## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2014-09-13/UA_Kie_Cho_2_2014-09-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2014-09-13/UA_Kie_Cho_2_2014-09-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kie_Cho_2_2014-09-13/UA_Kie_Cho_2_2014-09-13.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 14:18:00 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	7921719	20939674	0	0	1717032	597289	0	0.058465	360036488

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	19598677	19598677
2.0	1.943499	430490	430490
3.0	2.83369	7917	7917
4.0	3.673584	620	620
5.0	4.466023	371	371
6.0	5.213689	226	226
7.0	5.91911	192	192
8.0	6.584675	174	174
9.0	7.212635	131	131
10.0	7.805115	142	142
11.0	8.364119	104	104
12.0	8.891539	78	78
13.0	9.389159	87	87
14.0	9.858663	79	79
15.0	10.30164	60	60
16.0	10.719588	67	67
17.0	11.113921	64	64
18.0	11.485975	46	46
19.0	11.837007	46	46
20.0	12.168205	49	49
21.0	12.480691	43	43
22.0	12.775521	40	40
23.0	13.053692	28	28
24.0	13.316147	30	30
25.0	13.563773	35	35
26.0	13.797407	31	31
27.0	14.017841	32	32
28.0	14.225821	22	22
29.0	14.422049	30	30
30.0	14.60719	27	27
31.0	14.781871	32	32
32.0	14.946682	17	17
33.0	15.102181	22	22
34.0	15.248894	21	21
35.0	15.387318	11	11
36.0	15.517921	17	17
37.0	15.641144	26	26
38.0	15.757406	20	20
39.0	15.867098	16	16
40.0	15.970593	10	10
41.0	16.06824	17	17
42.0	16.16037	14	14
43.0	16.247294	15	15
44.0	16.329308	10	10
45.0	16.406687	15	15
46.0	16.479695	12	12
47.0	16.548577	17	17
48.0	16.613568	13	13
49.0	16.674886	6	6
50.0	16.73274	11	11
51.0	16.787325	9	9
52.0	16.838826	6	6
53.0	16.887417	10	10
54.0	16.933263	10	10
55.0	16.976519	10	10
56.0	17.01733	8	8
57.0	17.055836	9	9
58.0	17.092166	9	9
59.0	17.126443	13	13
60.0	17.158783	11	11
61.0	17.189297	7	7
62.0	17.218086	15	15
63.0	17.245249	7	7
64.0	17.270877	5	5
65.0	17.295057	8	8
66.0	17.31787	9	9
67.0	17.339395	6	6
68.0	17.359704	10	10
69.0	17.378865	9	9
70.0	17.396943	7	7
71.0	17.414001	12	12
72.0	17.430094	3	3
73.0	17.445278	10	10
74.0	17.459604	7	7
75.0	17.473121	7	7
76.0	17.485874	7	7
77.0	17.497906	7	7
78.0	17.509259	3	3
79.0	17.51997	5	5
80.0	17.530076	3	3
81.0	17.539611	3	3
82.0	17.548607	7	7
83.0	17.557095	4	4
84.0	17.565103	7	7
85.0	17.572659	4	4
86.0	17.579788	5	5
87.0	17.586514	2	2
88.0	17.59286	3	3
89.0	17.598848	4	4
90.0	17.604497	2	2
91.0	17.609827	6	6
92.0	17.614856	4	4
93.0	17.619601	5	5
94.0	17.624078	4	4
95.0	17.628302	0	0
96.0	17.632287	2	2
97.0	17.636047	1	1
98.0	17.639594	1	1
99.0	17.642941	4	4
100.0	17.646099	1	1
101.0	0	4	4
102.0	0	2	2
103.0	0	3	3
104.0	0	6	6
105.0	0	5	5
106.0	0	4	4
107.0	0	2	2
108.0	0	2	2
109.0	0	1	1
110.0	0	2	2
111.0	0	3	3
112.0	0	3	3
113.0	0	1	1
114.0	0	4	4
115.0	0	2	2
116.0	0	3	3
117.0	0	2	2
118.0	0	1	1
119.0	0	3	3
120.0	0	4	4
121.0	0	2	2
122.0	0	1	1
123.0	0	3	3
124.0	0	3	3
125.0	0	4	4
126.0	0	4	4
127.0	0	6	6
128.0	0	1	1
129.0	0	3	3
130.0	0	1	1
131.0	0	1	1
132.0	0	3	3
133.0	0	1	1
134.0	0	3	3
135.0	0	2	2
136.0	0	1	1
137.0	0	3	3
138.0	0	6	6
139.0	0	2	2
140.0	0	5	5
143.0	0	3	3
144.0	0	1	1
145.0	0	4	4
146.0	0	2	2
147.0	0	3	3
148.0	0	1	1
149.0	0	1	1
150.0	0	6	6
151.0	0	2	2
152.0	0	1	1
153.0	0	1	1
157.0	0	4	4
158.0	0	3	3
159.0	0	2	2
160.0	0	2	2
161.0	0	2	2
162.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
170.0	0	1	1
171.0	0	3	3
173.0	0	2	2
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
177.0	0	4	4
178.0	0	2	2
179.0	0	3	3
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	3	3
184.0	0	2	2
185.0	0	1	1
186.0	0	2	2
187.0	0	1	1
188.0	0	2	2
189.0	0	3	3
190.0	0	1	1
192.0	0	2	2
193.0	0	2	2
195.0	0	1	1
196.0	0	2	2
201.0	0	1	1
203.0	0	3	3
204.0	0	2	2
205.0	0	1	1
206.0	0	3	3
208.0	0	1	1
210.0	0	1	1
212.0	0	2	2
213.0	0	1	1
214.0	0	2	2
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	3	3
220.0	0	1	1
221.0	0	1	1
222.0	0	2	2
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
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	2	2
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
237.0	0	2	2
239.0	0	2	2
242.0	0	3	3
243.0	0	2	2
246.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	2	2
250.0	0	1	1
252.0	0	3	3
253.0	0	3	3
254.0	0	1	1
257.0	0	2	2
259.0	0	2	2
261.0	0	1	1
262.0	0	1	1
264.0	0	1	1
266.0	0	2	2
269.0	0	2	2
270.0	0	1	1
274.0	0	2	2
276.0	0	3	3
277.0	0	1	1
279.0	0	1	1
281.0	0	1	1
283.0	0	1	1
287.0	0	2	2
289.0	0	2	2
296.0	0	1	1
302.0	0	1	1
303.0	0	2	2
305.0	0	2	2
306.0	0	1	1
307.0	0	2	2
309.0	0	1	1
311.0	0	1	1
319.0	0	1	1
320.0	0	1	1
324.0	0	3	3
326.0	0	1	1
327.0	0	1	1
329.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	2	2
333.0	0	1	1
337.0	0	3	3
340.0	0	1	1
345.0	0	1	1
347.0	0	1	1
348.0	0	1	1
353.0	0	2	2
356.0	0	2	2
357.0	0	2	2
360.0	0	1	1
361.0	0	1	1
363.0	0	1	1
369.0	0	1	1
370.0	0	1	1
374.0	0	1	1
375.0	0	1	1
382.0	0	1	1
386.0	0	1	1
389.0	0	1	1
390.0	0	1	1
398.0	0	2	2
403.0	0	1	1
411.0	0	1	1
417.0	0	1	1
419.0	0	1	1
420.0	0	1	1
422.0	0	1	1
423.0	0	1	1
433.0	0	1	1
434.0	0	1	1
440.0	0	1	1
448.0	0	1	1
451.0	0	1	1
452.0	0	1	1
455.0	0	1	1
460.0	0	1	1
467.0	0	1	1
473.0	0	1	1
481.0	0	1	1
483.0	0	1	1
485.0	0	1	1
488.0	0	1	1
493.0	0	1	1
497.0	0	1	1
505.0	0	1	1
509.0	0	1	1
511.0	0	1	1
517.0	0	1	1
527.0	0	1	1
532.0	0	1	1
536.0	0	1	1
547.0	0	1	1
550.0	0	1	1
564.0	0	1	1
574.0	0	1	1
605.0	0	1	1
612.0	0	1	1
623.0	0	1	1
624.0	0	1	1
639.0	0	1	1
646.0	0	1	1
732.0	0	1	1
757.0	0	1	1
781.0	0	1	1
820.0	0	1	1
868.0	0	1	1