## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2015-09-18/UA_Lvi_Dro_1_2015-09-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2015-09-18/UA_Lvi_Dro_1_2015-09-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2015-09-18/UA_Lvi_Dro_1_2015-09-18.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 17:32:17 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	5983062	35595764	0	0	2159342	2519843	0	0.093282	239405348

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	30403076	30403076
2.0	1.861841	2075246	2075246
3.0	2.604612	121523	121523
4.0	3.244762	8236	8236
5.0	3.79647	1573	1573
6.0	4.271955	840	840
7.0	4.681747	588	588
8.0	5.034923	450	450
9.0	5.339305	374	374
10.0	5.601634	317	317
11.0	5.82772	252	252
12.0	6.02257	207	207
13.0	6.1905	194	194
14.0	6.335229	177	177
15.0	6.459962	170	170
16.0	6.567462	132	132
17.0	6.660111	135	135
18.0	6.739959	133	133
19.0	6.808775	113	113
20.0	6.868084	114	114
21.0	6.919199	111	111
22.0	6.963251	115	115
23.0	7.001218	88	88
24.0	7.033939	91	91
25.0	7.06214	87	87
26.0	7.086444	83	83
27.0	7.10739	79	79
28.0	7.125443	69	69
29.0	7.141001	62	62
30.0	7.15441	59	59
31.0	7.165966	53	53
32.0	7.175926	59	59
33.0	7.18451	63	63
34.0	7.191908	47	47
35.0	7.198283	47	47
36.0	7.203778	53	53
37.0	7.208514	39	39
38.0	7.212595	41	41
39.0	7.216113	33	33
40.0	7.219144	28	28
41.0	7.221757	26	26
42.0	7.224009	33	33
43.0	7.225949	40	40
44.0	7.227622	26	26
45.0	7.229063	31	31
46.0	7.230306	21	21
47.0	7.231376	20	20
48.0	7.232299	30	30
49.0	7.233094	12	12
50.0	7.23378	22	22
51.0	7.234371	19	19
52.0	7.23488	29	29
53.0	7.235318	21	21
54.0	7.235697	17	17
55.0	7.236022	21	21
56.0	7.236303	8	8
57.0	7.236545	10	10
58.0	7.236754	22	22
59.0	7.236934	12	12
60.0	7.237089	11	11
61.0	7.237222	18	18
62.0	7.237337	13	13
63.0	7.237437	17	17
64.0	7.237522	11	11
65.0	7.237596	16	16
66.0	7.237659	10	10
67.0	7.237714	17	17
68.0	7.237761	11	11
69.0	7.237802	14	14
70.0	7.237837	12	12
71.0	7.237867	8	8
72.0	7.237893	10	10
73.0	7.237915	9	9
74.0	7.237935	13	13
75.0	7.237951	14	14
76.0	7.237966	9	9
77.0	7.237978	8	8
78.0	7.237989	2	2
79.0	7.237998	20	20
80.0	7.238006	9	9
81.0	7.238013	7	7
82.0	7.238019	9	9
83.0	7.238024	7	7
84.0	7.238028	4	4
85.0	7.238032	8	8
86.0	7.238035	7	7
87.0	7.238038	7	7
88.0	7.23804	4	4
89.0	7.238042	10	10
90.0	7.238044	8	8
91.0	7.238046	6	6
92.0	7.238047	15	15
93.0	7.238048	8	8
94.0	7.238049	9	9
95.0	7.23805	8	8
96.0	7.238051	5	5
97.0	7.238051	10	10
98.0	7.238052	3	3
99.0	7.238052	4	4
100.0	7.238053	7	7
101.0	0	2	2
102.0	0	5	5
103.0	0	2	2
104.0	0	13	13
105.0	0	5	5
106.0	0	4	4
107.0	0	6	6
108.0	0	10	10
109.0	0	10	10
110.0	0	7	7
111.0	0	4	4
112.0	0	4	4
113.0	0	6	6
114.0	0	2	2
115.0	0	2	2
116.0	0	6	6
117.0	0	3	3
118.0	0	6	6
119.0	0	2	2
120.0	0	4	4
121.0	0	2	2
122.0	0	5	5
123.0	0	6	6
124.0	0	3	3
125.0	0	3	3
126.0	0	2	2
128.0	0	3	3
129.0	0	3	3
130.0	0	2	2
131.0	0	2	2
132.0	0	5	5
133.0	0	6	6
134.0	0	3	3
135.0	0	2	2
136.0	0	4	4
137.0	0	1	1
138.0	0	3	3
139.0	0	2	2
140.0	0	4	4
141.0	0	1	1
143.0	0	1	1
144.0	0	5	5
146.0	0	2	2
147.0	0	2	2
148.0	0	1	1
149.0	0	6	6
150.0	0	2	2
151.0	0	3	3
152.0	0	3	3
153.0	0	1	1
154.0	0	2	2
155.0	0	2	2
157.0	0	3	3
158.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	3	3
163.0	0	6	6
164.0	0	3	3
165.0	0	1	1
166.0	0	3	3
168.0	0	1	1
169.0	0	2	2
171.0	0	1	1
175.0	0	1	1
176.0	0	2	2
178.0	0	1	1
179.0	0	2	2
182.0	0	1	1
185.0	0	1	1
187.0	0	1	1
189.0	0	2	2
191.0	0	2	2
192.0	0	1	1
199.0	0	1	1
202.0	0	1	1
205.0	0	1	1
212.0	0	2	2
217.0	0	2	2
218.0	0	3	3
221.0	0	1	1
224.0	0	1	1
227.0	0	2	2
228.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
246.0	0	1	1
252.0	0	1	1
253.0	0	2	2
254.0	0	1	1
257.0	0	2	2
262.0	0	1	1
265.0	0	1	1
267.0	0	1	1
269.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	1	1
277.0	0	1	1
280.0	0	1	1
284.0	0	1	1
287.0	0	1	1
295.0	0	1	1
297.0	0	1	1
302.0	0	1	1
304.0	0	1	1
311.0	0	1	1
313.0	0	1	1
314.0	0	1	1
320.0	0	1	1
323.0	0	1	1
334.0	0	1	1
335.0	0	1	1
364.0	0	1	1
365.0	0	1	1
388.0	0	1	1
428.0	0	1	1
537.0	0	1	1