## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-06-18/US_Pen_Sta_1_2014-06-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-06-18/US_Pen_Sta_1_2014-06-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Sta_1_2014-06-18/US_Pen_Sta_1_2014-06-18.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 23:02:25 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	879348	68841788	0	0	486844	24494802	0	0.357068	72088769

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25904813	25904813
2.0	1.384828	10973926	10973926
3.0	1.532921	3840762	3840762
4.0	1.589911	1157979	1157979
5.0	1.611842	320420	320420
6.0	1.620282	86809	86809
7.0	1.62353	25671	25671
8.0	1.62478	9310	9310
9.0	1.625261	4605	4605
10.0	1.625446	2756	2756
11.0	1.625517	1877	1877
12.0	1.625545	1408	1408
13.0	1.625555	1006	1006
14.0	1.625559	834	834
15.0	1.625561	663	663
16.0	1.625561	544	544
17.0	1.625562	466	466
18.0	1.625562	375	375
19.0	1.625562	358	358
20.0	1.625562	287	287
21.0	1.625562	282	282
22.0	1.625562	245	245
23.0	1.625562	191	191
24.0	1.625562	223	223
25.0	1.625562	183	183
26.0	1.625562	146	146
27.0	1.625562	151	151
28.0	1.625562	130	130
29.0	1.625562	116	116
30.0	1.625562	106	106
31.0	1.625562	105	105
32.0	1.625562	94	94
33.0	1.625562	91	91
34.0	1.625562	76	76
35.0	1.625562	89	89
36.0	1.625562	61	61
37.0	1.625562	61	61
38.0	1.625562	58	58
39.0	1.625562	59	59
40.0	1.625562	53	53
41.0	1.625562	52	52
42.0	1.625562	55	55
43.0	1.625562	42	42
44.0	1.625562	42	42
45.0	1.625562	53	53
46.0	1.625562	36	36
47.0	1.625562	44	44
48.0	1.625562	47	47
49.0	1.625562	34	34
50.0	1.625562	30	30
51.0	1.625562	32	32
52.0	1.625562	41	41
53.0	1.625562	35	35
54.0	1.625562	26	26
55.0	1.625562	31	31
56.0	1.625562	22	22
57.0	1.625562	25	25
58.0	1.625562	29	29
59.0	1.625562	25	25
60.0	1.625562	27	27
61.0	1.625562	28	28
62.0	1.625562	22	22
63.0	1.625562	22	22
64.0	1.625562	29	29
65.0	1.625562	23	23
66.0	1.625562	9	9
67.0	1.625562	20	20
68.0	1.625562	26	26
69.0	1.625562	13	13
70.0	1.625562	14	14
71.0	1.625562	21	21
72.0	1.625562	19	19
73.0	1.625562	15	15
74.0	1.625562	13	13
75.0	1.625562	17	17
76.0	1.625562	14	14
77.0	1.625562	12	12
78.0	1.625562	14	14
79.0	1.625562	12	12
80.0	1.625562	12	12
81.0	1.625562	7	7
82.0	1.625562	13	13
83.0	1.625562	10	10
84.0	1.625562	11	11
85.0	1.625562	10	10
86.0	1.625562	13	13
87.0	1.625562	10	10
88.0	1.625562	12	12
89.0	1.625562	9	9
90.0	1.625562	9	9
91.0	1.625562	5	5
92.0	1.625562	7	7
93.0	1.625562	9	9
94.0	1.625562	8	8
95.0	1.625562	12	12
96.0	1.625562	16	16
97.0	1.625562	10	10
98.0	1.625562	7	7
99.0	1.625562	15	15
100.0	1.625562	14	14
101.0	0	7	7
102.0	0	10	10
103.0	0	10	10
104.0	0	11	11
105.0	0	5	5
106.0	0	9	9
107.0	0	4	4
108.0	0	8	8
109.0	0	6	6
110.0	0	10	10
111.0	0	6	6
112.0	0	8	8
113.0	0	6	6
114.0	0	9	9
115.0	0	5	5
116.0	0	2	2
117.0	0	8	8
118.0	0	5	5
119.0	0	4	4
120.0	0	5	5
121.0	0	7	7
122.0	0	6	6
123.0	0	5	5
124.0	0	4	4
125.0	0	5	5
126.0	0	5	5
127.0	0	6	6
128.0	0	2	2
129.0	0	4	4
130.0	0	10	10
131.0	0	2	2
132.0	0	6	6
133.0	0	1	1
134.0	0	5	5
135.0	0	2	2
136.0	0	6	6
137.0	0	1	1
138.0	0	4	4
139.0	0	2	2
140.0	0	4	4
141.0	0	3	3
142.0	0	6	6
143.0	0	6	6
144.0	0	4	4
145.0	0	2	2
146.0	0	3	3
147.0	0	3	3
148.0	0	2	2
149.0	0	5	5
150.0	0	5	5
151.0	0	2	2
152.0	0	3	3
153.0	0	3	3
154.0	0	2	2
155.0	0	2	2
156.0	0	3	3
157.0	0	2	2
158.0	0	3	3
159.0	0	1	1
160.0	0	3	3
161.0	0	5	5
162.0	0	2	2
163.0	0	1	1
164.0	0	4	4
165.0	0	2	2
166.0	0	4	4
168.0	0	2	2
169.0	0	1	1
170.0	0	3	3
171.0	0	1	1
172.0	0	2	2
174.0	0	3	3
175.0	0	2	2
176.0	0	2	2
177.0	0	4	4
178.0	0	3	3
180.0	0	2	2
181.0	0	3	3
183.0	0	1	1
185.0	0	1	1
186.0	0	4	4
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	5	5
192.0	0	1	1
193.0	0	3	3
194.0	0	3	3
195.0	0	2	2
196.0	0	1	1
197.0	0	1	1
199.0	0	3	3
200.0	0	1	1
201.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	1	1
208.0	0	1	1
209.0	0	2	2
210.0	0	1	1
212.0	0	2	2
213.0	0	2	2
214.0	0	1	1
217.0	0	3	3
218.0	0	4	4
219.0	0	2	2
221.0	0	1	1
222.0	0	1	1
224.0	0	2	2
226.0	0	1	1
227.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	3	3
233.0	0	2	2
234.0	0	1	1
237.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	1	1
244.0	0	5	5
245.0	0	1	1
249.0	0	1	1
251.0	0	1	1
254.0	0	2	2
256.0	0	2	2
257.0	0	2	2
263.0	0	1	1
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
270.0	0	1	1
271.0	0	2	2
272.0	0	1	1
273.0	0	1	1
275.0	0	1	1
280.0	0	1	1
284.0	0	1	1
286.0	0	3	3
287.0	0	1	1
288.0	0	4	4
289.0	0	1	1
290.0	0	1	1
292.0	0	1	1
295.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	2	2
307.0	0	2	2
308.0	0	2	2
309.0	0	1	1
311.0	0	1	1
319.0	0	1	1
321.0	0	1	1
322.0	0	1	1
327.0	0	1	1
331.0	0	1	1
336.0	0	1	1
340.0	0	1	1
342.0	0	1	1
345.0	0	3	3
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
351.0	0	1	1
361.0	0	1	1
363.0	0	1	1
367.0	0	1	1
376.0	0	1	1
378.0	0	1	1
379.0	0	1	1
382.0	0	3	3
383.0	0	1	1
389.0	0	1	1
390.0	0	1	1
395.0	0	1	1
396.0	0	1	1
401.0	0	1	1
404.0	0	1	1
405.0	0	1	1
416.0	0	1	1
417.0	0	1	1
420.0	0	1	1
433.0	0	1	1
436.0	0	1	1
437.0	0	1	1
449.0	0	1	1
460.0	0	1	1
462.0	0	2	2
467.0	0	1	1
471.0	0	1	1
477.0	0	1	1
479.0	0	1	1
492.0	0	1	1
494.0	0	1	1
497.0	0	1	1
505.0	0	1	1
507.0	0	1	1
523.0	0	1	1
531.0	0	1	1
535.0	0	1	1
537.0	0	1	1
540.0	0	1	1
541.0	0	1	1
542.0	0	1	1
550.0	0	1	1
554.0	0	1	1
558.0	0	1	1
579.0	0	1	1
583.0	0	1	1
587.0	0	2	2
588.0	0	1	1
614.0	0	1	1
615.0	0	1	1
616.0	0	2	2
626.0	0	1	1
642.0	0	1	1
643.0	0	1	1
646.0	0	1	1
650.0	0	1	1
659.0	0	1	1
660.0	0	1	1
668.0	0	1	1
673.0	0	1	1
684.0	0	2	2
742.0	0	1	1
803.0	0	1	1
819.0	0	1	1
820.0	0	1	1
847.0	0	1	1
854.0	0	1	1
899.0	0	2	2
988.0	0	1	1
1095.0	0	1	1
1378.0	0	1	1
1480.0	0	1	1