## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2016-06-13/FR_Dro_Got_1_2016-06-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2016-06-13/FR_Dro_Got_1_2016-06-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2016-06-13/FR_Dro_Got_1_2016-06-13.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 09:00:28 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	22657505	14499994	0	0	5179756	1146341	0	0.144654	86804895

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	12107609	12107609
2.0	1.846165	874456	874456
3.0	2.56216	66307	66307
4.0	3.168009	6641	6641
5.0	3.680658	1704	1704
6.0	4.114443	943	943
7.0	4.481496	715	715
8.0	4.792084	542	542
9.0	5.054893	397	397
10.0	5.277272	341	341
11.0	5.465442	301	301
12.0	5.624664	225	225
13.0	5.759392	212	212
14.0	5.873395	169	169
15.0	5.96986	155	155
16.0	6.051485	123	123
17.0	6.120553	92	92
18.0	6.178996	110	110
19.0	6.228449	78	78
20.0	6.270294	79	79
21.0	6.305702	77	77
22.0	6.335662	60	60
23.0	6.361014	56	56
24.0	6.382466	54	54
25.0	6.400618	48	48
26.0	6.415977	41	41
27.0	6.428974	49	49
28.0	6.439971	44	44
29.0	6.449276	46	46
30.0	6.45715	42	42
31.0	6.463813	42	42
32.0	6.469451	35	35
33.0	6.474221	30	30
34.0	6.478258	35	35
35.0	6.481673	30	30
36.0	6.484563	39	39
37.0	6.487009	22	22
38.0	6.489078	32	32
39.0	6.490829	28	28
40.0	6.492311	27	27
41.0	6.493565	20	20
42.0	6.494625	26	26
43.0	6.495523	22	22
44.0	6.496283	16	16
45.0	6.496925	17	17
46.0	6.497469	16	16
47.0	6.497929	30	30
48.0	6.498319	15	15
49.0	6.498648	13	13
50.0	6.498927	11	11
51.0	6.499163	9	9
52.0	6.499363	11	11
53.0	6.499532	11	11
54.0	6.499674	17	17
55.0	6.499795	14	14
56.0	6.499898	5	5
57.0	6.499984	14	14
58.0	6.500058	10	10
59.0	6.50012	7	7
60.0	6.500172	11	11
61.0	6.500216	6	6
62.0	6.500254	6	6
63.0	6.500286	15	15
64.0	6.500313	7	7
65.0	6.500335	9	9
66.0	6.500355	6	6
67.0	6.500371	6	6
68.0	6.500385	5	5
69.0	6.500396	9	9
70.0	6.500406	7	7
71.0	6.500415	5	5
72.0	6.500422	6	6
73.0	6.500428	2	2
74.0	6.500433	5	5
75.0	6.500437	3	3
76.0	6.500441	3	3
77.0	6.500444	3	3
78.0	6.500446	4	4
79.0	6.500449	4	4
80.0	6.50045	2	2
81.0	6.500452	5	5
82.0	6.500453	7	7
83.0	6.500454	1	1
84.0	6.500455	4	4
85.0	6.500456	6	6
86.0	6.500457	2	2
87.0	6.500457	6	6
88.0	6.500458	5	5
89.0	6.500458	5	5
90.0	6.500459	2	2
91.0	6.500459	3	3
92.0	6.500459	2	2
93.0	6.500459	1	1
94.0	6.50046	3	3
95.0	6.50046	5	5
96.0	6.50046	2	2
97.0	6.50046	1	1
98.0	6.50046	3	3
99.0	6.50046	1	1
100.0	6.50046	0	0
101.0	0	3	3
102.0	0	3	3
103.0	0	2	2
105.0	0	1	1
106.0	0	4	4
107.0	0	2	2
108.0	0	1	1
109.0	0	1	1
110.0	0	1	1
111.0	0	2	2
113.0	0	1	1
115.0	0	3	3
116.0	0	1	1
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
121.0	0	4	4
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	2	2
128.0	0	1	1
129.0	0	2	2
130.0	0	1	1
131.0	0	3	3
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
141.0	0	1	1
143.0	0	2	2
144.0	0	1	1
146.0	0	2	2
151.0	0	3	3
152.0	0	2	2
155.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	2	2
163.0	0	2	2
165.0	0	1	1
166.0	0	1	1
168.0	0	1	1
171.0	0	1	1
172.0	0	2	2
177.0	0	2	2
180.0	0	1	1
182.0	0	2	2
191.0	0	1	1
194.0	0	1	1
196.0	0	1	1
201.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
217.0	0	1	1
222.0	0	1	1
223.0	0	1	1
229.0	0	1	1
233.0	0	1	1
238.0	0	1	1
242.0	0	1	1
248.0	0	1	1
260.0	0	2	2
262.0	0	1	1
271.0	0	1	1
274.0	0	1	1
276.0	0	1	1
307.0	0	1	1
314.0	0	1	1
319.0	0	1	1
343.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
383.0	0	1	1
388.0	0	1	1
430.0	0	1	1
432.0	0	1	1
441.0	0	1	1
460.0	0	1	1