## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Ill_Urb_1_2015-07-11/US_Ill_Urb_1_2015-07-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Ill_Urb_1_2015-07-11/US_Ill_Urb_1_2015-07-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Ill_Urb_1_2015-07-11/US_Ill_Urb_1_2015-07-11.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 19:52:04 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	1723445	48523633	0	0	843862	10553630	0	0.222243	94710693

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	28657624	28657624
2.0	1.599095	6621564	6621564
3.0	1.95801	1336259	1336259
4.0	2.173033	245562	245562
5.0	2.301853	45516	45516
6.0	2.379028	10980	10980
7.0	2.425264	4206	4206
8.0	2.452963	2279	2279
9.0	2.469558	1590	1590
10.0	2.479499	1102	1102
11.0	2.485455	849	849
12.0	2.489023	696	696
13.0	2.491161	556	556
14.0	2.492442	383	383
15.0	2.493209	364	364
16.0	2.493669	262	262
17.0	2.493944	239	239
18.0	2.494109	210	210
19.0	2.494208	168	168
20.0	2.494267	165	165
21.0	2.494303	138	138
22.0	2.494324	103	103
23.0	2.494337	128	128
24.0	2.494344	81	81
25.0	2.494349	84	84
26.0	2.494352	86	86
27.0	2.494353	76	76
28.0	2.494354	62	62
29.0	2.494355	77	77
30.0	2.494355	63	63
31.0	2.494355	65	65
32.0	2.494355	59	59
33.0	2.494356	44	44
34.0	2.494356	43	43
35.0	2.494356	52	52
36.0	2.494356	39	39
37.0	2.494356	38	38
38.0	2.494356	43	43
39.0	2.494356	42	42
40.0	2.494356	36	36
41.0	2.494356	34	34
42.0	2.494356	22	22
43.0	2.494356	28	28
44.0	2.494356	29	29
45.0	2.494356	22	22
46.0	2.494356	25	25
47.0	2.494356	24	24
48.0	2.494356	21	21
49.0	2.494356	29	29
50.0	2.494356	22	22
51.0	2.494356	10	10
52.0	2.494356	20	20
53.0	2.494356	22	22
54.0	2.494356	17	17
55.0	2.494356	11	11
56.0	2.494356	13	13
57.0	2.494356	19	19
58.0	2.494356	10	10
59.0	2.494356	11	11
60.0	2.494356	9	9
61.0	2.494356	18	18
62.0	2.494356	13	13
63.0	2.494356	12	12
64.0	2.494356	8	8
65.0	2.494356	11	11
66.0	2.494356	13	13
67.0	2.494356	12	12
68.0	2.494356	10	10
69.0	2.494356	13	13
70.0	2.494356	18	18
71.0	2.494356	7	7
72.0	2.494356	6	6
73.0	2.494356	10	10
74.0	2.494356	11	11
75.0	2.494356	11	11
76.0	2.494356	12	12
77.0	2.494356	9	9
78.0	2.494356	11	11
79.0	2.494356	11	11
80.0	2.494356	9	9
81.0	2.494356	6	6
82.0	2.494356	9	9
83.0	2.494356	4	4
84.0	2.494356	6	6
85.0	2.494356	10	10
86.0	2.494356	10	10
87.0	2.494356	7	7
88.0	2.494356	8	8
89.0	2.494356	6	6
90.0	2.494356	5	5
91.0	2.494356	2	2
92.0	2.494356	6	6
93.0	2.494356	5	5
94.0	2.494356	9	9
95.0	2.494356	8	8
96.0	2.494356	2	2
97.0	2.494356	6	6
98.0	2.494356	3	3
99.0	2.494356	6	6
100.0	2.494356	5	5
101.0	0	7	7
102.0	0	3	3
103.0	0	5	5
104.0	0	3	3
105.0	0	7	7
106.0	0	3	3
107.0	0	1	1
108.0	0	5	5
109.0	0	3	3
110.0	0	1	1
111.0	0	6	6
112.0	0	2	2
113.0	0	3	3
114.0	0	3	3
115.0	0	2	2
116.0	0	2	2
117.0	0	4	4
118.0	0	1	1
119.0	0	2	2
120.0	0	3	3
121.0	0	2	2
122.0	0	1	1
123.0	0	1	1
124.0	0	1	1
126.0	0	4	4
127.0	0	8	8
128.0	0	2	2
129.0	0	2	2
130.0	0	6	6
131.0	0	1	1
132.0	0	4	4
134.0	0	2	2
135.0	0	1	1
136.0	0	4	4
137.0	0	4	4
138.0	0	2	2
139.0	0	2	2
140.0	0	1	1
141.0	0	4	4
142.0	0	4	4
144.0	0	1	1
145.0	0	4	4
146.0	0	3	3
147.0	0	3	3
148.0	0	2	2
149.0	0	2	2
150.0	0	3	3
151.0	0	5	5
152.0	0	4	4
153.0	0	1	1
154.0	0	3	3
155.0	0	1	1
156.0	0	1	1
157.0	0	3	3
158.0	0	1	1
159.0	0	2	2
160.0	0	1	1
161.0	0	2	2
163.0	0	3	3
164.0	0	1	1
165.0	0	2	2
166.0	0	2	2
167.0	0	3	3
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	1	1
173.0	0	1	1
174.0	0	2	2
176.0	0	1	1
177.0	0	3	3
178.0	0	3	3
179.0	0	1	1
180.0	0	2	2
181.0	0	4	4
183.0	0	1	1
184.0	0	1	1
186.0	0	3	3
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
190.0	0	2	2
191.0	0	2	2
192.0	0	1	1
193.0	0	1	1
194.0	0	1	1
196.0	0	1	1
198.0	0	1	1
200.0	0	2	2
201.0	0	3	3
202.0	0	3	3
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
207.0	0	2	2
209.0	0	1	1
210.0	0	1	1
212.0	0	1	1
213.0	0	3	3
215.0	0	2	2
217.0	0	3	3
219.0	0	2	2
222.0	0	1	1
224.0	0	1	1
226.0	0	1	1
227.0	0	1	1
232.0	0	2	2
233.0	0	2	2
234.0	0	1	1
235.0	0	1	1
237.0	0	1	1
240.0	0	2	2
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
253.0	0	1	1
255.0	0	2	2
256.0	0	1	1
257.0	0	1	1
260.0	0	1	1
261.0	0	3	3
262.0	0	1	1
266.0	0	1	1
269.0	0	2	2
270.0	0	1	1
271.0	0	1	1
273.0	0	3	3
274.0	0	2	2
275.0	0	1	1
279.0	0	1	1
281.0	0	1	1
284.0	0	1	1
286.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	1	1
291.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	2	2
303.0	0	1	1
305.0	0	1	1
307.0	0	2	2
308.0	0	1	1
313.0	0	1	1
320.0	0	1	1
322.0	0	2	2
334.0	0	2	2
345.0	0	1	1
346.0	0	1	1
348.0	0	1	1
350.0	0	1	1
351.0	0	1	1
355.0	0	1	1
356.0	0	1	1
363.0	0	2	2
367.0	0	1	1
375.0	0	1	1
389.0	0	1	1
393.0	0	2	2
396.0	0	1	1
404.0	0	1	1
405.0	0	1	1
409.0	0	1	1
412.0	0	1	1
413.0	0	2	2
416.0	0	1	1
420.0	0	1	1
434.0	0	1	1
435.0	0	1	1
437.0	0	1	1
441.0	0	1	1
445.0	0	1	1
450.0	0	1	1
451.0	0	1	1
455.0	0	1	1
466.0	0	1	1
471.0	0	1	1
485.0	0	1	1
487.0	0	1	1
493.0	0	2	2
507.0	0	1	1
515.0	0	1	1
527.0	0	1	1
530.0	0	1	1
546.0	0	1	1
548.0	0	1	1
554.0	0	1	1
573.0	0	1	1
576.0	0	1	1
581.0	0	1	1
586.0	0	1	1
600.0	0	1	1
605.0	0	1	1
607.0	0	1	1
608.0	0	1	1
615.0	0	1	1
616.0	0	1	1
623.0	0	1	1
645.0	0	1	1
646.0	0	1	1
648.0	0	1	1
677.0	0	2	2
680.0	0	1	1
681.0	0	1	1
687.0	0	1	1
703.0	0	1	1
705.0	0	1	1
720.0	0	1	1
724.0	0	1	1
861.0	0	1	1
917.0	0	1	1
1369.0	0	1	1