## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-10-13/FR_Dro_Got_1_2015-10-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-10-13/FR_Dro_Got_1_2015-10-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2015-10-13/FR_Dro_Got_1_2015-10-13.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 09:07:29 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	7337361	27300032	0	0	2685027	3416038	0	0.153657	99783536

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20097152	20097152
2.0	1.760642	2442354	2442354
3.0	2.339218	273180	273180
4.0	2.779307	32061	32061
5.0	3.114058	5055	5055
6.0	3.368683	1828	1828
7.0	3.562361	1089	1089
8.0	3.709682	773	773
9.0	3.821739	616	616
10.0	3.906975	473	473
11.0	3.971809	382	382
12.0	4.021125	314	314
13.0	4.058636	304	304
14.0	4.087169	245	245
15.0	4.108872	214	214
16.0	4.12538	158	158
17.0	4.137937	159	159
18.0	4.147489	144	144
19.0	4.154754	152	152
20.0	4.16028	124	124
21.0	4.164483	134	134
22.0	4.167681	102	102
23.0	4.170113	88	88
24.0	4.171963	70	70
25.0	4.17337	77	77
26.0	4.17444	84	84
27.0	4.175254	92	92
28.0	4.175873	81	81
29.0	4.176344	79	79
30.0	4.176703	73	73
31.0	4.176975	65	65
32.0	4.177183	81	81
33.0	4.17734	70	70
34.0	4.17746	59	59
35.0	4.177551	51	51
36.0	4.177621	58	58
37.0	4.177674	47	47
38.0	4.177714	60	60
39.0	4.177744	54	54
40.0	4.177767	61	61
41.0	4.177785	53	53
42.0	4.177799	55	55
43.0	4.177809	45	45
44.0	4.177817	45	45
45.0	4.177822	51	51
46.0	4.177827	42	42
47.0	4.17783	49	49
48.0	4.177833	47	47
49.0	4.177835	42	42
50.0	4.177836	46	46
51.0	4.177838	45	45
52.0	4.177839	36	36
53.0	4.177839	46	46
54.0	4.17784	48	48
55.0	4.17784	30	30
56.0	4.17784	30	30
57.0	4.177841	28	28
58.0	4.177841	33	33
59.0	4.177841	23	23
60.0	4.177841	32	32
61.0	4.177841	15	15
62.0	4.177841	25	25
63.0	4.177841	19	19
64.0	4.177841	25	25
65.0	4.177841	32	32
66.0	4.177841	22	22
67.0	4.177841	23	23
68.0	4.177841	21	21
69.0	4.177841	22	22
70.0	4.177841	18	18
71.0	4.177841	18	18
72.0	4.177841	20	20
73.0	4.177841	15	15
74.0	4.177841	23	23
75.0	4.177841	15	15
76.0	4.177841	18	18
77.0	4.177841	13	13
78.0	4.177841	15	15
79.0	4.177841	14	14
80.0	4.177841	14	14
81.0	4.177841	12	12
82.0	4.177841	12	12
83.0	4.177841	12	12
84.0	4.177841	12	12
85.0	4.177841	7	7
86.0	4.177841	8	8
87.0	4.177841	11	11
88.0	4.177841	8	8
89.0	4.177841	12	12
90.0	4.177841	13	13
91.0	4.177841	8	8
92.0	4.177841	18	18
93.0	4.177841	8	8
94.0	4.177841	15	15
95.0	4.177841	8	8
96.0	4.177841	13	13
97.0	4.177841	15	15
98.0	4.177841	11	11
99.0	4.177841	7	7
100.0	4.177841	13	13
101.0	0	11	11
102.0	0	13	13
103.0	0	10	10
104.0	0	4	4
105.0	0	4	4
106.0	0	7	7
107.0	0	5	5
108.0	0	7	7
109.0	0	7	7
110.0	0	6	6
111.0	0	8	8
112.0	0	6	6
113.0	0	4	4
114.0	0	7	7
115.0	0	4	4
116.0	0	7	7
117.0	0	7	7
118.0	0	1	1
119.0	0	4	4
120.0	0	2	2
121.0	0	5	5
122.0	0	5	5
123.0	0	4	4
124.0	0	6	6
125.0	0	5	5
126.0	0	5	5
127.0	0	7	7
128.0	0	5	5
129.0	0	8	8
130.0	0	8	8
131.0	0	9	9
132.0	0	8	8
133.0	0	4	4
134.0	0	8	8
135.0	0	9	9
136.0	0	6	6
137.0	0	1	1
138.0	0	6	6
139.0	0	6	6
140.0	0	5	5
141.0	0	10	10
142.0	0	5	5
143.0	0	5	5
144.0	0	7	7
145.0	0	5	5
146.0	0	3	3
147.0	0	1	1
148.0	0	8	8
149.0	0	6	6
150.0	0	14	14
151.0	0	5	5
152.0	0	7	7
153.0	0	6	6
154.0	0	5	5
155.0	0	3	3
156.0	0	4	4
157.0	0	4	4
158.0	0	5	5
159.0	0	3	3
160.0	0	4	4
161.0	0	3	3
162.0	0	4	4
163.0	0	4	4
164.0	0	4	4
165.0	0	4	4
166.0	0	8	8
167.0	0	3	3
168.0	0	4	4
169.0	0	2	2
170.0	0	4	4
171.0	0	5	5
172.0	0	4	4
173.0	0	3	3
174.0	0	2	2
175.0	0	2	2
176.0	0	3	3
177.0	0	4	4
178.0	0	1	1
179.0	0	6	6
180.0	0	4	4
181.0	0	1	1
182.0	0	5	5
183.0	0	2	2
184.0	0	6	6
185.0	0	2	2
186.0	0	4	4
187.0	0	6	6
188.0	0	2	2
189.0	0	4	4
190.0	0	2	2
191.0	0	3	3
192.0	0	2	2
193.0	0	2	2
194.0	0	2	2
195.0	0	1	1
196.0	0	4	4
197.0	0	4	4
199.0	0	2	2
200.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	2	2
204.0	0	3	3
206.0	0	1	1
207.0	0	1	1
208.0	0	2	2
209.0	0	2	2
210.0	0	4	4
211.0	0	1	1
212.0	0	2	2
213.0	0	4	4
214.0	0	4	4
216.0	0	2	2
218.0	0	3	3
219.0	0	1	1
221.0	0	2	2
222.0	0	2	2
224.0	0	3	3
226.0	0	1	1
227.0	0	1	1
230.0	0	2	2
232.0	0	1	1
234.0	0	4	4
236.0	0	2	2
237.0	0	1	1
238.0	0	2	2
239.0	0	2	2
241.0	0	3	3
242.0	0	3	3
243.0	0	1	1
244.0	0	2	2
247.0	0	2	2
248.0	0	4	4
250.0	0	1	1
252.0	0	2	2
253.0	0	1	1
255.0	0	3	3
256.0	0	1	1
258.0	0	2	2
265.0	0	2	2
266.0	0	5	5
267.0	0	2	2
269.0	0	2	2
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
277.0	0	2	2
280.0	0	1	1
281.0	0	2	2
282.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	2	2
286.0	0	2	2
288.0	0	1	1
290.0	0	2	2
291.0	0	1	1
293.0	0	1	1
294.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
303.0	0	1	1
306.0	0	1	1
309.0	0	1	1
317.0	0	1	1
323.0	0	1	1
325.0	0	1	1
326.0	0	1	1
328.0	0	1	1
335.0	0	1	1
336.0	0	1	1
338.0	0	1	1
340.0	0	1	1
341.0	0	2	2
347.0	0	1	1
349.0	0	2	2
353.0	0	1	1
358.0	0	2	2
359.0	0	1	1
363.0	0	2	2
365.0	0	1	1
366.0	0	1	1
367.0	0	1	1
368.0	0	1	1
371.0	0	1	1
372.0	0	1	1
383.0	0	1	1
384.0	0	1	1
390.0	0	1	1
395.0	0	1	1
397.0	0	1	1
405.0	0	1	1
407.0	0	1	1
424.0	0	1	1
428.0	0	1	1
434.0	0	2	2
438.0	0	1	1
456.0	0	1	1
460.0	0	1	1
466.0	0	2	2
468.0	0	1	1
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
478.0	0	1	1
482.0	0	1	1
495.0	0	1	1
501.0	0	1	1
504.0	0	1	1
511.0	0	1	1
512.0	0	1	1
543.0	0	2	2
548.0	0	1	1
557.0	0	1	1
558.0	0	1	1
668.0	0	1	1