## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-09-01/DE_Bay_Mun_1_2016-09-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-09-01/DE_Bay_Mun_1_2016-09-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/DE_Bay_Mun_1_2016-09-01/DE_Bay_Mun_1_2016-09-01.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 09:12:56 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	33316781	12282012	0	0	8152166	1029354	0	0.176412	69119153

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10209626	10209626
2.0	1.837199	686257	686257
3.0	2.538102	53890	53890
4.0	3.124896	6555	6555
5.0	3.616161	2084	2084
6.0	4.027446	1184	1184
7.0	4.371775	795	795
8.0	4.660046	625	625
9.0	4.901386	471	471
10.0	5.103437	382	382
11.0	5.272593	271	271
12.0	5.41421	230	230
13.0	5.532772	212	212
14.0	5.632032	196	196
15.0	5.715132	175	175
16.0	5.784704	172	172
17.0	5.842949	134	134
18.0	5.891712	123	123
19.0	5.932536	133	133
20.0	5.966714	111	111
21.0	5.995328	135	135
22.0	6.019283	98	98
23.0	6.039339	95	95
24.0	6.056129	97	97
25.0	6.070186	98	98
26.0	6.081955	85	85
27.0	6.091807	87	87
28.0	6.100056	55	55
29.0	6.106961	85	85
30.0	6.112743	55	55
31.0	6.117583	63	63
32.0	6.121635	49	49
33.0	6.125028	57	57
34.0	6.127868	45	45
35.0	6.130246	43	43
36.0	6.132236	39	39
37.0	6.133903	46	46
38.0	6.135298	39	39
39.0	6.136466	32	32
40.0	6.137444	30	30
41.0	6.138263	30	30
42.0	6.138949	27	27
43.0	6.139522	28	28
44.0	6.140003	22	22
45.0	6.140405	22	22
46.0	6.140742	18	18
47.0	6.141024	22	22
48.0	6.14126	14	14
49.0	6.141457	21	21
50.0	6.141623	27	27
51.0	6.141761	18	18
52.0	6.141877	19	19
53.0	6.141974	18	18
54.0	6.142056	18	18
55.0	6.142124	17	17
56.0	6.142181	15	15
57.0	6.142228	15	15
58.0	6.142268	11	11
59.0	6.142302	10	10
60.0	6.14233	16	16
61.0	6.142353	12	12
62.0	6.142373	8	8
63.0	6.142389	12	12
64.0	6.142403	12	12
65.0	6.142414	10	10
66.0	6.142424	14	14
67.0	6.142432	11	11
68.0	6.142439	7	7
69.0	6.142444	11	11
70.0	6.142449	8	8
71.0	6.142453	15	15
72.0	6.142456	12	12
73.0	6.142459	15	15
74.0	6.142461	7	7
75.0	6.142463	12	12
76.0	6.142465	15	15
77.0	6.142466	14	14
78.0	6.142468	4	4
79.0	6.142469	13	13
80.0	6.142469	9	9
81.0	6.14247	14	14
82.0	6.142471	15	15
83.0	6.142471	11	11
84.0	6.142471	6	6
85.0	6.142472	12	12
86.0	6.142472	7	7
87.0	6.142472	10	10
88.0	6.142472	7	7
89.0	6.142473	10	10
90.0	6.142473	10	10
91.0	6.142473	8	8
92.0	6.142473	8	8
93.0	6.142473	8	8
94.0	6.142473	8	8
95.0	6.142473	13	13
96.0	6.142473	10	10
97.0	6.142473	9	9
98.0	6.142473	6	6
99.0	6.142473	6	6
100.0	6.142473	6	6
101.0	0	3	3
102.0	0	6	6
103.0	0	9	9
104.0	0	7	7
105.0	0	8	8
106.0	0	4	4
107.0	0	7	7
108.0	0	9	9
109.0	0	10	10
110.0	0	5	5
111.0	0	4	4
112.0	0	6	6
113.0	0	3	3
114.0	0	6	6
115.0	0	6	6
116.0	0	3	3
117.0	0	3	3
118.0	0	4	4
119.0	0	3	3
120.0	0	5	5
121.0	0	4	4
122.0	0	3	3
123.0	0	7	7
124.0	0	3	3
125.0	0	3	3
126.0	0	3	3
128.0	0	1	1
129.0	0	3	3
130.0	0	1	1
131.0	0	3	3
132.0	0	2	2
133.0	0	5	5
135.0	0	2	2
136.0	0	1	1
137.0	0	7	7
138.0	0	5	5
139.0	0	1	1
141.0	0	1	1
142.0	0	5	5
143.0	0	2	2
144.0	0	2	2
145.0	0	2	2
146.0	0	1	1
147.0	0	5	5
149.0	0	1	1
150.0	0	2	2
151.0	0	4	4
152.0	0	2	2
153.0	0	2	2
154.0	0	3	3
155.0	0	5	5
158.0	0	2	2
159.0	0	3	3
160.0	0	2	2
161.0	0	1	1
162.0	0	1	1
164.0	0	1	1
166.0	0	1	1
167.0	0	1	1
169.0	0	3	3
170.0	0	1	1
171.0	0	3	3
172.0	0	2	2
173.0	0	2	2
175.0	0	2	2
176.0	0	3	3
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
183.0	0	2	2
184.0	0	3	3
187.0	0	3	3
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	3	3
193.0	0	2	2
196.0	0	2	2
198.0	0	1	1
200.0	0	2	2
201.0	0	1	1
206.0	0	2	2
208.0	0	1	1
210.0	0	2	2
213.0	0	1	1
215.0	0	3	3
216.0	0	1	1
218.0	0	2	2
220.0	0	1	1
222.0	0	2	2
225.0	0	1	1
229.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	1	1
238.0	0	1	1
240.0	0	1	1
244.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
259.0	0	1	1
262.0	0	1	1
263.0	0	3	3
265.0	0	2	2
275.0	0	1	1
276.0	0	1	1
281.0	0	2	2
286.0	0	1	1
288.0	0	1	1
289.0	0	1	1
291.0	0	1	1
293.0	0	1	1
297.0	0	2	2
299.0	0	1	1
302.0	0	2	2
308.0	0	1	1
309.0	0	1	1
311.0	0	1	1
313.0	0	1	1
316.0	0	1	1
318.0	0	1	1
322.0	0	1	1
325.0	0	1	1
336.0	0	1	1
341.0	0	1	1
342.0	0	1	1
343.0	0	1	1
344.0	0	1	1
349.0	0	1	1
350.0	0	1	1
365.0	0	1	1
371.0	0	1	1
372.0	0	2	2
374.0	0	1	1
378.0	0	1	1
381.0	0	1	1
396.0	0	1	1
399.0	0	1	1
407.0	0	1	1
408.0	0	1	1
412.0	0	1	1
414.0	0	1	1
452.0	0	1	1
467.0	0	1	1
516.0	0	1	1
616.0	0	1	1
680.0	0	1	1
735.0	0	1	1
740.0	0	1	1
776.0	0	1	1
824.0	0	1	1
1067.0	0	1	1
1086.0	0	1	1
1123.0	0	1	1
1248.0	0	1	1
1374.0	0	1	1
1409.0	0	1	1
1815.0	0	1	1
3086.0	0	1	1