## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-09-29/IT_Tre_San_1_2015-09-29.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-09-29/IT_Tre_San_1_2015-09-29.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/IT_Tre_San_1_2015-09-29/IT_Tre_San_1_2015-09-29.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 09:18:58 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	6350350	33129668	0	0	2132999	3619081	0	0.129062	140380314

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25499431	25499431
2.0	1.789781	2762562	2762562
3.0	2.413535	265507	265507
4.0	2.906165	26968	26968
5.0	3.295234	4235	4235
6.0	3.602514	1552	1552
7.0	3.845198	984	984
8.0	4.036865	705	705
9.0	4.18824	561	561
10.0	4.307793	443	443
11.0	4.402214	371	371
12.0	4.476785	318	318
13.0	4.535681	257	257
14.0	4.582195	233	233
15.0	4.618931	187	187
16.0	4.647945	167	167
17.0	4.670859	163	163
18.0	4.688957	152	152
19.0	4.70325	172	172
20.0	4.714538	112	112
21.0	4.723453	116	116
22.0	4.730494	112	112
23.0	4.736055	116	116
24.0	4.740447	93	93
25.0	4.743916	99	99
26.0	4.746655	84	84
27.0	4.748819	75	75
28.0	4.750528	83	83
29.0	4.751877	69	69
30.0	4.752943	78	78
31.0	4.753785	58	58
32.0	4.75445	70	70
33.0	4.754975	48	48
34.0	4.75539	70	70
35.0	4.755717	63	63
36.0	4.755976	42	42
37.0	4.75618	45	45
38.0	4.756341	48	48
39.0	4.756469	34	34
40.0	4.756569	37	37
41.0	4.756649	52	52
42.0	4.756712	35	35
43.0	4.756761	42	42
44.0	4.7568	43	43
45.0	4.756831	20	20
46.0	4.756856	24	24
47.0	4.756875	29	29
48.0	4.75689	27	27
49.0	4.756902	30	30
50.0	4.756912	25	25
51.0	4.756919	33	33
52.0	4.756925	19	19
53.0	4.75693	22	22
54.0	4.756934	21	21
55.0	4.756937	19	19
56.0	4.756939	20	20
57.0	4.756941	23	23
58.0	4.756942	29	29
59.0	4.756943	18	18
60.0	4.756944	15	15
61.0	4.756945	20	20
62.0	4.756945	24	24
63.0	4.756946	14	14
64.0	4.756946	14	14
65.0	4.756946	16	16
66.0	4.756947	22	22
67.0	4.756947	13	13
68.0	4.756947	9	9
69.0	4.756947	11	11
70.0	4.756947	7	7
71.0	4.756947	17	17
72.0	4.756947	9	9
73.0	4.756947	9	9
74.0	4.756947	15	15
75.0	4.756947	14	14
76.0	4.756947	18	18
77.0	4.756947	9	9
78.0	4.756947	11	11
79.0	4.756947	13	13
80.0	4.756948	13	13
81.0	4.756948	10	10
82.0	4.756948	11	11
83.0	4.756948	2	2
84.0	4.756948	14	14
85.0	4.756948	9	9
86.0	4.756948	12	12
87.0	4.756948	8	8
88.0	4.756948	6	6
89.0	4.756948	9	9
90.0	4.756948	9	9
91.0	4.756948	9	9
92.0	4.756948	7	7
93.0	4.756948	8	8
94.0	4.756948	6	6
95.0	4.756948	6	6
96.0	4.756948	5	5
97.0	4.756948	9	9
98.0	4.756948	4	4
99.0	4.756948	3	3
100.0	4.756948	7	7
101.0	0	3	3
102.0	0	6	6
103.0	0	7	7
104.0	0	9	9
105.0	0	7	7
106.0	0	7	7
107.0	0	6	6
108.0	0	8	8
109.0	0	6	6
110.0	0	7	7
111.0	0	7	7
112.0	0	12	12
113.0	0	8	8
114.0	0	5	5
115.0	0	8	8
116.0	0	5	5
117.0	0	7	7
118.0	0	4	4
119.0	0	3	3
120.0	0	3	3
121.0	0	4	4
122.0	0	2	2
123.0	0	4	4
124.0	0	6	6
125.0	0	4	4
126.0	0	6	6
127.0	0	4	4
128.0	0	5	5
129.0	0	5	5
130.0	0	3	3
131.0	0	4	4
132.0	0	4	4
133.0	0	3	3
134.0	0	6	6
135.0	0	3	3
136.0	0	3	3
137.0	0	8	8
138.0	0	4	4
139.0	0	1	1
140.0	0	4	4
142.0	0	2	2
143.0	0	3	3
144.0	0	2	2
145.0	0	5	5
146.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	3	3
151.0	0	3	3
152.0	0	1	1
153.0	0	4	4
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
166.0	0	2	2
169.0	0	2	2
170.0	0	1	1
172.0	0	3	3
173.0	0	4	4
174.0	0	4	4
175.0	0	2	2
176.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	1	1
180.0	0	2	2
181.0	0	3	3
183.0	0	3	3
184.0	0	1	1
185.0	0	1	1
186.0	0	3	3
187.0	0	3	3
188.0	0	1	1
190.0	0	1	1
194.0	0	1	1
195.0	0	1	1
198.0	0	1	1
199.0	0	2	2
200.0	0	1	1
201.0	0	4	4
202.0	0	1	1
203.0	0	2	2
204.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	2	2
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
217.0	0	1	1
218.0	0	3	3
220.0	0	1	1
222.0	0	1	1
225.0	0	1	1
227.0	0	2	2
229.0	0	1	1
230.0	0	4	4
231.0	0	1	1
232.0	0	2	2
233.0	0	2	2
234.0	0	2	2
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
241.0	0	3	3
242.0	0	1	1
243.0	0	2	2
244.0	0	1	1
246.0	0	2	2
248.0	0	1	1
250.0	0	1	1
259.0	0	1	1
260.0	0	2	2
261.0	0	1	1
262.0	0	2	2
265.0	0	1	1
267.0	0	1	1
268.0	0	1	1
271.0	0	1	1
273.0	0	1	1
274.0	0	1	1
276.0	0	1	1
296.0	0	1	1
299.0	0	1	1
300.0	0	1	1
308.0	0	2	2
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
313.0	0	1	1
322.0	0	1	1
326.0	0	1	1
332.0	0	1	1
334.0	0	1	1
346.0	0	1	1
352.0	0	1	1
353.0	0	1	1
356.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
365.0	0	1	1
369.0	0	1	1
378.0	0	1	1
391.0	0	1	1
393.0	0	1	1
398.0	0	1	1
403.0	0	2	2
422.0	0	2	2
448.0	0	1	1
453.0	0	1	1
459.0	0	1	1
476.0	0	1	1
478.0	0	1	1
497.0	0	1	1
509.0	0	1	1
529.0	0	1	1
595.0	0	1	1
883.0	0	1	1
1036.0	0	1	1