## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_Tre_1_2016-08-24/IT_Tre_Tre_1_2016-08-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_Tre_1_2016-08-24/IT_Tre_Tre_1_2016-08-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_Tre_1_2016-08-24/IT_Tre_Tre_1_2016-08-24.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 08:54:26 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	32477475	9099436	0	0	6112966	722565	0	0.149144	54220616

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	7591686	7591686
2.0	1.845504	470973	470973
3.0	2.560381	37098	37098
4.0	3.164812	5020	5020
5.0	3.675861	1862	1862
6.0	4.107955	1082	1082
7.0	4.473292	744	744
8.0	4.782186	525	525
9.0	5.043357	432	432
10.0	5.264179	322	322
11.0	5.450884	284	284
12.0	5.608744	272	272
13.0	5.742215	213	213
14.0	5.855065	194	194
15.0	5.950481	165	165
16.0	6.031155	153	153
17.0	6.099366	147	147
18.0	6.157038	131	131
19.0	6.2058	121	121
20.0	6.247028	97	97
21.0	6.281887	90	90
22.0	6.31136	84	84
23.0	6.33628	87	87
24.0	6.35735	78	78
25.0	6.375164	57	57
26.0	6.390227	72	72
27.0	6.402962	49	49
28.0	6.41373	60	60
29.0	6.422834	47	47
30.0	6.430531	52	52
31.0	6.43704	38	38
32.0	6.442542	30	30
33.0	6.447195	34	34
34.0	6.451129	41	41
35.0	6.454455	33	33
36.0	6.457267	35	35
37.0	6.459645	37	37
38.0	6.461655	31	31
39.0	6.463355	33	33
40.0	6.464792	20	20
41.0	6.466007	24	24
42.0	6.467035	31	31
43.0	6.467903	16	16
44.0	6.468638	30	30
45.0	6.469259	19	19
46.0	6.469784	24	24
47.0	6.470228	22	22
48.0	6.470603	24	24
49.0	6.470921	18	18
50.0	6.471189	24	24
51.0	6.471416	22	22
52.0	6.471608	21	21
53.0	6.47177	17	17
54.0	6.471907	19	19
55.0	6.472023	18	18
56.0	6.472121	16	16
57.0	6.472204	18	18
58.0	6.472274	12	12
59.0	6.472333	15	15
60.0	6.472383	8	8
61.0	6.472426	8	8
62.0	6.472461	5	5
63.0	6.472492	17	17
64.0	6.472517	14	14
65.0	6.472539	19	19
66.0	6.472557	16	16
67.0	6.472573	17	17
68.0	6.472586	15	15
69.0	6.472597	10	10
70.0	6.472606	9	9
71.0	6.472614	10	10
72.0	6.472621	4	4
73.0	6.472626	11	11
74.0	6.472631	8	8
75.0	6.472635	7	7
76.0	6.472639	8	8
77.0	6.472642	5	5
78.0	6.472644	8	8
79.0	6.472646	6	6
80.0	6.472648	8	8
81.0	6.472649	6	6
82.0	6.472651	9	9
83.0	6.472652	4	4
84.0	6.472653	6	6
85.0	6.472653	7	7
86.0	6.472654	7	7
87.0	6.472654	6	6
88.0	6.472655	7	7
89.0	6.472655	5	5
90.0	6.472656	6	6
91.0	6.472656	5	5
92.0	6.472656	6	6
93.0	6.472656	7	7
94.0	6.472656	3	3
95.0	6.472657	3	3
96.0	6.472657	2	2
97.0	6.472657	10	10
98.0	6.472657	3	3
99.0	6.472657	3	3
100.0	6.472657	1	1
101.0	0	2	2
102.0	0	3	3
103.0	0	6	6
104.0	0	1	1
105.0	0	4	4
106.0	0	5	5
107.0	0	4	4
108.0	0	5	5
109.0	0	4	4
110.0	0	3	3
111.0	0	2	2
112.0	0	2	2
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
116.0	0	2	2
117.0	0	2	2
118.0	0	2	2
119.0	0	1	1
120.0	0	1	1
121.0	0	2	2
122.0	0	2	2
123.0	0	2	2
124.0	0	3	3
125.0	0	3	3
126.0	0	2	2
127.0	0	3	3
128.0	0	1	1
130.0	0	4	4
131.0	0	1	1
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
139.0	0	5	5
140.0	0	3	3
141.0	0	3	3
142.0	0	1	1
143.0	0	4	4
144.0	0	2	2
145.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	4	4
151.0	0	4	4
152.0	0	1	1
153.0	0	5	5
154.0	0	1	1
156.0	0	2	2
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
167.0	0	2	2
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
177.0	0	2	2
181.0	0	1	1
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	3	3
190.0	0	1	1
191.0	0	4	4
192.0	0	1	1
193.0	0	2	2
194.0	0	1	1
198.0	0	1	1
201.0	0	1	1
202.0	0	1	1
204.0	0	1	1
215.0	0	1	1
216.0	0	2	2
218.0	0	1	1
219.0	0	1	1
221.0	0	1	1
225.0	0	2	2
233.0	0	1	1
234.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	2	2
259.0	0	1	1
262.0	0	1	1
271.0	0	1	1
280.0	0	1	1
284.0	0	2	2
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
299.0	0	1	1
301.0	0	1	1
306.0	0	1	1
309.0	0	1	1
317.0	0	1	1
327.0	0	1	1
336.0	0	2	2
352.0	0	1	1
361.0	0	1	1
383.0	0	1	1
388.0	0	1	1
415.0	0	1	1
424.0	0	1	1
430.0	0	1	1
433.0	0	1	1
449.0	0	1	1
463.0	0	1	1
527.0	0	1	1
529.0	0	1	1
573.0	0	1	1
779.0	0	1	1
808.0	0	1	1