## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Gua_1_2015-09-12/ES_Gra_Gua_1_2015-09-12.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Gua_1_2015-09-12/ES_Gra_Gua_1_2015-09-12.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Gua_1_2015-09-12/ES_Gra_Gua_1_2015-09-12.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 08:58:56 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	6243933	32614393	0	0	2602528	4001953	0	0.148398	121787787

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	24660593	24660593
2.0	1.765063	3044032	3044032
3.0	2.350385	346573	346573
4.0	2.798193	40223	40223
5.0	3.140794	5739	5739
6.0	3.402906	1290	1290
7.0	3.603438	599	599
8.0	3.756857	388	388
9.0	3.874233	288	288
10.0	3.964033	267	267
11.0	4.032736	203	203
12.0	4.085297	186	186
13.0	4.12551	193	193
14.0	4.156276	154	154
15.0	4.179814	129	129
16.0	4.197821	134	134
17.0	4.211598	108	108
18.0	4.222139	115	115
19.0	4.230203	100	100
20.0	4.236372	85	85
21.0	4.241092	94	94
22.0	4.244703	69	69
23.0	4.247466	64	64
24.0	4.24958	74	74
25.0	4.251197	66	66
26.0	4.252434	55	55
27.0	4.253381	52	52
28.0	4.254105	47	47
29.0	4.254659	42	42
30.0	4.255083	44	44
31.0	4.255407	35	35
32.0	4.255655	49	49
33.0	4.255845	31	31
34.0	4.25599	37	37
35.0	4.256101	41	41
36.0	4.256186	42	42
37.0	4.256251	30	30
38.0	4.256301	23	23
39.0	4.256339	24	24
40.0	4.256368	28	28
41.0	4.25639	28	28
42.0	4.256407	17	17
43.0	4.25642	15	15
44.0	4.25643	30	30
45.0	4.256438	13	13
46.0	4.256444	14	14
47.0	4.256448	13	13
48.0	4.256452	15	15
49.0	4.256454	11	11
50.0	4.256456	13	13
51.0	4.256458	15	15
52.0	4.256459	19	19
53.0	4.25646	18	18
54.0	4.256461	18	18
55.0	4.256461	16	16
56.0	4.256462	14	14
57.0	4.256462	14	14
58.0	4.256462	12	12
59.0	4.256462	18	18
60.0	4.256462	10	10
61.0	4.256462	15	15
62.0	4.256463	13	13
63.0	4.256463	16	16
64.0	4.256463	13	13
65.0	4.256463	3	3
66.0	4.256463	7	7
67.0	4.256463	9	9
68.0	4.256463	16	16
69.0	4.256463	6	6
70.0	4.256463	5	5
71.0	4.256463	12	12
72.0	4.256463	5	5
73.0	4.256463	8	8
74.0	4.256463	6	6
75.0	4.256463	10	10
76.0	4.256463	9	9
77.0	4.256463	4	4
78.0	4.256463	4	4
79.0	4.256463	7	7
80.0	4.256463	5	5
81.0	4.256463	8	8
82.0	4.256463	7	7
83.0	4.256463	10	10
84.0	4.256463	6	6
85.0	4.256463	3	3
86.0	4.256463	6	6
87.0	4.256463	4	4
88.0	4.256463	7	7
89.0	4.256463	1	1
90.0	4.256463	3	3
91.0	4.256463	4	4
92.0	4.256463	4	4
93.0	4.256463	9	9
94.0	4.256463	7	7
95.0	4.256463	2	2
96.0	4.256463	3	3
97.0	4.256463	4	4
98.0	4.256463	4	4
99.0	4.256463	1	1
100.0	4.256463	4	4
101.0	0	3	3
102.0	0	2	2
103.0	0	6	6
104.0	0	3	3
105.0	0	2	2
106.0	0	5	5
107.0	0	2	2
108.0	0	7	7
110.0	0	1	1
111.0	0	1	1
112.0	0	3	3
113.0	0	1	1
114.0	0	2	2
115.0	0	1	1
116.0	0	1	1
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
120.0	0	1	1
122.0	0	1	1
123.0	0	1	1
125.0	0	3	3
126.0	0	1	1
127.0	0	4	4
128.0	0	1	1
129.0	0	1	1
131.0	0	3	3
132.0	0	4	4
133.0	0	3	3
134.0	0	3	3
135.0	0	5	5
136.0	0	4	4
139.0	0	1	1
144.0	0	2	2
145.0	0	3	3
146.0	0	2	2
147.0	0	1	1
148.0	0	2	2
149.0	0	2	2
151.0	0	1	1
154.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	3	3
170.0	0	2	2
173.0	0	2	2
174.0	0	1	1
177.0	0	2	2
180.0	0	1	1
181.0	0	1	1
184.0	0	1	1
190.0	0	1	1
191.0	0	1	1
192.0	0	1	1
195.0	0	1	1
198.0	0	1	1
210.0	0	1	1
211.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
219.0	0	1	1
220.0	0	1	1
225.0	0	1	1
228.0	0	1	1
233.0	0	1	1
237.0	0	1	1
241.0	0	1	1
248.0	0	1	1
250.0	0	1	1
252.0	0	1	1
262.0	0	2	2
269.0	0	1	1
280.0	0	1	1
292.0	0	1	1
323.0	0	1	1
355.0	0	1	1
396.0	0	1	1