## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-09-09/FR_Dro_Got_1_2015-09-09.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-09-09/FR_Dro_Got_1_2015-09-09.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-09-09/FR_Dro_Got_1_2015-09-09.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 09:05:43 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	7223899	29777204	0	0	2637237	5932527	0	0.217171	64434736

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18500013	18500013
2.0	1.629941	3731049	3731049
3.0	2.026766	698173	698173
4.0	2.276742	123440	123440
5.0	2.434212	22189	22189
6.0	2.533409	4642	4642
7.0	2.595898	1627	1627
8.0	2.635261	840	840
9.0	2.660058	609	609
10.0	2.675679	487	487
11.0	2.685519	429	429
12.0	2.691717	323	323
13.0	2.695622	282	282
14.0	2.698082	256	256
15.0	2.699632	231	231
16.0	2.700608	214	214
17.0	2.701222	174	174
18.0	2.70161	166	166
19.0	2.701854	141	141
20.0	2.702008	136	136
21.0	2.702104	95	95
22.0	2.702165	97	97
23.0	2.702204	92	92
24.0	2.702228	102	102
25.0	2.702243	102	102
26.0	2.702253	83	83
27.0	2.702259	99	99
28.0	2.702263	74	74
29.0	2.702265	73	73
30.0	2.702267	77	77
31.0	2.702268	70	70
32.0	2.702268	60	60
33.0	2.702269	66	66
34.0	2.702269	55	55
35.0	2.702269	54	54
36.0	2.702269	60	60
37.0	2.702269	59	59
38.0	2.702269	55	55
39.0	2.702269	62	62
40.0	2.702269	46	46
41.0	2.702269	43	43
42.0	2.702269	54	54
43.0	2.702269	56	56
44.0	2.702269	51	51
45.0	2.702269	44	44
46.0	2.702269	41	41
47.0	2.702269	41	41
48.0	2.702269	37	37
49.0	2.702269	37	37
50.0	2.702269	39	39
51.0	2.702269	41	41
52.0	2.702269	36	36
53.0	2.702269	36	36
54.0	2.702269	35	35
55.0	2.702269	34	34
56.0	2.702269	26	26
57.0	2.702269	33	33
58.0	2.702269	34	34
59.0	2.702269	25	25
60.0	2.702269	28	28
61.0	2.702269	28	28
62.0	2.702269	21	21
63.0	2.702269	28	28
64.0	2.702269	28	28
65.0	2.702269	23	23
66.0	2.702269	23	23
67.0	2.702269	24	24
68.0	2.702269	24	24
69.0	2.702269	17	17
70.0	2.702269	22	22
71.0	2.702269	26	26
72.0	2.702269	23	23
73.0	2.702269	17	17
74.0	2.702269	12	12
75.0	2.702269	21	21
76.0	2.702269	19	19
77.0	2.702269	18	18
78.0	2.702269	12	12
79.0	2.702269	14	14
80.0	2.702269	12	12
81.0	2.702269	16	16
82.0	2.702269	15	15
83.0	2.702269	10	10
84.0	2.702269	7	7
85.0	2.702269	13	13
86.0	2.702269	8	8
87.0	2.702269	10	10
88.0	2.702269	5	5
89.0	2.702269	14	14
90.0	2.702269	14	14
91.0	2.702269	12	12
92.0	2.702269	7	7
93.0	2.702269	14	14
94.0	2.702269	8	8
95.0	2.702269	13	13
96.0	2.702269	8	8
97.0	2.702269	9	9
98.0	2.702269	15	15
99.0	2.702269	10	10
100.0	2.702269	7	7
101.0	0	11	11
102.0	0	5	5
103.0	0	7	7
104.0	0	6	6
105.0	0	13	13
106.0	0	11	11
107.0	0	9	9
108.0	0	10	10
109.0	0	8	8
110.0	0	5	5
111.0	0	6	6
112.0	0	8	8
113.0	0	11	11
114.0	0	13	13
115.0	0	8	8
116.0	0	10	10
117.0	0	9	9
118.0	0	7	7
119.0	0	10	10
120.0	0	10	10
121.0	0	7	7
122.0	0	4	4
123.0	0	6	6
124.0	0	5	5
125.0	0	4	4
126.0	0	8	8
127.0	0	7	7
128.0	0	7	7
129.0	0	5	5
130.0	0	6	6
131.0	0	10	10
132.0	0	7	7
133.0	0	5	5
134.0	0	5	5
135.0	0	2	2
136.0	0	4	4
137.0	0	4	4
138.0	0	6	6
139.0	0	6	6
140.0	0	7	7
141.0	0	5	5
142.0	0	5	5
143.0	0	5	5
144.0	0	6	6
145.0	0	4	4
146.0	0	5	5
147.0	0	8	8
148.0	0	1	1
149.0	0	4	4
150.0	0	7	7
151.0	0	4	4
152.0	0	6	6
153.0	0	5	5
154.0	0	3	3
155.0	0	3	3
156.0	0	3	3
157.0	0	2	2
158.0	0	7	7
159.0	0	6	6
160.0	0	5	5
161.0	0	2	2
162.0	0	2	2
163.0	0	6	6
164.0	0	5	5
165.0	0	3	3
166.0	0	2	2
167.0	0	5	5
168.0	0	4	4
169.0	0	6	6
170.0	0	5	5
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	5	5
176.0	0	1	1
177.0	0	2	2
178.0	0	2	2
179.0	0	2	2
180.0	0	3	3
181.0	0	6	6
182.0	0	2	2
183.0	0	6	6
184.0	0	3	3
185.0	0	3	3
186.0	0	3	3
187.0	0	2	2
188.0	0	2	2
189.0	0	2	2
190.0	0	5	5
191.0	0	4	4
192.0	0	6	6
193.0	0	4	4
195.0	0	4	4
196.0	0	4	4
197.0	0	1	1
198.0	0	4	4
199.0	0	5	5
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	5	5
204.0	0	2	2
205.0	0	4	4
206.0	0	5	5
207.0	0	6	6
208.0	0	4	4
209.0	0	1	1
210.0	0	4	4
211.0	0	3	3
212.0	0	1	1
213.0	0	2	2
214.0	0	1	1
215.0	0	3	3
216.0	0	2	2
218.0	0	2	2
219.0	0	1	1
220.0	0	2	2
221.0	0	2	2
222.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	4	4
227.0	0	1	1
228.0	0	2	2
230.0	0	3	3
232.0	0	2	2
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
237.0	0	1	1
238.0	0	3	3
239.0	0	3	3
240.0	0	1	1
241.0	0	1	1
242.0	0	2	2
243.0	0	2	2
244.0	0	1	1
245.0	0	1	1
251.0	0	4	4
255.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
261.0	0	1	1
267.0	0	3	3
268.0	0	2	2
270.0	0	1	1
271.0	0	2	2
274.0	0	2	2
275.0	0	1	1
277.0	0	4	4
282.0	0	2	2
283.0	0	3	3
284.0	0	2	2
287.0	0	1	1
289.0	0	3	3
290.0	0	1	1
291.0	0	1	1
292.0	0	2	2
293.0	0	2	2
295.0	0	1	1
297.0	0	1	1
298.0	0	1	1
300.0	0	1	1
302.0	0	1	1
306.0	0	1	1
312.0	0	2	2
313.0	0	1	1
315.0	0	2	2
316.0	0	1	1
318.0	0	1	1
321.0	0	1	1
322.0	0	1	1
325.0	0	1	1
326.0	0	1	1
327.0	0	1	1
328.0	0	2	2
329.0	0	1	1
330.0	0	2	2
331.0	0	1	1
332.0	0	1	1
334.0	0	1	1
336.0	0	1	1
341.0	0	1	1
345.0	0	2	2
351.0	0	2	2
354.0	0	1	1
361.0	0	1	1
362.0	0	1	1
365.0	0	1	1
368.0	0	2	2
369.0	0	1	1
373.0	0	1	1
374.0	0	1	1
379.0	0	1	1
392.0	0	1	1
393.0	0	1	1
395.0	0	2	2
396.0	0	1	1
398.0	0	2	2
399.0	0	1	1
400.0	0	1	1
401.0	0	2	2
402.0	0	2	2
405.0	0	1	1
407.0	0	1	1
409.0	0	1	1
418.0	0	1	1
421.0	0	1	1
432.0	0	1	1
436.0	0	1	1
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
459.0	0	1	1
463.0	0	1	1
472.0	0	1	1
499.0	0	1	1
502.0	0	1	1
513.0	0	1	1
516.0	0	1	1
523.0	0	1	1
528.0	0	1	1
530.0	0	1	1
531.0	0	1	1
532.0	0	1	1
553.0	0	1	1
560.0	0	1	1
574.0	0	1	1
582.0	0	1	1
611.0	0	1	1
614.0	0	1	1
626.0	0	1	1
650.0	0	1	1
687.0	0	1	1
692.0	0	1	1
701.0	0	1	1
722.0	0	1	1
781.0	0	1	1
890.0	0	1	1