## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//UA_Cho_16_55/UA_Cho_16_55.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Cho_16_55/UA_Cho_16_55.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Cho_16_55/UA_Cho_16_55.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 19:38:10 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	38983164	14093182	0	0	11484136	1216016	0	0.20718	76898836

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11641675	11641675
2.0	1.832544	775166	775166
3.0	2.525674	60343	60343
4.0	3.102735	7407	7407
5.0	3.583163	2601	2601
6.0	3.983141	1569	1569
7.0	4.316141	1077	1077
8.0	4.593377	774	774
9.0	4.824189	569	569
10.0	5.01635	498	498
11.0	5.176332	395	395
12.0	5.309525	319	319
13.0	5.420414	241	241
14.0	5.512733	231	231
15.0	5.589593	185	185
16.0	5.653583	176	176
17.0	5.706857	159	159
18.0	5.75121	156	156
19.0	5.788136	124	124
20.0	5.818878	111	111
21.0	5.844472	98	98
22.0	5.865781	104	104
23.0	5.883521	102	102
24.0	5.898291	88	88
25.0	5.910587	94	94
26.0	5.920824	88	88
27.0	5.929347	70	70
28.0	5.936443	78	78
29.0	5.94235	96	96
30.0	5.947268	72	72
31.0	5.951363	78	78
32.0	5.954772	71	71
33.0	5.95761	57	57
34.0	5.959973	55	55
35.0	5.96194	60	60
36.0	5.963578	61	61
37.0	5.964941	51	51
38.0	5.966077	51	51
39.0	5.967022	48	48
40.0	5.967809	47	47
41.0	5.968464	46	46
42.0	5.969009	34	34
43.0	5.969463	39	39
44.0	5.969841	41	41
45.0	5.970156	29	29
46.0	5.970418	27	27
47.0	5.970636	36	36
48.0	5.970818	33	33
49.0	5.970969	34	34
50.0	5.971095	23	23
51.0	5.971199	28	28
52.0	5.971287	16	16
53.0	5.971359	24	24
54.0	5.97142	21	21
55.0	5.97147	17	17
56.0	5.971512	26	26
57.0	5.971547	20	20
58.0	5.971576	24	24
59.0	5.9716	22	22
60.0	5.97162	12	12
61.0	5.971637	13	13
62.0	5.971651	15	15
63.0	5.971663	6	6
64.0	5.971672	18	18
65.0	5.97168	19	19
66.0	5.971687	13	13
67.0	5.971693	25	25
68.0	5.971697	21	21
69.0	5.971701	11	11
70.0	5.971704	12	12
71.0	5.971707	13	13
72.0	5.971709	13	13
73.0	5.971711	9	9
74.0	5.971713	13	13
75.0	5.971714	12	12
76.0	5.971715	13	13
77.0	5.971716	10	10
78.0	5.971717	14	14
79.0	5.971717	7	7
80.0	5.971718	13	13
81.0	5.971718	8	8
82.0	5.971719	15	15
83.0	5.971719	6	6
84.0	5.971719	10	10
85.0	5.971719	12	12
86.0	5.97172	8	8
87.0	5.97172	10	10
88.0	5.97172	7	7
89.0	5.97172	10	10
90.0	5.97172	17	17
91.0	5.97172	14	14
92.0	5.97172	13	13
93.0	5.97172	3	3
94.0	5.97172	7	7
95.0	5.97172	9	9
96.0	5.97172	10	10
97.0	5.97172	6	6
98.0	5.97172	12	12
99.0	5.97172	9	9
100.0	5.97172	10	10
101.0	0	6	6
102.0	0	12	12
103.0	0	9	9
104.0	0	4	4
105.0	0	6	6
106.0	0	3	3
107.0	0	10	10
108.0	0	16	16
109.0	0	6	6
110.0	0	8	8
111.0	0	6	6
112.0	0	9	9
113.0	0	6	6
114.0	0	3	3
115.0	0	7	7
116.0	0	8	8
117.0	0	9	9
118.0	0	6	6
119.0	0	4	4
120.0	0	4	4
121.0	0	9	9
122.0	0	10	10
123.0	0	4	4
124.0	0	11	11
125.0	0	3	3
126.0	0	7	7
127.0	0	6	6
128.0	0	6	6
129.0	0	4	4
130.0	0	5	5
131.0	0	5	5
132.0	0	11	11
133.0	0	5	5
134.0	0	4	4
135.0	0	4	4
136.0	0	2	2
137.0	0	5	5
138.0	0	8	8
139.0	0	1	1
140.0	0	6	6
141.0	0	7	7
142.0	0	5	5
144.0	0	6	6
145.0	0	3	3
146.0	0	1	1
147.0	0	7	7
148.0	0	3	3
149.0	0	3	3
150.0	0	5	5
151.0	0	1	1
152.0	0	8	8
153.0	0	1	1
154.0	0	4	4
155.0	0	4	4
156.0	0	2	2
157.0	0	3	3
158.0	0	1	1
159.0	0	3	3
160.0	0	1	1
161.0	0	5	5
162.0	0	3	3
163.0	0	1	1
164.0	0	1	1
165.0	0	5	5
166.0	0	6	6
167.0	0	4	4
168.0	0	2	2
169.0	0	2	2
170.0	0	2	2
171.0	0	1	1
172.0	0	4	4
173.0	0	1	1
174.0	0	1	1
175.0	0	3	3
176.0	0	1	1
177.0	0	2	2
178.0	0	3	3
179.0	0	3	3
180.0	0	1	1
181.0	0	2	2
182.0	0	1	1
183.0	0	2	2
184.0	0	3	3
185.0	0	2	2
186.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
190.0	0	3	3
191.0	0	1	1
192.0	0	1	1
194.0	0	3	3
196.0	0	4	4
197.0	0	3	3
198.0	0	4	4
199.0	0	1	1
200.0	0	2	2
201.0	0	2	2
203.0	0	2	2
204.0	0	2	2
206.0	0	3	3
207.0	0	2	2
208.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	1	1
214.0	0	2	2
216.0	0	1	1
217.0	0	3	3
219.0	0	1	1
220.0	0	2	2
221.0	0	1	1
222.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	2	2
239.0	0	1	1
240.0	0	3	3
241.0	0	1	1
243.0	0	2	2
244.0	0	2	2
245.0	0	2	2
247.0	0	1	1
252.0	0	1	1
253.0	0	1	1
255.0	0	2	2
257.0	0	1	1
258.0	0	1	1
263.0	0	2	2
264.0	0	2	2
265.0	0	1	1
268.0	0	1	1
269.0	0	3	3
270.0	0	1	1
272.0	0	2	2
277.0	0	1	1
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
283.0	0	1	1
284.0	0	1	1
286.0	0	1	1
287.0	0	1	1
289.0	0	1	1
292.0	0	2	2
294.0	0	1	1
295.0	0	1	1
297.0	0	1	1
299.0	0	2	2
304.0	0	1	1
305.0	0	1	1
306.0	0	1	1
314.0	0	1	1
316.0	0	2	2
317.0	0	1	1
322.0	0	2	2
323.0	0	2	2
328.0	0	3	3
330.0	0	1	1
337.0	0	2	2
339.0	0	1	1
346.0	0	1	1
348.0	0	1	1
349.0	0	1	1
353.0	0	1	1
355.0	0	1	1
357.0	0	1	1
361.0	0	1	1
372.0	0	1	1
375.0	0	2	2
378.0	0	2	2
383.0	0	1	1
385.0	0	1	1
387.0	0	1	1
390.0	0	1	1
392.0	0	1	1
394.0	0	1	1
395.0	0	1	1
398.0	0	1	1
412.0	0	1	1
425.0	0	1	1
436.0	0	2	2
437.0	0	1	1
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
446.0	0	1	1
451.0	0	1	1
455.0	0	1	1
457.0	0	1	1
458.0	0	1	1
462.0	0	3	3
468.0	0	1	1
478.0	0	1	1
480.0	0	1	1
481.0	0	1	1
492.0	0	1	1
503.0	0	1	1
508.0	0	1	1
513.0	0	1	1
524.0	0	1	1
527.0	0	1	1
575.0	0	1	1
584.0	0	1	1
588.0	0	1	1
594.0	0	1	1
606.0	0	1	1
623.0	0	1	1
624.0	0	1	1
627.0	0	1	1
640.0	0	1	1
653.0	0	1	1
665.0	0	1	1
784.0	0	1	1
811.0	0	1	1
816.0	0	1	1
846.0	0	1	1
881.0	0	1	1
921.0	0	1	1
934.0	0	1	1
1187.0	0	1	1
1214.0	0	1	1
1254.0	0	1	1
1529.0	0	1	1
2464.0	0	1	1
4863.0	0	1	1