## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2014-10-14/US_Vir_Cha_1_2014-10-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2014-10-14/US_Vir_Cha_1_2014-10-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2014-10-14/US_Vir_Cha_1_2014-10-14.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 20:41:25 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	1434647	52438706	0	0	699638	12607200	0	0.243754	90770119

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	28353038	28353038
2.0	1.561183	7474179	7474179
3.0	1.876109	1729681	1729681
4.0	2.05284	366537	366537
5.0	2.152018	75131	75131
6.0	2.207675	16451	16451
7.0	2.238909	4473	4473
8.0	2.256437	1749	1749
9.0	2.266273	967	967
10.0	2.271793	652	652
11.0	2.274891	467	467
12.0	2.276629	354	354
13.0	2.277605	298	298
14.0	2.278152	233	233
15.0	2.278459	162	162
16.0	2.278632	167	167
17.0	2.278729	145	145
18.0	2.278783	126	126
19.0	2.278813	95	95
20.0	2.27883	83	83
21.0	2.27884	74	74
22.0	2.278845	72	72
23.0	2.278848	73	73
24.0	2.27885	54	54
25.0	2.278851	54	54
26.0	2.278852	40	40
27.0	2.278852	42	42
28.0	2.278852	37	37
29.0	2.278852	41	41
30.0	2.278852	36	36
31.0	2.278852	28	28
32.0	2.278852	32	32
33.0	2.278852	37	37
34.0	2.278852	36	36
35.0	2.278852	21	21
36.0	2.278852	26	26
37.0	2.278852	30	30
38.0	2.278852	17	17
39.0	2.278852	23	23
40.0	2.278852	21	21
41.0	2.278852	24	24
42.0	2.278852	20	20
43.0	2.278852	11	11
44.0	2.278852	21	21
45.0	2.278852	15	15
46.0	2.278852	8	8
47.0	2.278852	9	9
48.0	2.278852	13	13
49.0	2.278852	9	9
50.0	2.278852	6	6
51.0	2.278852	14	14
52.0	2.278852	15	15
53.0	2.278852	7	7
54.0	2.278852	10	10
55.0	2.278852	8	8
56.0	2.278852	5	5
57.0	2.278852	8	8
58.0	2.278852	7	7
59.0	2.278852	7	7
60.0	2.278852	10	10
61.0	2.278852	7	7
62.0	2.278852	11	11
63.0	2.278852	12	12
64.0	2.278852	9	9
65.0	2.278852	12	12
66.0	2.278852	6	6
67.0	2.278852	3	3
68.0	2.278852	8	8
69.0	2.278852	8	8
70.0	2.278852	6	6
71.0	2.278852	3	3
72.0	2.278852	2	2
73.0	2.278852	5	5
74.0	2.278852	4	4
75.0	2.278852	4	4
76.0	2.278852	5	5
77.0	2.278852	4	4
78.0	2.278852	3	3
79.0	2.278852	2	2
80.0	2.278852	2	2
81.0	2.278852	8	8
82.0	2.278852	0	0
83.0	2.278852	3	3
84.0	2.278852	4	4
85.0	2.278852	0	0
86.0	2.278852	3	3
87.0	2.278852	0	0
88.0	2.278852	6	6
89.0	2.278852	3	3
90.0	2.278852	1	1
91.0	2.278852	1	1
92.0	2.278852	2	2
93.0	2.278852	3	3
94.0	2.278852	3	3
95.0	2.278852	3	3
96.0	2.278852	2	2
97.0	2.278852	3	3
98.0	2.278852	5	5
99.0	2.278852	5	5
100.0	2.278852	1	1
102.0	0	4	4
103.0	0	3	3
104.0	0	1	1
105.0	0	3	3
106.0	0	1	1
107.0	0	3	3
109.0	0	2	2
110.0	0	2	2
112.0	0	4	4
114.0	0	2	2
118.0	0	4	4
119.0	0	6	6
120.0	0	2	2
121.0	0	1	1
122.0	0	3	3
123.0	0	3	3
124.0	0	2	2
125.0	0	1	1
126.0	0	2	2
127.0	0	2	2
128.0	0	2	2
129.0	0	1	1
130.0	0	1	1
131.0	0	2	2
132.0	0	1	1
133.0	0	3	3
135.0	0	2	2
136.0	0	3	3
137.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
142.0	0	2	2
144.0	0	2	2
145.0	0	2	2
148.0	0	2	2
152.0	0	2	2
154.0	0	2	2
156.0	0	2	2
157.0	0	3	3
160.0	0	3	3
162.0	0	4	4
165.0	0	1	1
167.0	0	1	1
170.0	0	1	1
175.0	0	1	1
176.0	0	1	1
178.0	0	1	1
180.0	0	1	1
181.0	0	2	2
184.0	0	1	1
185.0	0	1	1
187.0	0	2	2
189.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
196.0	0	1	1
202.0	0	1	1
203.0	0	1	1
210.0	0	1	1
212.0	0	1	1
219.0	0	2	2
222.0	0	1	1
224.0	0	1	1
227.0	0	3	3
228.0	0	1	1
234.0	0	1	1
241.0	0	1	1
245.0	0	1	1
249.0	0	1	1
251.0	0	1	1
254.0	0	1	1
256.0	0	1	1
259.0	0	1	1
260.0	0	1	1
263.0	0	1	1
266.0	0	1	1
269.0	0	1	1
270.0	0	2	2
272.0	0	1	1
277.0	0	1	1
279.0	0	1	1
300.0	0	1	1
302.0	0	1	1
316.0	0	1	1
318.0	0	1	1
320.0	0	1	1
322.0	0	1	1
331.0	0	1	1
335.0	0	1	1
337.0	0	1	1
342.0	0	1	1
344.0	0	1	1
347.0	0	1	1
369.0	0	1	1
387.0	0	1	1
391.0	0	1	1
404.0	0	1	1
407.0	0	1	1
421.0	0	2	2
430.0	0	1	1
435.0	0	1	1
437.0	0	1	1
453.0	0	1	1
503.0	0	1	1
511.0	0	1	1
525.0	0	1	1
527.0	0	1	1
541.0	0	1	1
556.0	0	1	1
580.0	0	1	1
589.0	0	1	1
593.0	0	1	1
622.0	0	1	1
738.0	0	1	1
813.0	0	1	1
815.0	0	1	1
879.0	0	1	1
883.0	0	1	1
924.0	0	1	1
938.0	0	1	1
960.0	0	1	1
1003.0	0	1	1
1065.0	0	1	1
1105.0	0	1	1
1211.0	0	1	1
1316.0	0	1	1
1357.0	0	1	1
1380.0	0	1	1
1413.0	0	1	1
1415.0	0	1	1
1432.0	0	1	1
1485.0	0	1	1
1631.0	0	1	1
1813.0	0	1	1
2399.0	0	1	1
2468.0	0	1	1