289891	2	0	2
94.0	2.289891	1	0	4
95.0	2.289891	2	0	1
96.0	2.289891	1	0	6
97.0	2.289891	3	0	1
98.0	2.289891	5	0	2
99.0	2.289891	1	0	1
100.0	2.289891	0	0	1
101.0	0	3	0	1
102.0	0	0	0	2
103.0	0	3	0	2
104.0	0	1	0	0
105.0	0	3	0	1
106.0	0	0	0	2
107.0	0	1	0	3
108.0	0	2	0	3
109.0	0	3	0	1
110.0	0	2	0	2
111.0	0	2	0	4
112.0	0	0	0	1
113.0	0	2	0	3
114.0	0	4	0	0
115.0	0	4	0	1
116.0	0	0	0	1
117.0	0	3	0	2
118.0	0	1	0	2
119.0	0	0	0	1
120.0	0	3	0	0
122.0	0	1	0	3
123.0	0	1	0	3
124.0	0	1	0	1
125.0	0	2	0	1
126.0	0	1	0	1
127.0	0	2	0	0
128.0	0	0	0	1
129.0	0	2	0	0
130.0	0	1	0	1
131.0	0	0	0	1
133.0	0	1	0	1
134.0	0	0	0	1
135.0	0	1	0	1
136.0	0	0	0	1
137.0	0	1	0	2
138.0	0	0	0	1
139.0	0	0	0	2
140.0	0	2	0	0
141.0	0	1	0	1
142.0	0	1	0	1
143.0	0	2	0	1
144.0	0	2	0	0
145.0	0	3	0	2
146.0	0	1	0	1
147.0	0	1	0	1
148.0	0	0	0	3
149.0	0	1	0	0
150.0	0	0	0	2
151.0	0	2	0	1
152.0	0	1	0	0
153.0	0	1	0	2
155.0	0	3	0	0
157.0	0	0	0	1
158.0	0	3	0	0
159.0	0	1	0	0
160.0	0	0	0	1
163.0	0	0	0	1
166.0	0	1	0	0
168.0	0	1	0	0
169.0	0	0	0	1
170.0	0	1	0	0
174.0	0	0	0	1
177.0	0	0	0	1
181.0	0	1	0	0
185.0	0	1	0	0
186.0	0	0	0	1
187.0	0	1	0	0
189.0	0	1	0	0
193.0	0	0	0	1
196.0	0	0	0	1
199.0	0	1	0	0
205.0	0	1	0	0
207.0	0	0	0	1
212.0	0	1	0	1
215.0	0	0	0	1
216.0	0	0	0	1
219.0	0	1	0	0
221.0	0	1	0	0
222.0	0	0	0	1
223.0	0	2	0	0
232.0	0	0	0	1
235.0	0	0	0	1
236.0	0	1	0	0
245.0	0	0	0	1
250.0	0	1	0	0
258.0	0	1	0	0
259.0	0	0	0	1
266.0	0	1	0	0
280.0	0	0	0	1
285.0	0	0	0	1
287.0	0	0	0	1
294.0	0	1	0	0
295.0	0	1	0	0
306.0	0	1	0	0
317.0	0	0	0	1
319.0	0	0	0	1
327.0	0	1	0	0
328.0	0	1	0	0
352.0	0	0	0	1
361.0	0	1	0	0
382.0	0	0	0	1
403.0	0	1	0	0
415.0	0	0	0	1
439.0	0	1	0	0
467.0	0	0	0	1
481.0	0	1	0	0
513.0	0	0	0	1
542.0	0	1	0	0
559.0	0	0	0	1
579.0	0	1	0	0
687.0	0	0	0	1
714.0	0	1	0	0
906.0	0	0	0	1
930.0	0	1	0	0