## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//PA_li_15_spring/PA_li_15_spring.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_15_spring/PA_li_15_spring.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_15_spring/PA_li_15_spring.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: Thu Jun 11 08:23:18 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	3148711	123540413	0	0	2180785	24496037	0	0.204504	268817280

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	76732690	76732690
2.0	1.631555	16270700	16270700
3.0	2.030417	2902677	2902677
4.0	2.28232	478951	478951
5.0	2.441411	84906	84906
6.0	2.541885	21130	21130
7.0	2.60534	8653	8653
8.0	2.645416	4851	4851
9.0	2.670726	3255	3255
10.0	2.68671	2215	2215
11.0	2.696805	1646	1646
12.0	2.703181	1235	1235
13.0	2.707208	926	926
14.0	2.709751	786	786
15.0	2.711357	610	610
16.0	2.712371	512	512
17.0	2.713011	403	403
18.0	2.713416	379	379
19.0	2.713672	317	317
20.0	2.713833	292	292
21.0	2.713935	261	261
22.0	2.713999	226	226
23.0	2.71404	207	207
24.0	2.714065	206	206
25.0	2.714082	194	194
26.0	2.714092	154	154
27.0	2.714098	137	137
28.0	2.714102	125	125
29.0	2.714105	131	131
30.0	2.714107	96	96
31.0	2.714108	112	112
32.0	2.714108	97	97
33.0	2.714109	79	79
34.0	2.714109	65	65
35.0	2.714109	85	85
36.0	2.714109	70	70
37.0	2.714109	77	77
38.0	2.714109	55	55
39.0	2.714109	60	60
40.0	2.714109	52	52
41.0	2.714109	63	63
42.0	2.714109	56	56
43.0	2.714109	53	53
44.0	2.714109	44	44
45.0	2.714109	48	48
46.0	2.714109	41	41
47.0	2.714109	46	46
48.0	2.714109	54	54
49.0	2.714109	44	44
50.0	2.714109	28	28
51.0	2.714109	24	24
52.0	2.714109	38	38
53.0	2.714109	25	25
54.0	2.714109	41	41
55.0	2.714109	37	37
56.0	2.714109	35	35
57.0	2.714109	24	24
58.0	2.714109	19	19
59.0	2.714109	27	27
60.0	2.714109	31	31
61.0	2.714109	21	21
62.0	2.714109	24	24
63.0	2.714109	27	27
64.0	2.714109	22	22
65.0	2.714109	14	14
66.0	2.714109	18	18
67.0	2.714109	12	12
68.0	2.714109	17	17
69.0	2.714109	16	16
70.0	2.714109	19	19
71.0	2.714109	17	17
72.0	2.714109	17	17
73.0	2.714109	10	10
74.0	2.714109	16	16
75.0	2.714109	13	13
76.0	2.714109	16	16
77.0	2.714109	14	14
78.0	2.714109	14	14
79.0	2.714109	18	18
80.0	2.714109	15	15
81.0	2.714109	12	12
82.0	2.714109	12	12
83.0	2.714109	20	20
84.0	2.714109	18	18
85.0	2.714109	13	13
86.0	2.714109	10	10
87.0	2.714109	6	6
88.0	2.714109	11	11
89.0	2.714109	14	14
90.0	2.714109	6	6
91.0	2.714109	10	10
92.0	2.714109	11	11
93.0	2.714109	8	8
94.0	2.714109	7	7
95.0	2.714109	4	4
96.0	2.714109	14	14
97.0	2.714109	11	11
98.0	2.714109	5	5
99.0	2.714109	10	10
100.0	2.714109	9	9
101.0	0	6	6
102.0	0	13	13
103.0	0	12	12
104.0	0	10	10
105.0	0	10	10
106.0	0	8	8
107.0	0	6	6
108.0	0	5	5
109.0	0	5	5
110.0	0	10	10
111.0	0	9	9
112.0	0	5	5
113.0	0	7	7
114.0	0	6	6
115.0	0	6	6
116.0	0	7	7
118.0	0	6	6
119.0	0	6	6
120.0	0	6	6
121.0	0	8	8
122.0	0	6	6
123.0	0	4	4
124.0	0	3	3
125.0	0	6	6
126.0	0	3	3
127.0	0	2	2
128.0	0	3	3
129.0	0	7	7
130.0	0	8	8
131.0	0	6	6
132.0	0	5	5
133.0	0	14	14
134.0	0	3	3
135.0	0	8	8
136.0	0	8	8
137.0	0	1	1
138.0	0	2	2
139.0	0	2	2
140.0	0	2	2
141.0	0	5	5
142.0	0	5	5
143.0	0	12	12
144.0	0	3	3
145.0	0	4	4
146.0	0	4	4
147.0	0	3	3
148.0	0	3	3
149.0	0	2	2
150.0	0	6	6
151.0	0	3	3
153.0	0	2	2
154.0	0	6	6
155.0	0	2	2
156.0	0	3	3
157.0	0	2	2
158.0	0	5	5
159.0	0	4	4
160.0	0	5	5
161.0	0	3	3
162.0	0	3	3
163.0	0	2	2
164.0	0	5	5
165.0	0	3	3
166.0	0	1	1
167.0	0	2	2
168.0	0	4	4
169.0	0	3	3
170.0	0	2	2
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	4	4
176.0	0	2	2
177.0	0	1	1
178.0	0	5	5
180.0	0	5	5
182.0	0	1	1
183.0	0	1	1
184.0	0	4	4
185.0	0	4	4
186.0	0	2	2
188.0	0	3	3
189.0	0	2	2
190.0	0	3	3
191.0	0	2	2
192.0	0	2	2
194.0	0	5	5
196.0	0	1	1
197.0	0	1	1
198.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	3	3
204.0	0	3	3
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
212.0	0	3	3
215.0	0	1	1
216.0	0	2	2
217.0	0	2	2
219.0	0	3	3
220.0	0	2	2
221.0	0	2	2
223.0	0	1	1
224.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	4	4
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	2	2
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	2	2
237.0	0	1	1
238.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	3	3
243.0	0	5	5
244.0	0	1	1
245.0	0	2	2
247.0	0	1	1
249.0	0	1	1
252.0	0	2	2
253.0	0	3	3
254.0	0	1	1
256.0	0	2	2
257.0	0	1	1
258.0	0	1	1
261.0	0	3	3
262.0	0	4	4
263.0	0	1	1
264.0	0	3	3
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
270.0	0	2	2
271.0	0	1	1
273.0	0	1	1
274.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
282.0	0	3	3
286.0	0	3	3
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	1	1
294.0	0	2	2
296.0	0	2	2
297.0	0	1	1
301.0	0	2	2
303.0	0	1	1
304.0	0	1	1
305.0	0	2	2
306.0	0	1	1
307.0	0	1	1
309.0	0	1	1
311.0	0	2	2
312.0	0	1	1
314.0	0	1	1
317.0	0	1	1
321.0	0	2	2
322.0	0	1	1
323.0	0	1	1
332.0	0	1	1
339.0	0	1	1
341.0	0	2	2
342.0	0	1	1
346.0	0	1	1
348.0	0	1	1
349.0	0	1	1
356.0	0	1	1
359.0	0	1	1
361.0	0	1	1
363.0	0	1	1
365.0	0	1	1
367.0	0	1	1
375.0	0	1	1
376.0	0	1	1
378.0	0	1	1
380.0	0	1	1
381.0	0	1	1
382.0	0	1	1
383.0	0	1	1
386.0	0	1	1
389.0	0	1	1
390.0	0	1	1
391.0	0	1	1
392.0	0	1	1
394.0	0	2	2
395.0	0	1	1
397.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
408.0	0	1	1
409.0	0	1	1
410.0	0	1	1
414.0	0	2	2
417.0	0	1	1
420.0	0	4	4
421.0	0	1	1
423.0	0	1	1
424.0	0	1	1
427.0	0	1	1
429.0	0	1	1
432.0	0	2	2
434.0	0	1	1
436.0	0	2	2
439.0	0	1	1
442.0	0	1	1
444.0	0	1	1
451.0	0	2	2
452.0	0	1	1
456.0	0	1	1
461.0	0	1	1
473.0	0	2	2
475.0	0	1	1
476.0	0	1	1
478.0	0	1	1
480.0	0	1	1
483.0	0	1	1
493.0	0	1	1
497.0	0	1	1
500.0	0	1	1
512.0	0	1	1
513.0	0	1	1
519.0	0	1	1
520.0	0	1	1
524.0	0	1	1
527.0	0	1	1
531.0	0	1	1
538.0	0	2	2
546.0	0	1	1
548.0	0	1	1
549.0	0	1	1
556.0	0	1	1
558.0	0	1	1
562.0	0	1	1
563.0	0	1	1
564.0	0	1	1
570.0	0	1	1
572.0	0	1	1
573.0	0	1	1
574.0	0	1	1
576.0	0	2	2
580.0	0	1	1
581.0	0	1	1
585.0	0	1	1
586.0	0	1	1
588.0	0	1	1
592.0	0	1	1
598.0	0	1	1
605.0	0	1	1
606.0	0	1	1
630.0	0	1	1
651.0	0	1	1
657.0	0	1	1
658.0	0	1	1
663.0	0	1	1
666.0	0	1	1
686.0	0	1	1
687.0	0	1	1
688.0	0	1	1
689.0	0	1	1
693.0	0	1	1
701.0	0	1	1
703.0	0	1	1
719.0	0	1	1
727.0	0	1	1
739.0	0	1	1
781.0	0	2	2
787.0	0	1	1
800.0	0	1	1
802.0	0	1	1
810.0	0	1	1
814.0	0	1	1
830.0	0	1	1
836.0	0	1	1
844.0	0	1	1
852.0	0	1	1
860.0	0	1	1
882.0	0	1	1
935.0	0	1	1
988.0	0	1	1
1010.0	0	1	1
1030.0	0	1	1
1047.0	0	1	1
1121.0	0	1	1
1132.0	0	1	1
1161.0	0	1	1
1202.0	0	1	1
1287.0	0	1	1