## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-07-24/CH_Vau_Cha_1_2014-07-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-07-24/CH_Vau_Cha_1_2014-07-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CH_Vau_Cha_1_2014-07-24/CH_Vau_Cha_1_2014-07-24.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 08:44:19 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	24957399	9407189	0	0	4776693	507641	0	0.132322	83998403

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8382327	8382327
2.0	1.894051	183061	183061
3.0	2.693378	5153	5153
4.0	3.408017	1125	1125
5.0	4.046941	603	603
6.0	4.618172	420	420
7.0	5.128881	313	313
8.0	5.585481	243	243
9.0	5.993705	187	187
10.0	6.358678	171	171
11.0	6.684982	147	147
12.0	6.976715	129	129
13.0	7.237539	109	109
14.0	7.470729	106	106
15.0	7.679212	91	91
16.0	7.865607	91	91
17.0	8.032254	65	65
18.0	8.181245	81	81
19.0	8.31445	64	64
20.0	8.433542	55	55
21.0	8.540017	58	58
22.0	8.63521	72	72
23.0	8.720318	46	46
24.0	8.796409	49	49
25.0	8.864438	49	49
26.0	8.92526	37	37
27.0	8.979637	45	45
28.0	9.028254	51	51
29.0	9.071719	44	44
30.0	9.110579	49	49
31.0	9.145322	37	37
32.0	9.176385	46	46
33.0	9.204156	36	36
34.0	9.228984	33	33
35.0	9.251183	30	30
36.0	9.271029	27	27
37.0	9.288773	40	40
38.0	9.304636	32	32
39.0	9.318819	33	33
40.0	9.3315	26	26
41.0	9.342836	30	30
42.0	9.352972	20	20
43.0	9.362034	24	24
44.0	9.370136	31	31
45.0	9.377379	27	27
46.0	9.383855	21	21
47.0	9.389645	20	20
48.0	9.394821	8	8
49.0	9.399449	21	21
50.0	9.403587	18	18
51.0	9.407286	14	14
52.0	9.410593	14	14
53.0	9.41355	19	19
54.0	9.416194	20	20
55.0	9.418557	12	12
56.0	9.420671	14	14
57.0	9.42256	12	12
58.0	9.424249	23	23
59.0	9.425759	23	23
60.0	9.427109	16	16
61.0	9.428316	18	18
62.0	9.429395	16	16
63.0	9.43036	11	11
64.0	9.431223	13	13
65.0	9.431994	13	13
66.0	9.432684	17	17
67.0	9.4333	11	11
68.0	9.433851	13	13
69.0	9.434344	12	12
70.0	9.434785	13	13
71.0	9.435178	8	8
72.0	9.435531	8	8
73.0	9.435845	16	16
74.0	9.436127	14	14
75.0	9.436379	5	5
76.0	9.436604	10	10
77.0	9.436805	12	12
78.0	9.436985	13	13
79.0	9.437145	7	7
80.0	9.437289	13	13
81.0	9.437418	9	9
82.0	9.437533	11	11
83.0	9.437635	11	11
84.0	9.437727	12	12
85.0	9.437809	8	8
86.0	9.437883	9	9
87.0	9.437948	7	7
88.0	9.438007	4	4
89.0	9.438059	12	12
90.0	9.438106	4	4
91.0	9.438148	10	10
92.0	9.438186	6	6
93.0	9.438219	5	5
94.0	9.438249	11	11
95.0	9.438276	8	8
96.0	9.4383	8	8
97.0	9.438321	8	8
98.0	9.438341	10	10
99.0	9.438358	9	9
100.0	9.438373	8	8
101.0	0	6	6
102.0	0	2	2
103.0	0	7	7
104.0	0	11	11
105.0	0	4	4
106.0	0	5	5
107.0	0	9	9
108.0	0	5	5
109.0	0	5	5
110.0	0	7	7
111.0	0	9	9
112.0	0	6	6
113.0	0	5	5
114.0	0	4	4
115.0	0	5	5
116.0	0	5	5
117.0	0	3	3
118.0	0	3	3
119.0	0	6	6
120.0	0	4	4
121.0	0	8	8
122.0	0	3	3
123.0	0	7	7
124.0	0	6	6
125.0	0	6	6
126.0	0	7	7
127.0	0	5	5
128.0	0	3	3
129.0	0	5	5
130.0	0	6	6
131.0	0	3	3
132.0	0	8	8
133.0	0	3	3
134.0	0	5	5
135.0	0	1	1
136.0	0	1	1
137.0	0	3	3
138.0	0	1	1
139.0	0	1	1
140.0	0	3	3
141.0	0	6	6
142.0	0	5	5
143.0	0	5	5
144.0	0	3	3
145.0	0	3	3
146.0	0	4	4
147.0	0	3	3
148.0	0	3	3
149.0	0	5	5
150.0	0	4	4
151.0	0	2	2
152.0	0	3	3
153.0	0	1	1
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	3	3
160.0	0	4	4
161.0	0	3	3
162.0	0	4	4
163.0	0	1	1
164.0	0	3	3
165.0	0	1	1
166.0	0	6	6
167.0	0	5	5
168.0	0	4	4
169.0	0	5	5
170.0	0	5	5
171.0	0	5	5
172.0	0	1	1
173.0	0	1	1
174.0	0	3	3
175.0	0	6	6
176.0	0	4	4
177.0	0	2	2
178.0	0	3	3
179.0	0	5	5
180.0	0	1	1
181.0	0	4	4
182.0	0	3	3
183.0	0	3	3
184.0	0	3	3
185.0	0	5	5
188.0	0	6	6
189.0	0	1	1
190.0	0	2	2
191.0	0	2	2
192.0	0	3	3
193.0	0	2	2
194.0	0	1	1
195.0	0	1	1
196.0	0	3	3
197.0	0	3	3
198.0	0	2	2
199.0	0	1	1
200.0	0	5	5
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	3	3
206.0	0	2	2
207.0	0	2	2
208.0	0	2	2
209.0	0	4	4
210.0	0	2	2
211.0	0	2	2
212.0	0	2	2
213.0	0	2	2
214.0	0	2	2
215.0	0	4	4
217.0	0	2	2
218.0	0	3	3
219.0	0	1	1
220.0	0	1	1
221.0	0	6	6
222.0	0	2	2
224.0	0	2	2
226.0	0	4	4
228.0	0	2	2
229.0	0	1	1
230.0	0	1	1
231.0	0	2	2
232.0	0	2	2
233.0	0	2	2
234.0	0	2	2
235.0	0	2	2
236.0	0	2	2
238.0	0	3	3
239.0	0	3	3
240.0	0	1	1
241.0	0	3	3
242.0	0	2	2
243.0	0	1	1
244.0	0	3	3
245.0	0	1	1
246.0	0	3	3
247.0	0	2	2
248.0	0	1	1
249.0	0	3	3
252.0	0	2	2
253.0	0	2	2
254.0	0	1	1
255.0	0	3	3
257.0	0	1	1
258.0	0	2	2
260.0	0	1	1
261.0	0	1	1
262.0	0	2	2
264.0	0	1	1
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	2	2
269.0	0	4	4
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
275.0	0	1	1
277.0	0	2	2
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
283.0	0	2	2
285.0	0	1	1
286.0	0	1	1
287.0	0	2	2
288.0	0	2	2
289.0	0	1	1
291.0	0	1	1
292.0	0	2	2
293.0	0	1	1
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
304.0	0	2	2
307.0	0	1	1
308.0	0	3	3
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
317.0	0	2	2
321.0	0	2	2
322.0	0	1	1
323.0	0	1	1
324.0	0	2	2
325.0	0	1	1
328.0	0	2	2
329.0	0	2	2
331.0	0	1	1
333.0	0	1	1
335.0	0	1	1
339.0	0	1	1
341.0	0	1	1
342.0	0	1	1
346.0	0	2	2
348.0	0	1	1
349.0	0	1	1
350.0	0	1	1
353.0	0	1	1
354.0	0	1	1
355.0	0	1	1
357.0	0	1	1
358.0	0	1	1
360.0	0	3	3
361.0	0	1	1
363.0	0	1	1
365.0	0	1	1
370.0	0	1	1
371.0	0	2	2
372.0	0	1	1
373.0	0	1	1
374.0	0	2	2
378.0	0	1	1
387.0	0	1	1
388.0	0	2	2
389.0	0	1	1
390.0	0	3	3
392.0	0	3	3
396.0	0	2	2
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
403.0	0	3	3
405.0	0	2	2
410.0	0	2	2
412.0	0	2	2
413.0	0	1	1
415.0	0	1	1
418.0	0	1	1
420.0	0	1	1
421.0	0	2	2
422.0	0	1	1
425.0	0	1	1
426.0	0	1	1
427.0	0	1	1
431.0	0	1	1
433.0	0	1	1
436.0	0	1	1
437.0	0	1	1
438.0	0	1	1
440.0	0	1	1
442.0	0	1	1
444.0	0	1	1
447.0	0	1	1
449.0	0	1	1
451.0	0	1	1
455.0	0	1	1
456.0	0	1	1
458.0	0	1	1
459.0	0	2	2
460.0	0	1	1
461.0	0	1	1
469.0	0	1	1
470.0	0	1	1
471.0	0	1	1
472.0	0	1	1
474.0	0	1	1
478.0	0	1	1
479.0	0	1	1
481.0	0	2	2
483.0	0	1	1
492.0	0	1	1
495.0	0	1	1
497.0	0	1	1
502.0	0	1	1
504.0	0	1	1
510.0	0	1	1
522.0	0	1	1
524.0	0	2	2
525.0	0	1	1
526.0	0	1	1
532.0	0	1	1
533.0	0	1	1
535.0	0	1	1
536.0	0	2	2
537.0	0	1	1
539.0	0	1	1
544.0	0	1	1
546.0	0	1	1
550.0	0	1	1
553.0	0	1	1
556.0	0	2	2
559.0	0	1	1
561.0	0	1	1
565.0	0	1	1
569.0	0	1	1
572.0	0	1	1
575.0	0	1	1
578.0	0	2	2
581.0	0	1	1
582.0	0	1	1
590.0	0	1	1
594.0	0	1	1
599.0	0	1	1
600.0	0	1	1
603.0	0	2	2
610.0	0	1	1
614.0	0	1	1
626.0	0	1	1
627.0	0	1	1
632.0	0	1	1
636.0	0	1	1
650.0	0	1	1
664.0	0	1	1
667.0	0	1	1
671.0	0	1	1
672.0	0	1	1
673.0	0	1	1
682.0	0	1	1
685.0	0	2	2
690.0	0	1	1
695.0	0	1	1
699.0	0	1	1
702.0	0	1	1
708.0	0	1	1
727.0	0	1	1
754.0	0	1	1
762.0	0	1	1
768.0	0	1	1
773.0	0	1	1
777.0	0	1	1
781.0	0	1	1
785.0	0	1	1
795.0	0	1	1
806.0	0	1	1
812.0	0	2	2
820.0	0	1	1
825.0	0	1	1
842.0	0	1	1
853.0	0	1	1
882.0	0	1	1
892.0	0	1	1
898.0	0	1	1
906.0	0	1	1
924.0	0	1	1
950.0	0	1	1
977.0	0	1	1
992.0	0	1	1
1013.0	0	1	1
1020.0	0	1	1
1021.0	0	1	1
1048.0	0	1	1
1060.0	0	1	1
1077.0	0	1	1
1078.0	0	1	1
1093.0	0	1	1
1109.0	0	1	1
1159.0	0	2	2
1172.0	0	1	1
1214.0	0	1	1
1278.0	0	1	1
1310.0	0	1	1
1433.0	0	1	1
1450.0	0	1	1
1531.0	0	1	1
1559.0	0	1	1
1988.0	0	1	1