## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-09-03/DE_Bay_Mun_1_2014-09-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-09-03/DE_Bay_Mun_1_2014-09-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2014-09-03/DE_Bay_Mun_1_2014-09-03.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 08:35:21 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	8234036	17652434	0	0	1691347	551563	0	0.064183	276562328

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	16400336	16400336
2.0	1.938166	344276	344276
3.0	2.818322	6653	6653
4.0	3.644055	791	791
5.0	4.41873	485	485
6.0	5.145503	334	334
7.0	5.827338	272	272
8.0	6.467012	207	207
9.0	7.067133	152	152
10.0	7.630146	150	150
11.0	8.158346	117	117
12.0	8.653885	102	102
13.0	9.118783	91	91
14.0	9.554935	84	84
15.0	9.964118	77	77
16.0	10.348	84	84
17.0	10.708145	59	59
18.0	11.046021	65	65
19.0	11.363004	68	68
20.0	11.660388	48	48
21.0	11.939383	42	42
22.0	12.201127	52	52
23.0	12.446686	43	43
24.0	12.677061	50	50
25.0	12.893192	38	38
26.0	13.095958	44	44
27.0	13.286187	37	37
28.0	13.464653	34	34
29.0	13.632083	39	39
30.0	13.789161	27	27
31.0	13.936526	25	25
32.0	14.07478	27	27
33.0	14.204484	25	25
34.0	14.326168	26	26
35.0	14.440328	23	23
36.0	14.547429	21	21
37.0	14.647908	21	21
38.0	14.742174	25	25
39.0	14.830611	25	25
40.0	14.913579	18	18
41.0	14.991417	16	16
42.0	15.064443	15	15
43.0	15.132952	8	8
44.0	15.197226	17	17
45.0	15.257525	14	14
46.0	15.314096	16	16
47.0	15.367169	14	14
48.0	15.41696	16	16
49.0	15.463673	16	16
50.0	15.507497	18	18
51.0	15.548611	15	15
52.0	15.587183	17	17
53.0	15.62337	12	12
54.0	15.657319	12	12
55.0	15.689169	11	11
56.0	15.71905	7	7
57.0	15.747083	13	13
58.0	15.773382	20	20
59.0	15.798056	10	10
60.0	15.821204	10	10
61.0	15.84292	11	11
62.0	15.863294	13	13
63.0	15.882408	8	8
64.0	15.90034	4	4
65.0	15.917163	6	6
66.0	15.932946	8	8
67.0	15.947753	8	8
68.0	15.961644	6	6
69.0	15.974677	11	11
70.0	15.986904	15	15
71.0	15.998374	5	5
72.0	16.009136	15	15
73.0	16.019232	16	16
74.0	16.028703	9	9
75.0	16.037589	8	8
76.0	16.045926	6	6
77.0	16.053747	5	5
78.0	16.061085	7	7
79.0	16.067968	8	8
80.0	16.074426	5	5
81.0	16.080485	4	4
82.0	16.086169	8	8
83.0	16.091502	10	10
84.0	16.096505	4	4
85.0	16.101199	6	6
86.0	16.105602	8	8
87.0	16.109733	7	7
88.0	16.113609	7	7
89.0	16.117245	5	5
90.0	16.120656	5	5
91.0	16.123856	6	6
92.0	16.126859	6	6
93.0	16.129675	3	3
94.0	16.132318	5	5
95.0	16.134797	4	4
96.0	16.137123	8	8
97.0	16.139305	2	2
98.0	16.141352	3	3
99.0	16.143273	7	7
100.0	16.145074	5	5
102.0	0	4	4
103.0	0	4	4
104.0	0	4	4
105.0	0	2	2
106.0	0	9	9
107.0	0	5	5
108.0	0	3	3
109.0	0	3	3
110.0	0	4	4
111.0	0	4	4
112.0	0	5	5
113.0	0	4	4
114.0	0	1	1
115.0	0	6	6
116.0	0	2	2
117.0	0	1	1
118.0	0	3	3
119.0	0	4	4
120.0	0	3	3
121.0	0	6	6
122.0	0	2	2
123.0	0	5	5
124.0	0	6	6
125.0	0	3	3
126.0	0	1	1
127.0	0	4	4
128.0	0	1	1
129.0	0	5	5
130.0	0	1	1
131.0	0	2	2
132.0	0	5	5
133.0	0	3	3
134.0	0	4	4
135.0	0	3	3
136.0	0	2	2
137.0	0	4	4
138.0	0	1	1
139.0	0	2	2
140.0	0	3	3
141.0	0	3	3
142.0	0	3	3
143.0	0	2	2
144.0	0	1	1
145.0	0	1	1
146.0	0	3	3
147.0	0	5	5
148.0	0	3	3
150.0	0	4	4
151.0	0	2	2
152.0	0	5	5
153.0	0	6	6
154.0	0	2	2
155.0	0	2	2
156.0	0	1	1
157.0	0	4	4
158.0	0	4	4
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
163.0	0	2	2
165.0	0	2	2
166.0	0	2	2
167.0	0	2	2
168.0	0	3	3
169.0	0	4	4
170.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	4	4
177.0	0	2	2
178.0	0	5	5
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
182.0	0	2	2
183.0	0	4	4
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	3	3
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
196.0	0	2	2
197.0	0	2	2
198.0	0	3	3
200.0	0	1	1
201.0	0	1	1
203.0	0	2	2
207.0	0	2	2
208.0	0	2	2
209.0	0	2	2
210.0	0	1	1
211.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	4	4
216.0	0	3	3
217.0	0	1	1
218.0	0	1	1
219.0	0	3	3
221.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	2	2
233.0	0	1	1
234.0	0	1	1
235.0	0	3	3
236.0	0	2	2
238.0	0	2	2
239.0	0	2	2
241.0	0	3	3
242.0	0	1	1
244.0	0	1	1
245.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	2	2
255.0	0	2	2
256.0	0	1	1
257.0	0	2	2
259.0	0	1	1
267.0	0	1	1
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	2	2
274.0	0	1	1
275.0	0	1	1
277.0	0	1	1
278.0	0	2	2
279.0	0	1	1
281.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	1	1
286.0	0	1	1
292.0	0	1	1
294.0	0	1	1
295.0	0	1	1
297.0	0	3	3
298.0	0	2	2
299.0	0	1	1
300.0	0	1	1
302.0	0	1	1
307.0	0	1	1
308.0	0	1	1
311.0	0	1	1
312.0	0	3	3
315.0	0	1	1
316.0	0	1	1
318.0	0	1	1
325.0	0	1	1
326.0	0	1	1
328.0	0	2	2
331.0	0	2	2
332.0	0	1	1
334.0	0	1	1
338.0	0	1	1
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
350.0	0	1	1
351.0	0	3	3
353.0	0	2	2
354.0	0	1	1
355.0	0	2	2
357.0	0	1	1
360.0	0	1	1
363.0	0	1	1
366.0	0	1	1
367.0	0	1	1
377.0	0	1	1
378.0	0	1	1
379.0	0	1	1
382.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	1	1
390.0	0	1	1
392.0	0	1	1
395.0	0	2	2
397.0	0	1	1
398.0	0	1	1
399.0	0	2	2
400.0	0	1	1
402.0	0	1	1
403.0	0	1	1
404.0	0	1	1
406.0	0	1	1
408.0	0	1	1
411.0	0	1	1
412.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	1	1
424.0	0	1	1
426.0	0	1	1
429.0	0	1	1
433.0	0	1	1
442.0	0	1	1
448.0	0	1	1
449.0	0	1	1
450.0	0	1	1
453.0	0	1	1
455.0	0	1	1
456.0	0	1	1
464.0	0	1	1
466.0	0	1	1
473.0	0	1	1
479.0	0	1	1
485.0	0	1	1
493.0	0	1	1
497.0	0	1	1
499.0	0	1	1
514.0	0	1	1
538.0	0	1	1
542.0	0	1	1
558.0	0	1	1
561.0	0	1	1
574.0	0	1	1
575.0	0	1	1
586.0	0	1	1
594.0	0	1	1
598.0	0	1	1
605.0	0	2	2
608.0	0	1	1
619.0	0	1	1
624.0	0	1	1
625.0	0	1	1
626.0	0	1	1
631.0	0	1	1
632.0	0	1	1
657.0	0	1	1
660.0	0	1	1
662.0	0	1	1
668.0	0	1	1
669.0	0	1	1
671.0	0	1	1
690.0	0	1	1
698.0	0	1	1
710.0	0	1	1
764.0	0	1	1
766.0	0	1	1
781.0	0	1	1
812.0	0	1	1
818.0	0	1	1
827.0	0	1	1
842.0	0	1	1
879.0	0	1	1
907.0	0	1	1
908.0	0	1	1
1060.0	0	1	1
1114.0	0	1	1