## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-10-11/ES_Ciu_Tom_1_2016-10-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-10-11/ES_Ciu_Tom_1_2016-10-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-10-11/ES_Ciu_Tom_1_2016-10-11.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 08:48:08 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	29369641	9277073	0	0	7620959	780846	0	0.191609	51971709

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	7698851	7698851
2.0	1.836522	482294	482294
3.0	2.536291	36560	36560
4.0	3.121664	4837	4837
5.0	3.611341	1671	1671
6.0	4.020966	1012	1012
7.0	4.363627	725	725
8.0	4.65027	530	530
9.0	4.890054	401	401
10.0	5.090638	332	332
11.0	5.258431	249	249
12.0	5.398794	206	206
13.0	5.51621	203	203
14.0	5.614432	156	156
15.0	5.696596	147	147
16.0	5.765328	146	146
17.0	5.822824	127	127
18.0	5.870921	111	111
19.0	5.911155	110	110
20.0	5.944812	99	99
21.0	5.972966	117	117
22.0	5.996518	81	81
23.0	6.01622	96	96
24.0	6.032701	72	72
25.0	6.046487	75	75
26.0	6.05802	65	65
27.0	6.067668	77	77
28.0	6.075738	64	64
29.0	6.082489	56	56
30.0	6.088136	71	71
31.0	6.09286	53	53
32.0	6.096812	62	62
33.0	6.100118	50	50
34.0	6.102883	50	50
35.0	6.105197	31	31
36.0	6.107132	39	39
37.0	6.108751	33	33
38.0	6.110105	34	34
39.0	6.111238	39	39
40.0	6.112185	33	33
41.0	6.112978	30	30
42.0	6.113641	36	36
43.0	6.114196	29	29
44.0	6.11466	30	30
45.0	6.115048	26	26
46.0	6.115372	18	18
47.0	6.115644	16	16
48.0	6.115871	24	24
49.0	6.116061	18	18
50.0	6.11622	16	16
51.0	6.116353	22	22
52.0	6.116465	14	14
53.0	6.116558	23	23
54.0	6.116636	19	19
55.0	6.116701	14	14
56.0	6.116755	23	23
57.0	6.116801	8	8
58.0	6.116839	21	21
59.0	6.116871	20	20
60.0	6.116897	13	13
61.0	6.11692	14	14
62.0	6.116938	12	12
63.0	6.116954	14	14
64.0	6.116967	8	8
65.0	6.116978	14	14
66.0	6.116987	7	7
67.0	6.116995	15	15
68.0	6.117001	8	8
69.0	6.117007	13	13
70.0	6.117011	10	10
71.0	6.117015	7	7
72.0	6.117018	12	12
73.0	6.117021	16	16
74.0	6.117023	15	15
75.0	6.117025	8	8
76.0	6.117026	4	4
77.0	6.117027	14	14
78.0	6.117028	11	11
79.0	6.117029	10	10
80.0	6.11703	14	14
81.0	6.117031	8	8
82.0	6.117031	10	10
83.0	6.117032	9	9
84.0	6.117032	8	8
85.0	6.117032	6	6
86.0	6.117033	8	8
87.0	6.117033	8	8
88.0	6.117033	10	10
89.0	6.117033	10	10
90.0	6.117033	10	10
91.0	6.117033	7	7
92.0	6.117033	4	4
93.0	6.117034	7	7
94.0	6.117034	9	9
95.0	6.117034	2	2
96.0	6.117034	5	5
97.0	6.117034	6	6
98.0	6.117034	10	10
99.0	6.117034	8	8
100.0	6.117034	6	6
101.0	0	2	2
102.0	0	4	4
103.0	0	6	6
104.0	0	6	6
105.0	0	3	3
106.0	0	7	7
107.0	0	7	7
108.0	0	7	7
109.0	0	6	6
110.0	0	5	5
111.0	0	3	3
112.0	0	6	6
113.0	0	5	5
114.0	0	5	5
115.0	0	5	5
116.0	0	4	4
117.0	0	3	3
118.0	0	7	7
119.0	0	3	3
120.0	0	7	7
121.0	0	1	1
122.0	0	4	4
123.0	0	4	4
124.0	0	4	4
125.0	0	3	3
126.0	0	1	1
127.0	0	4	4
128.0	0	2	2
129.0	0	7	7
130.0	0	1	1
131.0	0	2	2
132.0	0	2	2
133.0	0	3	3
134.0	0	5	5
135.0	0	4	4
136.0	0	4	4
137.0	0	2	2
138.0	0	4	4
139.0	0	1	1
140.0	0	3	3
141.0	0	1	1
142.0	0	2	2
143.0	0	2	2
144.0	0	2	2
145.0	0	3	3
146.0	0	2	2
147.0	0	3	3
148.0	0	1	1
149.0	0	3	3
150.0	0	1	1
151.0	0	2	2
152.0	0	3	3
153.0	0	4	4
154.0	0	1	1
155.0	0	3	3
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
159.0	0	2	2
160.0	0	1	1
162.0	0	3	3
164.0	0	3	3
166.0	0	3	3
167.0	0	2	2
168.0	0	3	3
169.0	0	1	1
170.0	0	5	5
171.0	0	3	3
172.0	0	1	1
173.0	0	3	3
175.0	0	1	1
177.0	0	2	2
180.0	0	2	2
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
185.0	0	2	2
186.0	0	1	1
187.0	0	1	1
188.0	0	2	2
190.0	0	2	2
191.0	0	2	2
192.0	0	1	1
195.0	0	2	2
197.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
204.0	0	1	1
208.0	0	1	1
209.0	0	2	2
217.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
227.0	0	2	2
228.0	0	2	2
231.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	1	1
238.0	0	2	2
242.0	0	1	1
243.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
253.0	0	2	2
254.0	0	1	1
255.0	0	1	1
257.0	0	1	1
260.0	0	2	2
262.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
272.0	0	1	1
273.0	0	2	2
276.0	0	1	1
278.0	0	1	1
281.0	0	1	1
282.0	0	1	1
284.0	0	1	1
287.0	0	2	2
289.0	0	1	1
291.0	0	1	1
293.0	0	1	1
303.0	0	1	1
307.0	0	1	1
308.0	0	1	1
311.0	0	1	1
315.0	0	1	1
316.0	0	1	1
317.0	0	1	1
322.0	0	1	1
323.0	0	1	1
328.0	0	1	1
329.0	0	1	1
331.0	0	1	1
332.0	0	2	2
333.0	0	1	1
335.0	0	1	1
341.0	0	1	1
343.0	0	1	1
345.0	0	2	2
347.0	0	1	1
348.0	0	1	1
350.0	0	1	1
353.0	0	1	1
354.0	0	1	1
359.0	0	1	1
364.0	0	1	1
365.0	0	1	1
372.0	0	1	1
382.0	0	1	1
390.0	0	1	1
409.0	0	2	2
415.0	0	1	1
429.0	0	1	1
437.0	0	1	1
440.0	0	1	1
444.0	0	1	1
456.0	0	1	1
485.0	0	1	1
489.0	0	1	1
491.0	0	1	1
540.0	0	1	1
560.0	0	1	1
562.0	0	1	1
601.0	0	1	1
606.0	0	1	1
625.0	0	1	1
631.0	0	1	1
651.0	0	1	1
663.0	0	1	1
704.0	0	1	1
791.0	0	1	1
838.0	0	1	1
840.0	0	1	1
845.0	0	1	1
873.0	0	1	1
875.0	0	1	1
1069.0	0	1	1
1861.0	0	1	1
4221.0	0	1	1