## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//PA_li_15_fall/PA_li_15_fall.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_15_fall/PA_li_15_fall.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_15_fall/PA_li_15_fall.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: Sun Jun 07 08:10:55 UTC 2020

## 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	739967	51575292	0	0	321356	5627219	0	0.111423	218828142

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	40083768	40083768
2.0	1.790027	4325155	4325155
3.0	2.414169	463262	463262
4.0	2.907258	55390	55390
5.0	3.296811	9221	9221
6.0	3.604569	2575	2575
7.0	3.847705	1273	1273
8.0	4.03979	799	799
9.0	4.191542	543	543
10.0	4.31143	427	427
11.0	4.406145	341	341
12.0	4.480972	293	293
13.0	4.540087	257	257
14.0	4.58679	210	210
15.0	4.623686	195	195
16.0	4.652836	147	147
17.0	4.675864	138	138
18.0	4.694057	134	134
19.0	4.708431	96	96
20.0	4.719786	87	87
21.0	4.728757	84	84
22.0	4.735844	103	103
23.0	4.741443	70	70
24.0	4.745866	58	58
25.0	4.749361	66	66
26.0	4.752122	53	53
27.0	4.754303	43	43
28.0	4.756026	47	47
29.0	4.757388	50	50
30.0	4.758463	38	38
31.0	4.759313	49	49
32.0	4.759984	27	27
33.0	4.760514	40	40
34.0	4.760933	34	34
35.0	4.761264	24	24
36.0	4.761526	39	39
37.0	4.761732	23	23
38.0	4.761896	21	21
39.0	4.762025	36	36
40.0	4.762126	19	19
41.0	4.762207	28	28
42.0	4.76227	21	21
43.0	4.762321	19	19
44.0	4.76236	20	20
45.0	4.762392	22	22
46.0	4.762416	19	19
47.0	4.762436	15	15
48.0	4.762452	14	14
49.0	4.762464	17	17
50.0	4.762473	18	18
51.0	4.762481	10	10
52.0	4.762487	10	10
53.0	4.762492	10	10
54.0	4.762496	17	17
55.0	4.762498	9	9
56.0	4.762501	13	13
57.0	4.762503	16	16
58.0	4.762504	9	9
59.0	4.762505	8	8
60.0	4.762506	12	12
61.0	4.762507	7	7
62.0	4.762508	7	7
63.0	4.762508	8	8
64.0	4.762508	9	9
65.0	4.762509	6	6
66.0	4.762509	10	10
67.0	4.762509	4	4
68.0	4.762509	6	6
69.0	4.762509	6	6
70.0	4.762509	7	7
71.0	4.762509	7	7
72.0	4.762509	7	7
73.0	4.76251	7	7
74.0	4.76251	8	8
75.0	4.76251	6	6
76.0	4.76251	4	4
77.0	4.76251	3	3
78.0	4.76251	3	3
79.0	4.76251	6	6
80.0	4.76251	4	4
81.0	4.76251	5	5
82.0	4.76251	5	5
83.0	4.76251	4	4
84.0	4.76251	5	5
85.0	4.76251	5	5
86.0	4.76251	1	1
87.0	4.76251	3	3
88.0	4.76251	5	5
89.0	4.76251	5	5
90.0	4.76251	3	3
91.0	4.76251	3	3
92.0	4.76251	6	6
93.0	4.76251	4	4
94.0	4.76251	2	2
95.0	4.76251	4	4
96.0	4.76251	4	4
97.0	4.76251	1	1
98.0	4.76251	3	3
99.0	4.76251	2	2
100.0	4.76251	5	5
101.0	0	5	5
102.0	0	3	3
103.0	0	5	5
104.0	0	1	1
105.0	0	3	3
107.0	0	2	2
108.0	0	1	1
109.0	0	6	6
111.0	0	9	9
112.0	0	1	1
113.0	0	3	3
114.0	0	3	3
115.0	0	3	3
116.0	0	1	1
118.0	0	1	1
119.0	0	1	1
120.0	0	4	4
121.0	0	6	6
122.0	0	2	2
123.0	0	1	1
124.0	0	4	4
125.0	0	3	3
127.0	0	1	1
128.0	0	2	2
129.0	0	1	1
130.0	0	1	1
133.0	0	4	4
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
138.0	0	2	2
139.0	0	2	2
140.0	0	1	1
141.0	0	1	1
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
147.0	0	3	3
149.0	0	1	1
150.0	0	2	2
151.0	0	2	2
152.0	0	2	2
153.0	0	1	1
155.0	0	3	3
156.0	0	3	3
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	1	1
163.0	0	4	4
164.0	0	1	1
165.0	0	1	1
166.0	0	4	4
167.0	0	4	4
168.0	0	3	3
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
182.0	0	2	2
183.0	0	1	1
187.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	2	2
198.0	0	2	2
199.0	0	1	1
200.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
218.0	0	1	1
219.0	0	2	2
224.0	0	3	3
226.0	0	2	2
233.0	0	1	1
235.0	0	2	2
239.0	0	1	1
240.0	0	1	1
242.0	0	1	1
245.0	0	1	1
251.0	0	1	1
253.0	0	2	2
257.0	0	1	1
261.0	0	1	1
264.0	0	2	2
265.0	0	1	1
269.0	0	1	1
271.0	0	1	1
280.0	0	1	1
287.0	0	2	2
290.0	0	2	2
294.0	0	1	1
296.0	0	1	1
301.0	0	1	1
303.0	0	1	1
317.0	0	1	1
326.0	0	1	1
330.0	0	1	1
333.0	0	1	1
335.0	0	1	1
337.0	0	1	1
338.0	0	1	1
346.0	0	1	1
350.0	0	1	1
351.0	0	1	1
359.0	0	1	1
364.0	0	1	1
368.0	0	1	1
371.0	0	1	1
386.0	0	1	1
398.0	0	1	1
417.0	0	1	1
419.0	0	1	1
429.0	0	1	1
436.0	0	1	1
443.0	0	1	1
504.0	0	1	1
535.0	0	1	1
538.0	0	1	1
565.0	0	1	1
571.0	0	1	1
586.0	0	1	1
645.0	0	1	1
690.0	0	1	1
720.0	0	1	1
756.0	0	1	1
763.0	0	1	1
782.0	0	1	1
821.0	0	1	1
866.0	0	1	1
871.0	0	1	1
940.0	0	1	1
1302.0	0	1	1
1497.0	0	1	1
1772.0	0	1	1
2566.0	0	1	1