## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-07-24/FI_Pir_Aka_1_2016-07-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-07-24/FI_Pir_Aka_1_2016-07-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-07-24/FI_Pir_Aka_1_2016-07-24.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 08:41:42 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	23719931	11222014	0	0	5157773	891706	0	0.150359	66821427

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9370982	9370982
2.0	1.845404	650545	650545
3.0	2.560113	49814	49814
4.0	3.16433	5369	5369
5.0	3.675138	1519	1519
6.0	4.106977	900	900
7.0	4.472056	506	506
8.0	4.780695	353	353
9.0	5.04162	317	317
10.0	5.262207	239	239
11.0	5.448692	200	200
12.0	5.606348	201	201
13.0	5.73963	178	178
14.0	5.852308	162	162
15.0	5.947566	163	163
16.0	6.028098	139	139
17.0	6.096179	127	127
18.0	6.153736	113	113
19.0	6.202395	97	97
20.0	6.243531	107	107
21.0	6.278308	84	84
22.0	6.307708	79	79
23.0	6.332563	80	80
24.0	6.353576	60	60
25.0	6.37134	52	52
26.0	6.386358	49	49
27.0	6.399054	61	61
28.0	6.409788	51	51
29.0	6.418862	36	36
30.0	6.426533	47	47
31.0	6.433019	38	38
32.0	6.438501	31	31
33.0	6.443136	30	30
34.0	6.447055	31	31
35.0	6.450368	19	19
36.0	6.453168	22	22
37.0	6.455536	24	24
38.0	6.457538	24	24
39.0	6.45923	20	20
40.0	6.46066	17	17
41.0	6.46187	32	32
42.0	6.462892	28	28
43.0	6.463757	21	21
44.0	6.464487	16	16
45.0	6.465105	8	8
46.0	6.465627	14	14
47.0	6.466069	14	14
48.0	6.466442	29	29
49.0	6.466758	14	14
50.0	6.467025	22	22
51.0	6.46725	16	16
52.0	6.467441	16	16
53.0	6.467602	27	27
54.0	6.467738	15	15
55.0	6.467854	13	13
56.0	6.467951	15	15
57.0	6.468033	15	15
58.0	6.468103	14	14
59.0	6.468162	15	15
60.0	6.468211	17	17
61.0	6.468254	15	15
62.0	6.468289	17	17
63.0	6.468319	11	11
64.0	6.468345	5	5
65.0	6.468366	8	8
66.0	6.468384	6	6
67.0	6.4684	14	14
68.0	6.468413	9	9
69.0	6.468424	9	9
70.0	6.468433	11	11
71.0	6.468441	9	9
72.0	6.468447	9	9
73.0	6.468453	10	10
74.0	6.468458	8	8
75.0	6.468462	12	12
76.0	6.468465	4	4
77.0	6.468468	10	10
78.0	6.46847	5	5
79.0	6.468472	8	8
80.0	6.468474	8	8
81.0	6.468476	4	4
82.0	6.468477	8	8
83.0	6.468478	2	2
84.0	6.468479	5	5
85.0	6.468479	6	6
86.0	6.46848	5	5
87.0	6.468481	5	5
88.0	6.468481	2	2
89.0	6.468481	6	6
90.0	6.468482	5	5
91.0	6.468482	7	7
92.0	6.468482	4	4
93.0	6.468482	4	4
94.0	6.468483	1	1
95.0	6.468483	2	2
96.0	6.468483	4	4
97.0	6.468483	3	3
98.0	6.468483	5	5
99.0	6.468483	0	0
100.0	6.468483	2	2
101.0	0	3	3
102.0	0	1	1
103.0	0	2	2
104.0	0	2	2
105.0	0	1	1
106.0	0	1	1
108.0	0	1	1
109.0	0	2	2
110.0	0	1	1
111.0	0	3	3
112.0	0	3	3
113.0	0	1	1
114.0	0	3	3
115.0	0	3	3
117.0	0	3	3
118.0	0	1	1
119.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	2	2
129.0	0	2	2
130.0	0	3	3
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
139.0	0	3	3
140.0	0	1	1
141.0	0	3	3
142.0	0	1	1
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	2	2
147.0	0	1	1
148.0	0	2	2
150.0	0	3	3
152.0	0	1	1
154.0	0	1	1
156.0	0	2	2
157.0	0	2	2
162.0	0	2	2
163.0	0	1	1
164.0	0	2	2
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
173.0	0	1	1
178.0	0	1	1
180.0	0	2	2
183.0	0	1	1
188.0	0	1	1
192.0	0	3	3
193.0	0	1	1
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
210.0	0	1	1
212.0	0	1	1
213.0	0	1	1
216.0	0	1	1
220.0	0	1	1
221.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	2	2
235.0	0	2	2
245.0	0	1	1
251.0	0	1	1
252.0	0	1	1
258.0	0	1	1
275.0	0	2	2
278.0	0	1	1
280.0	0	1	1
286.0	0	1	1
304.0	0	1	1
321.0	0	1	1
346.0	0	1	1
357.0	0	1	1
374.0	0	1	1
547.0	0	1	1
976.0	0	1	1