## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-09-11/US_Wis_Cro_1_2012-09-11.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-09-11/US_Wis_Cro_1_2012-09-11.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Wis_Cro_1_2012-09-11/US_Wis_Cro_1_2012-09-11.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 18:22:40 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	1860248	31432028	0	0	497411	207183	0	0.014087	2373809973

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	30759308	30759308
2.0	1.986846	54601	54601
3.0	2.960711	5921	5921
4.0	3.921766	1798	1798
5.0	4.87018	803	803
6.0	5.806118	440	440
7.0	6.729745	296	296
8.0	7.641223	201	201
9.0	8.540711	142	142
10.0	9.428367	117	117
11.0	10.304348	86	86
12.0	11.168805	100	100
13.0	12.021892	85	85
14.0	12.863757	65	65
15.0	13.694549	69	69
16.0	14.514412	60	60
17.0	15.323491	65	65
18.0	16.121927	48	48
19.0	16.909861	51	51
20.0	17.687431	48	48
21.0	18.454772	46	46
22.0	19.21202	38	38
23.0	19.959307	49	49
24.0	20.696765	34	34
25.0	21.424522	34	34
26.0	22.142706	33	33
27.0	22.851443	31	31
28.0	23.550857	25	25
29.0	24.241072	34	34
30.0	24.922207	33	33
31.0	25.594383	27	27
32.0	26.257718	38	38
33.0	26.912326	23	23
34.0	27.558324	20	20
35.0	28.195825	20	20
36.0	28.82494	33	33
37.0	29.44578	26	26
38.0	30.058453	26	26
39.0	30.663068	26	26
40.0	31.259729	27	27
41.0	31.848542	19	19
42.0	32.429609	23	23
43.0	33.003034	20	20
44.0	33.568915	8	8
45.0	34.127353	15	15
46.0	34.678446	15	15
47.0	35.222289	8	8
48.0	35.758979	17	17
49.0	36.288609	9	9
50.0	36.811273	3	3
51.0	37.327061	7	7
52.0	37.836065	4	4
53.0	38.338373	3	3
54.0	38.834074	8	8
55.0	39.323255	3	3
56.0	39.806001	6	6
57.0	40.282397	6	6
58.0	40.752527	4	4
59.0	41.216472	3	3
60.0	41.674315	6	6
61.0	42.126136	2	2
62.0	42.572013	6	6
63.0	43.012025	3	3
64.0	43.44625	4	4
65.0	43.874762	7	7
66.0	44.297638	2	2
67.0	44.714952	3	3
68.0	45.126776	7	7
69.0	45.533183	4	4
70.0	45.934245	4	4
71.0	46.33003	2	2
72.0	46.72061	5	5
73.0	47.106052	3	3
74.0	47.486424	4	4
75.0	47.861793	2	2
76.0	48.232224	4	4
77.0	48.597782	3	3
78.0	48.958532	7	7
79.0	49.314537	6	6
80.0	49.665859	1	1
81.0	50.012559	3	3
82.0	50.354699	0	0
83.0	50.692339	1	1
84.0	51.025537	3	3
85.0	51.354353	1	1
86.0	51.678843	2	2
87.0	51.999065	1	1
88.0	52.315075	3	3
89.0	52.626928	3	3
90.0	52.934679	1	1
91.0	53.238382	1	1
92.0	53.53809	1	1
93.0	53.833855	1	1
94.0	54.12573	1	1
95.0	54.413766	2	2
96.0	54.698013	2	2
97.0	54.978521	1	1
98.0	55.25534	4	4
99.0	55.528517	1	1
100.0	55.798101	1	1
101.0	0	3	3
103.0	0	2	2
106.0	0	1	1
107.0	0	2	2
109.0	0	2	2
111.0	0	1	1
112.0	0	2	2
115.0	0	1	1
116.0	0	1	1
119.0	0	2	2
120.0	0	3	3
121.0	0	2	2
122.0	0	2	2
123.0	0	1	1
124.0	0	3	3
125.0	0	1	1
126.0	0	1	1
127.0	0	3	3
128.0	0	1	1
129.0	0	1	1
130.0	0	2	2
131.0	0	1	1
132.0	0	3	3
135.0	0	3	3
137.0	0	2	2
138.0	0	3	3
139.0	0	2	2
141.0	0	2	2
144.0	0	1	1
145.0	0	3	3
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
153.0	0	1	1
157.0	0	1	1
158.0	0	3	3
159.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	3	3
164.0	0	1	1
165.0	0	2	2
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	1	1
175.0	0	3	3
180.0	0	2	2
182.0	0	1	1
183.0	0	1	1
185.0	0	2	2
188.0	0	1	1
190.0	0	1	1
191.0	0	2	2
195.0	0	1	1
196.0	0	1	1
198.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
207.0	0	1	1
211.0	0	2	2
216.0	0	1	1
224.0	0	1	1
225.0	0	1	1
226.0	0	1	1
228.0	0	1	1
231.0	0	1	1
232.0	0	3	3
234.0	0	1	1
237.0	0	1	1
239.0	0	2	2
243.0	0	1	1
244.0	0	1	1
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	1	1
256.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
272.0	0	1	1
275.0	0	1	1
279.0	0	1	1
281.0	0	1	1
284.0	0	1	1
293.0	0	1	1
295.0	0	1	1
301.0	0	1	1
304.0	0	1	1
305.0	0	1	1
317.0	0	1	1
319.0	0	1	1
320.0	0	1	1
321.0	0	1	1
325.0	0	1	1
329.0	0	1	1
347.0	0	1	1
352.0	0	1	1
353.0	0	1	1
361.0	0	2	2
368.0	0	1	1
374.0	0	1	1
376.0	0	1	1
377.0	0	1	1
382.0	0	2	2
385.0	0	1	1
390.0	0	1	1
394.0	0	1	1
408.0	0	1	1
413.0	0	1	1
415.0	0	1	1
424.0	0	1	1
440.0	0	1	1
441.0	0	2	2
446.0	0	1	1
447.0	0	1	1
448.0	0	1	1
454.0	0	1	1
457.0	0	1	1
465.0	0	1	1
473.0	0	1	1
484.0	0	1	1
490.0	0	1	1
493.0	0	1	1
496.0	0	1	1
514.0	0	1	1
554.0	0	1	1
558.0	0	1	1
591.0	0	1	1
596.0	0	1	1
603.0	0	1	1
633.0	0	1	1
649.0	0	1	1
653.0	0	1	1
665.0	0	1	1
738.0	0	1	1
748.0	0	1	1
792.0	0	1	1
808.0	0	1	1
812.0	0	1	1
846.0	0	1	1
851.0	0	1	1
896.0	0	1	1
933.0	0	1	1
953.0	0	1	1
1045.0	0	1	1
1089.0	0	1	1
1099.0	0	1	1
1199.0	0	1	1
1284.0	0	1	1
1290.0	0	1	1
1452.0	0	1	1
1489.0	0	1	1
1530.0	0	1	1
2082.0	0	1	1
2291.0	0	1	1
10130.0	0	1	1