## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-06-20/RU_Cri_Yal_1_2014-06-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-06-20/RU_Cri_Yal_1_2014-06-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-06-20/RU_Cri_Yal_1_2014-06-20.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 08:38:59 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	4862691	29153244	0	0	1288165	833611	0	0.046785	500012343

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	27203851	27203851
2.0	1.943362	656868	656868
3.0	2.833294	12497	12497
4.0	3.672822	815	815
5.0	4.464802	390	390
6.0	5.211925	285	285
7.0	5.916733	213	213
8.0	6.581621	182	182
9.0	7.208852	156	156
10.0	7.800558	165	165
11.0	8.358751	150	150
12.0	8.88533	152	152
13.0	9.382083	120	120
14.0	9.850702	100	100
15.0	10.292779	111	111
16.0	10.709818	93	93
17.0	11.103237	85	85
18.0	11.474373	69	69
19.0	11.824489	67	67
20.0	12.154775	68	68
21.0	12.466355	65	65
22.0	12.760287	45	45
23.0	13.037572	62	62
24.0	13.299151	54	54
25.0	13.545916	33	33
26.0	13.778704	50	50
27.0	13.998308	50	50
28.0	14.205473	45	45
29.0	14.400906	37	37
30.0	14.585269	45	45
31.0	14.75919	28	28
32.0	14.923261	33	33
33.0	15.07804	22	22
34.0	15.224052	24	24
35.0	15.361794	24	24
36.0	15.491735	28	28
37.0	15.614316	30	30
38.0	15.729954	27	27
39.0	15.839043	23	23
40.0	15.941954	19	19
41.0	16.039035	27	27
42.0	16.130619	14	14
43.0	16.217015	24	24
44.0	16.298518	16	16
45.0	16.375404	17	17
46.0	16.447936	18	18
47.0	16.51636	8	8
48.0	16.580909	18	18
49.0	16.641801	17	17
50.0	16.699245	21	21
51.0	16.753436	10	10
52.0	16.804557	10	10
53.0	16.852783	14	14
54.0	16.898277	13	13
55.0	16.941194	11	11
56.0	16.981681	9	9
57.0	17.019875	17	17
58.0	17.055906	12	12
59.0	17.089896	12	12
60.0	17.12196	10	10
61.0	17.152209	9	9
62.0	17.180744	17	17
63.0	17.207664	13	13
64.0	17.233058	5	5
65.0	17.257015	10	10
66.0	17.279614	6	6
67.0	17.300934	5	5
68.0	17.321046	9	9
69.0	17.340019	8	8
70.0	17.357917	6	6
71.0	17.374801	7	7
72.0	17.39073	10	10
73.0	17.405756	8	8
74.0	17.419931	5	5
75.0	17.433303	10	10
76.0	17.445918	14	14
77.0	17.457819	9	9
78.0	17.469045	6	6
79.0	17.479635	4	4
80.0	17.489626	4	4
81.0	17.499051	9	9
82.0	17.507942	5	5
83.0	17.51633	2	2
84.0	17.524242	7	7
85.0	17.531706	2	2
86.0	17.538748	2	2
87.0	17.545391	6	6
88.0	17.551657	3	3
89.0	17.557569	8	8
90.0	17.563145	6	6
91.0	17.568406	6	6
92.0	17.573369	7	7
93.0	17.578051	3	3
94.0	17.582468	3	3
95.0	17.586634	6	6
96.0	17.590565	7	7
97.0	17.594273	6	6
98.0	17.597771	2	2
99.0	17.60107	4	4
100.0	17.604183	2	2
101.0	0	3	3
102.0	0	4	4
103.0	0	2	2
104.0	0	4	4
105.0	0	2	2
106.0	0	3	3
107.0	0	5	5
108.0	0	3	3
109.0	0	1	1
110.0	0	3	3
111.0	0	5	5
112.0	0	3	3
113.0	0	5	5
114.0	0	7	7
115.0	0	3	3
116.0	0	1	1
117.0	0	4	4
118.0	0	2	2
119.0	0	2	2
120.0	0	3	3
122.0	0	3	3
123.0	0	1	1
124.0	0	2	2
125.0	0	4	4
126.0	0	3	3
127.0	0	3	3
129.0	0	3	3
130.0	0	1	1
131.0	0	2	2
133.0	0	2	2
134.0	0	2	2
135.0	0	3	3
136.0	0	2	2
137.0	0	2	2
138.0	0	2	2
139.0	0	3	3
140.0	0	1	1
141.0	0	1	1
143.0	0	1	1
144.0	0	1	1
145.0	0	2	2
147.0	0	2	2
148.0	0	1	1
149.0	0	3	3
150.0	0	1	1
151.0	0	3	3
152.0	0	4	4
153.0	0	1	1
154.0	0	3	3
156.0	0	2	2
157.0	0	5	5
158.0	0	4	4
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	3	3
164.0	0	3	3
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
170.0	0	2	2
171.0	0	2	2
173.0	0	1	1
175.0	0	5	5
176.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	1	1
180.0	0	3	3
181.0	0	1	1
182.0	0	3	3
183.0	0	2	2
184.0	0	3	3
185.0	0	3	3
186.0	0	2	2
187.0	0	2	2
191.0	0	2	2
192.0	0	3	3
193.0	0	1	1
195.0	0	3	3
199.0	0	3	3
201.0	0	2	2
202.0	0	2	2
203.0	0	1	1
204.0	0	1	1
207.0	0	1	1
209.0	0	1	1
211.0	0	4	4
214.0	0	2	2
215.0	0	1	1
216.0	0	3	3
217.0	0	1	1
218.0	0	2	2
219.0	0	2	2
222.0	0	3	3
224.0	0	1	1
227.0	0	4	4
228.0	0	2	2
229.0	0	2	2
230.0	0	3	3
231.0	0	1	1
232.0	0	2	2
235.0	0	2	2
237.0	0	1	1
239.0	0	3	3
240.0	0	2	2
241.0	0	1	1
247.0	0	1	1
250.0	0	1	1
252.0	0	3	3
253.0	0	1	1
254.0	0	3	3
256.0	0	1	1
257.0	0	1	1
259.0	0	3	3
262.0	0	1	1
264.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
271.0	0	3	3
272.0	0	3	3
273.0	0	1	1
275.0	0	1	1
276.0	0	2	2
277.0	0	2	2
282.0	0	1	1
286.0	0	2	2
292.0	0	1	1
295.0	0	1	1
298.0	0	1	1
303.0	0	1	1
306.0	0	2	2
310.0	0	1	1
311.0	0	4	4
312.0	0	1	1
313.0	0	1	1
315.0	0	2	2
319.0	0	1	1
321.0	0	1	1
329.0	0	1	1
330.0	0	1	1
333.0	0	1	1
334.0	0	1	1
337.0	0	1	1
342.0	0	1	1
344.0	0	1	1
346.0	0	1	1
347.0	0	1	1
354.0	0	2	2
358.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
376.0	0	2	2
377.0	0	1	1
385.0	0	1	1
387.0	0	1	1
394.0	0	2	2
398.0	0	1	1
409.0	0	1	1
411.0	0	1	1
421.0	0	1	1
422.0	0	1	1
426.0	0	1	1
434.0	0	1	1
438.0	0	1	1
440.0	0	1	1
441.0	0	1	1
456.0	0	1	1
460.0	0	1	1
466.0	0	1	1
480.0	0	1	1
507.0	0	1	1
510.0	0	1	1
518.0	0	1	1
531.0	0	1	1
532.0	0	1	1
622.0	0	1	1
687.0	0	1	1
750.0	0	1	1