## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-10-27/FR_Ess_Vil_1_2014-10-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-10-27/FR_Ess_Vil_1_2014-10-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Ess_Vil_1_2014-10-27/FR_Ess_Vil_1_2014-10-27.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 09:42:46 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	3183293	33293887	0	0	929800	1204287	0	0.047848	449057540

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	30327286	30327286
2.0	1.92854	981057	981057
3.0	2.790727	28987	28987
4.0	3.591302	1492	1492
5.0	4.334668	432	432
6.0	5.024913	331	331
7.0	5.665833	263	263
8.0	6.260953	169	169
9.0	6.813546	161	161
10.0	7.326651	118	118
11.0	7.80309	107	107
12.0	8.245482	106	106
13.0	8.656261	92	92
14.0	9.037685	81	81
15.0	9.391853	77	77
16.0	9.720712	67	67
17.0	10.026071	66	66
18.0	10.30961	68	68
19.0	10.572886	55	55
20.0	10.817349	64	64
21.0	11.044342	47	47
22.0	11.255115	40	40
23.0	11.450826	43	43
24.0	11.632551	53	53
25.0	11.80129	35	35
26.0	11.957971	40	40
27.0	12.103456	34	34
28.0	12.238545	35	35
29.0	12.36398	26	26
30.0	12.480451	25	25
31.0	12.588599	21	21
32.0	12.68902	24	24
33.0	12.782264	23	23
34.0	12.868845	26	26
35.0	12.949238	21	21
36.0	13.023887	32	32
37.0	13.093202	13	13
38.0	13.157563	22	22
39.0	13.217325	11	11
40.0	13.272817	24	24
41.0	13.324343	13	13
42.0	13.372187	11	11
43.0	13.416612	13	13
44.0	13.457862	18	18
45.0	13.496165	18	18
46.0	13.531731	13	13
47.0	13.564755	20	20
48.0	13.595419	12	12
49.0	13.623892	16	16
50.0	13.65033	16	16
51.0	13.674879	12	12
52.0	13.697674	12	12
53.0	13.71884	10	10
54.0	13.738493	11	11
55.0	13.756742	8	8
56.0	13.773687	16	16
57.0	13.789421	14	14
58.0	13.80403	12	12
59.0	13.817596	15	15
60.0	13.830192	8	8
61.0	13.841888	14	14
62.0	13.852748	8	8
63.0	13.862833	11	11
64.0	13.872196	11	11
65.0	13.880891	5	5
66.0	13.888964	10	10
67.0	13.89646	3	3
68.0	13.903421	5	5
69.0	13.909884	8	8
70.0	13.915885	6	6
71.0	13.921458	7	7
72.0	13.926632	7	7
73.0	13.931436	7	7
74.0	13.935897	2	2
75.0	13.94004	11	11
76.0	13.943886	8	8
77.0	13.947458	5	5
78.0	13.950774	4	4
79.0	13.953853	8	8
80.0	13.956713	8	8
81.0	13.959367	6	6
82.0	13.961833	6	6
83.0	13.964122	10	10
84.0	13.966247	13	13
85.0	13.968221	7	7
86.0	13.970053	4	4
87.0	13.971755	4	4
88.0	13.973335	7	7
89.0	13.974802	5	5
90.0	13.976164	5	5
91.0	13.977429	3	3
92.0	13.978604	6	6
93.0	13.979694	2	2
94.0	13.980707	3	3
95.0	13.981647	5	5
96.0	13.98252	2	2
97.0	13.983331	7	7
98.0	13.984084	3	3
99.0	13.984783	5	5
100.0	13.985432	2	2
101.0	0	2	2
102.0	0	5	5
103.0	0	3	3
104.0	0	6	6
105.0	0	4	4
106.0	0	3	3
107.0	0	5	5
108.0	0	3	3
109.0	0	4	4
110.0	0	8	8
111.0	0	6	6
112.0	0	7	7
113.0	0	5	5
114.0	0	5	5
115.0	0	3	3
117.0	0	4	4
118.0	0	4	4
119.0	0	8	8
120.0	0	3	3
121.0	0	1	1
122.0	0	3	3
123.0	0	1	1
124.0	0	4	4
125.0	0	5	5
126.0	0	1	1
127.0	0	4	4
128.0	0	4	4
129.0	0	2	2
130.0	0	2	2
131.0	0	2	2
132.0	0	6	6
134.0	0	3	3
135.0	0	6	6
136.0	0	2	2
138.0	0	6	6
139.0	0	2	2
140.0	0	3	3
141.0	0	1	1
142.0	0	2	2
143.0	0	3	3
144.0	0	2	2
145.0	0	3	3
146.0	0	1	1
148.0	0	1	1
149.0	0	2	2
150.0	0	2	2
151.0	0	4	4
152.0	0	5	5
153.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	7	7
158.0	0	3	3
159.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	3	3
164.0	0	5	5
165.0	0	3	3
167.0	0	4	4
168.0	0	3	3
169.0	0	2	2
170.0	0	1	1
173.0	0	2	2
174.0	0	1	1
175.0	0	3	3
176.0	0	3	3
177.0	0	1	1
178.0	0	3	3
179.0	0	3	3
180.0	0	1	1
181.0	0	2	2
182.0	0	2	2
183.0	0	2	2
184.0	0	2	2
186.0	0	2	2
187.0	0	1	1
189.0	0	1	1
190.0	0	3	3
191.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	2	2
198.0	0	2	2
199.0	0	2	2
200.0	0	1	1
201.0	0	2	2
202.0	0	2	2
203.0	0	2	2
205.0	0	3	3
207.0	0	2	2
208.0	0	2	2
209.0	0	1	1
211.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
223.0	0	3	3
224.0	0	1	1
227.0	0	2	2
228.0	0	1	1
230.0	0	1	1
232.0	0	2	2
233.0	0	2	2
234.0	0	1	1
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
238.0	0	2	2
241.0	0	1	1
242.0	0	2	2
244.0	0	1	1
245.0	0	2	2
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
269.0	0	1	1
271.0	0	1	1
272.0	0	2	2
273.0	0	1	1
274.0	0	3	3
275.0	0	1	1
276.0	0	1	1
277.0	0	2	2
278.0	0	2	2
280.0	0	1	1
282.0	0	2	2
283.0	0	1	1
285.0	0	1	1
286.0	0	1	1
287.0	0	1	1
288.0	0	2	2
291.0	0	1	1
292.0	0	1	1
293.0	0	1	1
296.0	0	1	1
298.0	0	1	1
303.0	0	1	1
304.0	0	1	1
313.0	0	1	1
314.0	0	1	1
316.0	0	1	1
317.0	0	1	1
318.0	0	1	1
321.0	0	1	1
323.0	0	1	1
329.0	0	1	1
336.0	0	1	1
337.0	0	1	1
338.0	0	1	1
340.0	0	1	1
342.0	0	1	1
345.0	0	2	2
347.0	0	1	1
349.0	0	1	1
352.0	0	1	1
354.0	0	1	1
357.0	0	1	1
358.0	0	1	1
360.0	0	1	1
363.0	0	1	1
364.0	0	1	1
365.0	0	1	1
368.0	0	1	1
380.0	0	1	1
382.0	0	1	1
385.0	0	1	1
388.0	0	1	1
393.0	0	2	2
408.0	0	2	2
409.0	0	1	1
413.0	0	1	1
415.0	0	1	1
424.0	0	1	1
440.0	0	1	1
442.0	0	1	1
443.0	0	1	1
447.0	0	1	1
454.0	0	1	1
459.0	0	1	1
469.0	0	1	1
478.0	0	1	1
479.0	0	1	1
481.0	0	1	1
487.0	0	1	1
491.0	0	1	1
495.0	0	1	1
496.0	0	1	1
518.0	0	1	1
523.0	0	1	1
542.0	0	1	1
548.0	0	1	1
553.0	0	1	1
559.0	0	1	1
560.0	0	2	2
567.0	0	1	1
592.0	0	1	1
598.0	0	1	1
603.0	0	2	2
676.0	0	1	1
678.0	0	1	1
682.0	0	1	1
706.0	0	1	1
710.0	0	1	1
785.0	0	1	1
803.0	0	1	1
1022.0	0	1	1
1048.0	0	1	1