## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//ON_su_15_spring/ON_su_15_spring.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/ON_su_15_spring/ON_su_15_spring.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/ON_su_15_spring/ON_su_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: Thu Jun 11 08:08:30 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	3900755	122274572	0	0	2661993	19227521	0	0.165494	346866908

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	84049875	84049875
2.0	1.70292	13674084	13674084
3.0	2.197018	1987377	1987377
4.0	2.544329	291376	291376
5.0	2.788461	52973	52973
6.0	2.960066	15159	15159
7.0	3.080691	6907	6907
8.0	3.165481	4202	4202
9.0	3.225081	2885	2885
10.0	3.266976	1999	1999
11.0	3.296424	1484	1484
12.0	3.317124	1121	1121
13.0	3.331675	926	926
14.0	3.341902	705	705
15.0	3.349092	583	583
16.0	3.354145	497	497
17.0	3.357697	415	415
18.0	3.360194	326	326
19.0	3.361949	273	273
20.0	3.363183	266	266
21.0	3.36405	223	223
22.0	3.36466	174	174
23.0	3.365088	176	176
24.0	3.36539	150	150
25.0	3.365601	154	154
26.0	3.36575	136	136
27.0	3.365855	104	104
28.0	3.365928	109	109
29.0	3.36598	97	97
30.0	3.366016	103	103
31.0	3.366042	91	91
32.0	3.36606	74	74
33.0	3.366072	73	73
34.0	3.366081	65	65
35.0	3.366087	48	48
36.0	3.366092	62	62
37.0	3.366095	55	55
38.0	3.366097	44	44
39.0	3.366099	51	51
40.0	3.3661	47	47
41.0	3.3661	52	52
42.0	3.366101	47	47
43.0	3.366101	31	31
44.0	3.366102	35	35
45.0	3.366102	31	31
46.0	3.366102	50	50
47.0	3.366102	46	46
48.0	3.366102	28	28
49.0	3.366102	28	28
50.0	3.366102	27	27
51.0	3.366102	28	28
52.0	3.366102	27	27
53.0	3.366102	29	29
54.0	3.366102	17	17
55.0	3.366102	25	25
56.0	3.366102	26	26
57.0	3.366102	24	24
58.0	3.366102	26	26
59.0	3.366102	18	18
60.0	3.366102	18	18
61.0	3.366102	12	12
62.0	3.366102	19	19
63.0	3.366102	12	12
64.0	3.366102	16	16
65.0	3.366102	19	19
66.0	3.366102	12	12
67.0	3.366102	16	16
68.0	3.366102	16	16
69.0	3.366102	11	11
70.0	3.366102	13	13
71.0	3.366102	13	13
72.0	3.366102	15	15
73.0	3.366102	15	15
74.0	3.366102	11	11
75.0	3.366102	15	15
76.0	3.366102	16	16
77.0	3.366102	10	10
78.0	3.366102	13	13
79.0	3.366102	12	12
80.0	3.366102	7	7
81.0	3.366102	7	7
82.0	3.366102	9	9
83.0	3.366102	10	10
84.0	3.366102	7	7
85.0	3.366102	5	5
86.0	3.366102	9	9
87.0	3.366102	6	6
88.0	3.366102	9	9
89.0	3.366102	3	3
90.0	3.366102	9	9
91.0	3.366102	7	7
92.0	3.366102	1	1
93.0	3.366102	8	8
94.0	3.366102	4	4
95.0	3.366102	2	2
96.0	3.366102	10	10
97.0	3.366102	4	4
98.0	3.366102	6	6
99.0	3.366102	7	7
100.0	3.366102	6	6
101.0	0	6	6
102.0	0	7	7
103.0	0	5	5
104.0	0	6	6
105.0	0	3	3
106.0	0	4	4
107.0	0	4	4
108.0	0	7	7
109.0	0	2	2
111.0	0	6	6
112.0	0	4	4
113.0	0	3	3
114.0	0	2	2
115.0	0	4	4
116.0	0	8	8
117.0	0	4	4
118.0	0	5	5
119.0	0	3	3
120.0	0	4	4
121.0	0	4	4
122.0	0	3	3
123.0	0	5	5
124.0	0	1	1
125.0	0	2	2
126.0	0	6	6
127.0	0	1	1
128.0	0	6	6
129.0	0	1	1
130.0	0	4	4
131.0	0	2	2
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	6	6
137.0	0	5	5
138.0	0	1	1
139.0	0	6	6
140.0	0	2	2
141.0	0	6	6
142.0	0	4	4
143.0	0	5	5
144.0	0	2	2
145.0	0	1	1
146.0	0	4	4
147.0	0	2	2
148.0	0	2	2
150.0	0	4	4
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	3	3
155.0	0	3	3
156.0	0	3	3
157.0	0	3	3
158.0	0	1	1
159.0	0	1	1
161.0	0	2	2
163.0	0	1	1
168.0	0	2	2
169.0	0	2	2
170.0	0	2	2
171.0	0	3	3
173.0	0	2	2
174.0	0	1	1
176.0	0	2	2
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	4	4
185.0	0	1	1
186.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	2	2
197.0	0	2	2
198.0	0	2	2
199.0	0	1	1
200.0	0	2	2
202.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	2	2
208.0	0	3	3
210.0	0	1	1
211.0	0	2	2
212.0	0	3	3
216.0	0	1	1
217.0	0	1	1
218.0	0	3	3
219.0	0	2	2
220.0	0	2	2
221.0	0	1	1
222.0	0	1	1
223.0	0	3	3
225.0	0	4	4
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	1	1
237.0	0	1	1
239.0	0	2	2
241.0	0	3	3
242.0	0	1	1
246.0	0	2	2
247.0	0	2	2
249.0	0	2	2
250.0	0	2	2
251.0	0	4	4
253.0	0	3	3
257.0	0	2	2
258.0	0	3	3
260.0	0	2	2
262.0	0	1	1
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	2	2
270.0	0	1	1
271.0	0	2	2
272.0	0	3	3
274.0	0	1	1
279.0	0	1	1
280.0	0	1	1
282.0	0	2	2
284.0	0	2	2
287.0	0	1	1
289.0	0	1	1
292.0	0	1	1
293.0	0	1	1
295.0	0	1	1
296.0	0	2	2
297.0	0	1	1
300.0	0	1	1
301.0	0	2	2
304.0	0	1	1
306.0	0	2	2
308.0	0	1	1
312.0	0	2	2
313.0	0	1	1
317.0	0	2	2
318.0	0	2	2
322.0	0	1	1
323.0	0	2	2
324.0	0	1	1
327.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	2	2
337.0	0	1	1
339.0	0	1	1
346.0	0	1	1
348.0	0	1	1
352.0	0	1	1
353.0	0	1	1
355.0	0	1	1
357.0	0	2	2
358.0	0	2	2
360.0	0	1	1
364.0	0	1	1
365.0	0	2	2
366.0	0	1	1
367.0	0	1	1
371.0	0	2	2
374.0	0	2	2
378.0	0	1	1
384.0	0	1	1
385.0	0	2	2
389.0	0	1	1
392.0	0	1	1
403.0	0	1	1
406.0	0	1	1
411.0	0	2	2
413.0	0	2	2
414.0	0	1	1
421.0	0	1	1
424.0	0	1	1
430.0	0	1	1
432.0	0	1	1
439.0	0	1	1
442.0	0	1	1
443.0	0	1	1
459.0	0	1	1
461.0	0	1	1
470.0	0	1	1
473.0	0	1	1
476.0	0	1	1
482.0	0	1	1
505.0	0	1	1
511.0	0	2	2
520.0	0	1	1
521.0	0	2	2
529.0	0	1	1
534.0	0	1	1
536.0	0	1	1
562.0	0	1	1
564.0	0	1	1
568.0	0	1	1
573.0	0	1	1
583.0	0	1	1
657.0	0	1	1
679.0	0	1	1
681.0	0	1	1
694.0	0	1	1
700.0	0	1	1
703.0	0	1	1
757.0	0	1	1
782.0	0	1	1
832.0	0	1	1
883.0	0	1	1
891.0	0	1	1
914.0	0	1	1
918.0	0	1	1
956.0	0	1	1
1039.0	0	1	1
1254.0	0	1	1
1266.0	0	1	1