## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2014-06-25/US_Wis_Cro_1_2014-06-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2014-06-25/US_Wis_Cro_1_2014-06-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2014-06-25/US_Wis_Cro_1_2014-06-25.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 21:31:14 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	943004	55681866	0	0	452707	12165225	0	0.220674	108102762

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	32799013	32799013
2.0	1.597451	7621840	7621840
3.0	1.954399	1537511	1537511
4.0	2.167658	288802	288802
5.0	2.29507	55650	55650
6.0	2.371192	13164	13164
7.0	2.416671	4366	4366
8.0	2.443843	2191	2191
9.0	2.460077	1251	1251
10.0	2.469776	926	926
11.0	2.47557	699	699
12.0	2.479032	533	533
13.0	2.481101	392	392
14.0	2.482337	331	331
15.0	2.483075	252	252
16.0	2.483516	220	220
17.0	2.48378	179	179
18.0	2.483937	165	165
19.0	2.484031	153	153
20.0	2.484087	124	124
21.0	2.484121	120	120
22.0	2.484141	120	120
23.0	2.484153	115	115
24.0	2.48416	109	109
25.0	2.484164	87	87
26.0	2.484167	79	79
27.0	2.484168	84	84
28.0	2.484169	75	75
29.0	2.48417	62	62
30.0	2.48417	52	52
31.0	2.48417	50	50
32.0	2.48417	60	60
33.0	2.484171	50	50
34.0	2.484171	54	54
35.0	2.484171	50	50
36.0	2.484171	52	52
37.0	2.484171	33	33
38.0	2.484171	38	38
39.0	2.484171	35	35
40.0	2.484171	33	33
41.0	2.484171	31	31
42.0	2.484171	35	35
43.0	2.484171	30	30
44.0	2.484171	29	29
45.0	2.484171	39	39
46.0	2.484171	30	30
47.0	2.484171	29	29
48.0	2.484171	17	17
49.0	2.484171	18	18
50.0	2.484171	21	21
51.0	2.484171	30	30
52.0	2.484171	21	21
53.0	2.484171	12	12
54.0	2.484171	19	19
55.0	2.484171	27	27
56.0	2.484171	17	17
57.0	2.484171	16	16
58.0	2.484171	11	11
59.0	2.484171	13	13
60.0	2.484171	14	14
61.0	2.484171	15	15
62.0	2.484171	14	14
63.0	2.484171	11	11
64.0	2.484171	12	12
65.0	2.484171	19	19
66.0	2.484171	20	20
67.0	2.484171	13	13
68.0	2.484171	8	8
69.0	2.484171	19	19
70.0	2.484171	12	12
71.0	2.484171	9	9
72.0	2.484171	14	14
73.0	2.484171	19	19
74.0	2.484171	9	9
75.0	2.484171	12	12
76.0	2.484171	11	11
77.0	2.484171	14	14
78.0	2.484171	11	11
79.0	2.484171	13	13
80.0	2.484171	5	5
81.0	2.484171	10	10
82.0	2.484171	11	11
83.0	2.484171	8	8
84.0	2.484171	13	13
85.0	2.484171	6	6
86.0	2.484171	10	10
87.0	2.484171	11	11
88.0	2.484171	8	8
89.0	2.484171	6	6
90.0	2.484171	8	8
91.0	2.484171	2	2
92.0	2.484171	1	1
93.0	2.484171	7	7
94.0	2.484171	7	7
95.0	2.484171	6	6
96.0	2.484171	5	5
97.0	2.484171	7	7
98.0	2.484171	3	3
99.0	2.484171	4	4
100.0	2.484171	4	4
101.0	0	10	10
102.0	0	5	5
103.0	0	6	6
104.0	0	2	2
105.0	0	6	6
106.0	0	5	5
107.0	0	3	3
108.0	0	8	8
109.0	0	6	6
110.0	0	5	5
111.0	0	4	4
112.0	0	5	5
113.0	0	3	3
114.0	0	6	6
115.0	0	5	5
116.0	0	2	2
117.0	0	4	4
118.0	0	2	2
119.0	0	3	3
120.0	0	5	5
121.0	0	5	5
122.0	0	6	6
123.0	0	1	1
124.0	0	4	4
125.0	0	3	3
126.0	0	4	4
127.0	0	4	4
128.0	0	4	4
129.0	0	3	3
130.0	0	6	6
131.0	0	4	4
132.0	0	4	4
133.0	0	3	3
134.0	0	3	3
135.0	0	3	3
136.0	0	2	2
137.0	0	5	5
138.0	0	8	8
139.0	0	6	6
141.0	0	2	2
143.0	0	3	3
144.0	0	2	2
145.0	0	1	1
146.0	0	5	5
147.0	0	2	2
148.0	0	3	3
151.0	0	6	6
152.0	0	4	4
153.0	0	2	2
154.0	0	5	5
155.0	0	3	3
156.0	0	2	2
157.0	0	3	3
158.0	0	6	6
159.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	3	3
165.0	0	3	3
166.0	0	1	1
167.0	0	3	3
168.0	0	1	1
169.0	0	4	4
170.0	0	2	2
172.0	0	2	2
173.0	0	3	3
174.0	0	2	2
175.0	0	3	3
176.0	0	4	4
177.0	0	1	1
178.0	0	2	2
179.0	0	4	4
180.0	0	2	2
181.0	0	2	2
183.0	0	2	2
184.0	0	3	3
185.0	0	2	2
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
190.0	0	2	2
192.0	0	1	1
193.0	0	1	1
194.0	0	3	3
195.0	0	1	1
196.0	0	3	3
197.0	0	2	2
198.0	0	3	3
199.0	0	1	1
200.0	0	2	2
201.0	0	3	3
202.0	0	1	1
204.0	0	1	1
205.0	0	3	3
206.0	0	2	2
207.0	0	1	1
208.0	0	2	2
209.0	0	1	1
211.0	0	3	3
212.0	0	3	3
214.0	0	2	2
215.0	0	2	2
219.0	0	2	2
220.0	0	2	2
221.0	0	1	1
222.0	0	3	3
223.0	0	1	1
224.0	0	1	1
225.0	0	1	1
227.0	0	1	1
232.0	0	4	4
233.0	0	1	1
234.0	0	3	3
235.0	0	2	2
236.0	0	1	1
238.0	0	1	1
240.0	0	2	2
242.0	0	2	2
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
248.0	0	1	1
252.0	0	2	2
254.0	0	2	2
257.0	0	1	1
259.0	0	1	1
260.0	0	2	2
265.0	0	1	1
266.0	0	2	2
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
281.0	0	1	1
282.0	0	2	2
285.0	0	1	1
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
294.0	0	1	1
295.0	0	2	2
299.0	0	1	1
300.0	0	1	1
301.0	0	1	1
302.0	0	1	1
303.0	0	1	1
305.0	0	2	2
306.0	0	1	1
307.0	0	1	1
308.0	0	2	2
309.0	0	1	1
310.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
317.0	0	2	2
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
325.0	0	2	2
330.0	0	1	1
332.0	0	1	1
335.0	0	1	1
336.0	0	1	1
338.0	0	2	2
339.0	0	1	1
340.0	0	1	1
341.0	0	2	2
346.0	0	2	2
347.0	0	1	1
348.0	0	1	1
350.0	0	2	2
351.0	0	1	1
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
359.0	0	2	2
362.0	0	1	1
364.0	0	1	1
368.0	0	1	1
372.0	0	1	1
373.0	0	1	1
376.0	0	1	1
377.0	0	1	1
381.0	0	1	1
383.0	0	1	1
387.0	0	1	1
389.0	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
399.0	0	1	1
403.0	0	1	1
404.0	0	1	1
407.0	0	3	3
411.0	0	2	2
413.0	0	1	1
420.0	0	1	1
421.0	0	1	1
425.0	0	1	1
429.0	0	2	2
438.0	0	1	1
441.0	0	1	1
448.0	0	1	1
455.0	0	1	1
456.0	0	1	1
457.0	0	1	1
461.0	0	1	1
465.0	0	1	1
472.0	0	1	1
481.0	0	1	1
482.0	0	2	2
487.0	0	1	1
492.0	0	1	1
493.0	0	1	1
519.0	0	1	1
520.0	0	1	1
522.0	0	1	1
532.0	0	1	1
538.0	0	1	1
544.0	0	1	1
571.0	0	1	1
572.0	0	1	1
578.0	0	1	1
582.0	0	1	1
586.0	0	1	1
598.0	0	1	1
605.0	0	1	1
608.0	0	1	1
622.0	0	1	1
635.0	0	1	1
660.0	0	1	1
665.0	0	1	1
666.0	0	1	1
667.0	0	1	1
676.0	0	1	1
683.0	0	1	1
696.0	0	1	1
703.0	0	1	1
715.0	0	1	1
725.0	0	1	1
731.0	0	1	1
736.0	0	2	2
738.0	0	1	1
792.0	0	1	1
829.0	0	1	1
856.0	0	1	1
861.0	0	1	1
895.0	0	1	1
963.0	0	1	1
1031.0	0	1	1
1105.0	0	1	1
1134.0	0	1	1
1270.0	0	1	1
1482.0	0	1	1