## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//MI_bh_14_fall/MI_bh_14_fall.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/MI_bh_14_fall/MI_bh_14_fall.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/MI_bh_14_fall/MI_bh_14_fall.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 08:05:55 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	1410083	108743942	0	0	927305	25494714	0	0.237173	194040614

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	60833103	60833103
2.0	1.57097	15830586	15830586
3.0	1.896977	3337196	3337196
4.0	2.083117	622186	622186
5.0	2.189398	114858	114858
6.0	2.25008	25181	25181
7.0	2.284729	8745	8745
8.0	2.304512	4414	4414
9.0	2.315807	2902	2902
10.0	2.322257	2143	2143
11.0	2.325939	1586	1586
12.0	2.328042	1283	1283
13.0	2.329242	1026	1026
14.0	2.329928	841	841
15.0	2.330319	717	717
16.0	2.330542	611	611
17.0	2.33067	532	532
18.0	2.330743	469	469
19.0	2.330784	390	390
20.0	2.330808	352	352
21.0	2.330822	276	276
22.0	2.330829	271	271
23.0	2.330834	257	257
24.0	2.330836	237	237
25.0	2.330838	209	209
26.0	2.330839	172	172
27.0	2.330839	178	178
28.0	2.330839	146	146
29.0	2.33084	149	149
30.0	2.33084	119	119
31.0	2.33084	113	113
32.0	2.33084	102	102
33.0	2.33084	119	119
34.0	2.33084	96	96
35.0	2.33084	84	84
36.0	2.33084	76	76
37.0	2.33084	82	82
38.0	2.33084	74	74
39.0	2.33084	66	66
40.0	2.33084	57	57
41.0	2.33084	61	61
42.0	2.33084	58	58
43.0	2.33084	61	61
44.0	2.33084	68	68
45.0	2.33084	58	58
46.0	2.33084	40	40
47.0	2.33084	39	39
48.0	2.33084	46	46
49.0	2.33084	50	50
50.0	2.33084	45	45
51.0	2.33084	39	39
52.0	2.33084	36	36
53.0	2.33084	40	40
54.0	2.33084	39	39
55.0	2.33084	29	29
56.0	2.33084	23	23
57.0	2.33084	27	27
58.0	2.33084	24	24
59.0	2.33084	18	18
60.0	2.33084	27	27
61.0	2.33084	22	22
62.0	2.33084	30	30
63.0	2.33084	14	14
64.0	2.33084	19	19
65.0	2.33084	24	24
66.0	2.33084	19	19
67.0	2.33084	24	24
68.0	2.33084	24	24
69.0	2.33084	31	31
70.0	2.33084	19	19
71.0	2.33084	22	22
72.0	2.33084	13	13
73.0	2.33084	19	19
74.0	2.33084	19	19
75.0	2.33084	17	17
76.0	2.33084	13	13
77.0	2.33084	11	11
78.0	2.33084	14	14
79.0	2.33084	15	15
80.0	2.33084	13	13
81.0	2.33084	12	12
82.0	2.33084	17	17
83.0	2.33084	14	14
84.0	2.33084	17	17
85.0	2.33084	14	14
86.0	2.33084	13	13
87.0	2.33084	9	9
88.0	2.33084	10	10
89.0	2.33084	10	10
90.0	2.33084	19	19
91.0	2.33084	12	12
92.0	2.33084	10	10
93.0	2.33084	13	13
94.0	2.33084	13	13
95.0	2.33084	8	8
96.0	2.33084	8	8
97.0	2.33084	7	7
98.0	2.33084	12	12
99.0	2.33084	8	8
100.0	2.33084	12	12
101.0	0	11	11
102.0	0	14	14
103.0	0	8	8
104.0	0	11	11
105.0	0	4	4
106.0	0	5	5
107.0	0	5	5
108.0	0	6	6
109.0	0	5	5
110.0	0	8	8
111.0	0	3	3
112.0	0	6	6
113.0	0	13	13
114.0	0	3	3
115.0	0	5	5
116.0	0	2	2
117.0	0	5	5
118.0	0	2	2
119.0	0	5	5
120.0	0	4	4
121.0	0	10	10
122.0	0	8	8
123.0	0	2	2
124.0	0	4	4
125.0	0	4	4
126.0	0	6	6
127.0	0	5	5
128.0	0	4	4
129.0	0	5	5
130.0	0	7	7
131.0	0	2	2
132.0	0	7	7
133.0	0	3	3
134.0	0	10	10
135.0	0	7	7
136.0	0	6	6
137.0	0	4	4
138.0	0	5	5
139.0	0	7	7
140.0	0	6	6
141.0	0	2	2
142.0	0	7	7
143.0	0	4	4
144.0	0	4	4
146.0	0	3	3
147.0	0	5	5
148.0	0	2	2
149.0	0	5	5
150.0	0	3	3
151.0	0	5	5
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
155.0	0	2	2
157.0	0	3	3
158.0	0	6	6
159.0	0	4	4
160.0	0	4	4
161.0	0	5	5
162.0	0	1	1
163.0	0	2	2
164.0	0	6	6
165.0	0	4	4
166.0	0	1	1
167.0	0	2	2
168.0	0	4	4
169.0	0	1	1
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
177.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	4	4
182.0	0	2	2
183.0	0	1	1
184.0	0	2	2
185.0	0	4	4
186.0	0	1	1
187.0	0	1	1
188.0	0	3	3
189.0	0	3	3
190.0	0	4	4
191.0	0	2	2
192.0	0	3	3
193.0	0	2	2
196.0	0	1	1
197.0	0	2	2
199.0	0	2	2
200.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	2	2
205.0	0	1	1
206.0	0	3	3
210.0	0	1	1
211.0	0	4	4
212.0	0	1	1
213.0	0	6	6
214.0	0	3	3
215.0	0	2	2
216.0	0	1	1
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
222.0	0	2	2
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
228.0	0	2	2
229.0	0	2	2
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
236.0	0	1	1
238.0	0	1	1
241.0	0	1	1
242.0	0	3	3
244.0	0	2	2
245.0	0	1	1
247.0	0	2	2
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
254.0	0	1	1
255.0	0	1	1
258.0	0	2	2
259.0	0	1	1
262.0	0	1	1
264.0	0	1	1
266.0	0	2	2
269.0	0	1	1
274.0	0	1	1
275.0	0	1	1
281.0	0	1	1
282.0	0	2	2
283.0	0	1	1
284.0	0	1	1
285.0	0	2	2
286.0	0	2	2
289.0	0	1	1
293.0	0	1	1
295.0	0	1	1
297.0	0	1	1
299.0	0	1	1
300.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
308.0	0	1	1
310.0	0	1	1
314.0	0	1	1
317.0	0	2	2
320.0	0	1	1
322.0	0	1	1
328.0	0	2	2
329.0	0	1	1
330.0	0	1	1
331.0	0	2	2
334.0	0	1	1
335.0	0	1	1
337.0	0	1	1
339.0	0	1	1
342.0	0	2	2
344.0	0	1	1
346.0	0	1	1
355.0	0	1	1
359.0	0	1	1
360.0	0	2	2
364.0	0	2	2
369.0	0	2	2
372.0	0	1	1
374.0	0	1	1
377.0	0	1	1
379.0	0	1	1
381.0	0	2	2
388.0	0	1	1
390.0	0	1	1
393.0	0	1	1
399.0	0	1	1
400.0	0	1	1
403.0	0	1	1
406.0	0	1	1
408.0	0	1	1
410.0	0	1	1
417.0	0	1	1
420.0	0	1	1
424.0	0	1	1
428.0	0	1	1
431.0	0	1	1
435.0	0	1	1
443.0	0	1	1
451.0	0	1	1
456.0	0	1	1
462.0	0	2	2
468.0	0	2	2
470.0	0	2	2
473.0	0	1	1
475.0	0	1	1
477.0	0	2	2
480.0	0	1	1
481.0	0	1	1
486.0	0	2	2
489.0	0	1	1
506.0	0	1	1
507.0	0	1	1
509.0	0	1	1
511.0	0	1	1
514.0	0	1	1
517.0	0	1	1
523.0	0	1	1
524.0	0	1	1
530.0	0	1	1
532.0	0	1	1
549.0	0	1	1
555.0	0	1	1
557.0	0	1	1
559.0	0	1	1
565.0	0	1	1
576.0	0	1	1
604.0	0	1	1
611.0	0	1	1
615.0	0	1	1
616.0	0	1	1
619.0	0	1	1
620.0	0	1	1
621.0	0	1	1
623.0	0	2	2
636.0	0	1	1
639.0	0	1	1
653.0	0	1	1
655.0	0	1	1
665.0	0	1	1
673.0	0	1	1
674.0	0	1	1
695.0	0	1	1
745.0	0	1	1
751.0	0	1	1
758.0	0	1	1
781.0	0	1	1
783.0	0	1	1
786.0	0	1	1
795.0	0	1	1
807.0	0	1	1
812.0	0	1	1
818.0	0	1	1
871.0	0	1	1
951.0	0	1	1
1037.0	0	1	1
1533.0	0	1	1
1926.0	0	1	1
2167.0	0	1	1
2239.0	0	1	1
2394.0	0	1	1
4119.0	0	1	1