## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//PA_st_15_spring/PA_st_15_spring.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_st_15_spring/PA_st_15_spring.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_st_15_spring/PA_st_15_spring.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: Sun Jun 07 08:30:08 UTC 2020

## 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	1651057	49254545	0	0	728148	12209848	0	0.251076	82142076

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26649291	26649291
2.0	1.549017	7404466	7404466
3.0	1.850436	1677846	1677846
4.0	2.015921	326965	326965
5.0	2.106774	59146	59146
6.0	2.156654	11450	11450
7.0	2.184039	3040	3040
8.0	2.199074	1269	1269
9.0	2.207329	772	772
10.0	2.211861	545	545
11.0	2.214349	439	439
12.0	2.215715	357	357
13.0	2.216464	295	295
14.0	2.216876	266	266
15.0	2.217102	191	191
16.0	2.217226	172	172
17.0	2.217295	169	169
18.0	2.217332	138	138
19.0	2.217352	109	109
20.0	2.217364	102	102
21.0	2.21737	108	108
22.0	2.217373	96	96
23.0	2.217375	76	76
24.0	2.217376	85	85
25.0	2.217377	75	75
26.0	2.217377	79	79
27.0	2.217377	51	51
28.0	2.217377	56	56
29.0	2.217377	47	47
30.0	2.217377	47	47
31.0	2.217377	43	43
32.0	2.217377	44	44
33.0	2.217377	39	39
34.0	2.217377	47	47
35.0	2.217377	27	27
36.0	2.217377	29	29
37.0	2.217377	25	25
38.0	2.217377	22	22
39.0	2.217377	30	30
40.0	2.217377	25	25
41.0	2.217377	30	30
42.0	2.217377	25	25
43.0	2.217377	30	30
44.0	2.217377	22	22
45.0	2.217377	19	19
46.0	2.217377	23	23
47.0	2.217377	20	20
48.0	2.217377	21	21
49.0	2.217377	11	11
50.0	2.217377	13	13
51.0	2.217377	24	24
52.0	2.217377	10	10
53.0	2.217377	21	21
54.0	2.217377	17	17
55.0	2.217377	11	11
56.0	2.217377	14	14
57.0	2.217377	8	8
58.0	2.217377	10	10
59.0	2.217377	12	12
60.0	2.217377	14	14
61.0	2.217377	9	9
62.0	2.217377	14	14
63.0	2.217377	10	10
64.0	2.217377	15	15
65.0	2.217377	6	6
66.0	2.217377	7	7
67.0	2.217377	8	8
68.0	2.217377	7	7
69.0	2.217377	6	6
70.0	2.217377	4	4
71.0	2.217377	5	5
72.0	2.217377	7	7
73.0	2.217377	7	7
74.0	2.217377	4	4
75.0	2.217377	10	10
76.0	2.217377	5	5
77.0	2.217377	4	4
78.0	2.217377	8	8
79.0	2.217377	7	7
80.0	2.217377	2	2
81.0	2.217377	5	5
82.0	2.217377	4	4
83.0	2.217377	3	3
84.0	2.217377	7	7
85.0	2.217377	5	5
86.0	2.217377	9	9
87.0	2.217377	3	3
88.0	2.217377	4	4
89.0	2.217377	4	4
90.0	2.217377	6	6
91.0	2.217377	3	3
92.0	2.217377	4	4
93.0	2.217377	6	6
94.0	2.217377	6	6
95.0	2.217377	2	2
96.0	2.217377	3	3
97.0	2.217377	1	1
98.0	2.217377	4	4
99.0	2.217377	5	5
100.0	2.217377	6	6
101.0	0	4	4
102.0	0	3	3
103.0	0	6	6
104.0	0	6	6
105.0	0	5	5
106.0	0	3	3
107.0	0	2	2
108.0	0	3	3
109.0	0	4	4
110.0	0	4	4
111.0	0	2	2
112.0	0	5	5
113.0	0	3	3
114.0	0	4	4
115.0	0	1	1
116.0	0	2	2
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
120.0	0	3	3
121.0	0	1	1
122.0	0	3	3
123.0	0	1	1
124.0	0	1	1
125.0	0	3	3
126.0	0	1	1
129.0	0	2	2
130.0	0	2	2
131.0	0	1	1
132.0	0	3	3
134.0	0	2	2
135.0	0	1	1
136.0	0	2	2
137.0	0	3	3
138.0	0	1	1
140.0	0	2	2
141.0	0	1	1
142.0	0	2	2
143.0	0	3	3
144.0	0	2	2
145.0	0	2	2
146.0	0	3	3
147.0	0	4	4
148.0	0	1	1
149.0	0	1	1
151.0	0	1	1
152.0	0	1	1
155.0	0	6	6
156.0	0	2	2
157.0	0	1	1
158.0	0	2	2
159.0	0	4	4
161.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	2	2
165.0	0	4	4
168.0	0	1	1
169.0	0	1	1
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
175.0	0	4	4
176.0	0	2	2
177.0	0	1	1
180.0	0	2	2
181.0	0	2	2
182.0	0	2	2
183.0	0	1	1
184.0	0	1	1
185.0	0	4	4
186.0	0	1	1
188.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
196.0	0	1	1
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
202.0	0	3	3
203.0	0	3	3
205.0	0	2	2
206.0	0	1	1
207.0	0	3	3
210.0	0	1	1
211.0	0	1	1
212.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
218.0	0	2	2
219.0	0	2	2
220.0	0	1	1
221.0	0	1	1
222.0	0	2	2
224.0	0	1	1
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	2	2
236.0	0	1	1
237.0	0	1	1
242.0	0	1	1
246.0	0	2	2
248.0	0	1	1
250.0	0	3	3
252.0	0	1	1
253.0	0	1	1
259.0	0	1	1
262.0	0	1	1
269.0	0	1	1
270.0	0	1	1
273.0	0	1	1
277.0	0	1	1
280.0	0	1	1
292.0	0	1	1
295.0	0	1	1
300.0	0	1	1
302.0	0	1	1
306.0	0	2	2
309.0	0	2	2
310.0	0	2	2
316.0	0	1	1
324.0	0	1	1
326.0	0	1	1
328.0	0	1	1
342.0	0	1	1
349.0	0	1	1
354.0	0	1	1
360.0	0	1	1
361.0	0	1	1
375.0	0	1	1
390.0	0	1	1
425.0	0	1	1