## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-07-26/UA_Kha_Kha_1_2014-07-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-07-26/UA_Kha_Kha_1_2014-07-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Kha_Kha_1_2014-07-26/UA_Kha_Kha_1_2014-07-26.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 09:07:56 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	4779486	24431974	0	0	1186069	886702	0	0.055169	328402142

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22419524	22419524
2.0	1.928304	553216	553216
3.0	2.790051	12970	12970
4.0	3.590014	1262	1262
5.0	4.332623	638	638
6.0	5.021989	463	463
7.0	5.66193	319	319
8.0	6.25599	262	262
9.0	6.807458	170	170
10.0	7.319387	183	183
11.0	7.794613	125	125
12.0	8.235767	112	112
13.0	8.645291	126	126
14.0	9.025454	105	105
15.0	9.378361	90	90
16.0	9.705966	81	81
17.0	10.010083	76	76
18.0	10.292395	67	67
19.0	10.554467	59	59
20.0	10.797749	61	61
21.0	11.023588	59	59
22.0	11.233236	43	43
23.0	11.427853	47	47
24.0	11.608516	45	45
25.0	11.776227	48	48
26.0	11.931913	40	40
27.0	12.076437	46	46
28.0	12.210599	56	56
29.0	12.335142	45	45
30.0	12.450756	37	37
31.0	12.558081	36	36
32.0	12.657711	34	34
33.0	12.750198	38	38
34.0	12.836054	32	32
35.0	12.915754	33	33
36.0	12.98974	34	34
37.0	13.058422	29	29
38.0	13.122179	30	30
39.0	13.181365	24	24
40.0	13.236308	18	18
41.0	13.287312	12	12
42.0	13.334658	21	21
43.0	13.378611	20	20
44.0	13.419411	24	24
45.0	13.457287	13	13
46.0	13.492447	14	14
47.0	13.525087	20	20
48.0	13.555386	22	22
49.0	13.583512	22	22
50.0	13.609623	19	19
51.0	13.633861	24	24
52.0	13.656361	18	18
53.0	13.677248	18	18
54.0	13.696638	7	7
55.0	13.714638	12	12
56.0	13.731347	8	8
57.0	13.746858	12	12
58.0	13.761257	19	19
59.0	13.774623	7	7
60.0	13.787031	11	11
61.0	13.79855	12	12
62.0	13.809243	9	9
63.0	13.819169	19	19
64.0	13.828383	15	15
65.0	13.836937	12	12
66.0	13.844878	14	14
67.0	13.852249	15	15
68.0	13.859092	13	13
69.0	13.865444	11	11
70.0	13.871341	13	13
71.0	13.876815	15	15
72.0	13.881896	12	12
73.0	13.886613	9	9
74.0	13.890992	6	6
75.0	13.895057	11	11
76.0	13.898831	7	7
77.0	13.902334	4	4
78.0	13.905586	9	9
79.0	13.908604	8	8
80.0	13.911406	8	8
81.0	13.914008	7	7
82.0	13.916423	7	7
83.0	13.918664	6	6
84.0	13.920745	9	9
85.0	13.922677	12	12
86.0	13.92447	14	14
87.0	13.926135	6	6
88.0	13.927681	7	7
89.0	13.929115	9	9
90.0	13.930447	3	3
91.0	13.931683	11	11
92.0	13.932831	13	13
93.0	13.933896	6	6
94.0	13.934885	8	8
95.0	13.935803	6	6
96.0	13.936655	6	6
97.0	13.937446	7	7
98.0	13.938181	8	8
99.0	13.938862	8	8
100.0	13.939495	2	2
101.0	0	5	5
102.0	0	3	3
103.0	0	4	4
104.0	0	14	14
105.0	0	9	9
106.0	0	8	8
107.0	0	4	4
108.0	0	7	7
109.0	0	3	3
110.0	0	8	8
111.0	0	4	4
112.0	0	8	8
113.0	0	6	6
114.0	0	4	4
115.0	0	4	4
116.0	0	8	8
117.0	0	4	4
118.0	0	5	5
119.0	0	5	5
120.0	0	5	5
121.0	0	3	3
122.0	0	6	6
123.0	0	8	8
124.0	0	3	3
125.0	0	5	5
126.0	0	1	1
127.0	0	3	3
128.0	0	5	5
129.0	0	5	5
130.0	0	1	1
131.0	0	3	3
132.0	0	5	5
133.0	0	3	3
134.0	0	2	2
135.0	0	7	7
136.0	0	6	6
137.0	0	3	3
138.0	0	3	3
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	4	4
146.0	0	1	1
147.0	0	5	5
148.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	4	4
152.0	0	6	6
153.0	0	1	1
154.0	0	2	2
155.0	0	4	4
156.0	0	1	1
158.0	0	3	3
159.0	0	2	2
160.0	0	3	3
161.0	0	4	4
162.0	0	3	3
163.0	0	1	1
164.0	0	5	5
165.0	0	2	2
166.0	0	1	1
167.0	0	3	3
168.0	0	4	4
169.0	0	3	3
170.0	0	4	4
171.0	0	2	2
172.0	0	4	4
173.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	5	5
177.0	0	2	2
178.0	0	2	2
179.0	0	1	1
180.0	0	4	4
181.0	0	2	2
183.0	0	3	3
184.0	0	3	3
185.0	0	1	1
186.0	0	5	5
187.0	0	1	1
188.0	0	3	3
189.0	0	3	3
190.0	0	2	2
191.0	0	1	1
192.0	0	3	3
193.0	0	4	4
194.0	0	3	3
195.0	0	2	2
196.0	0	3	3
197.0	0	1	1
198.0	0	4	4
199.0	0	2	2
200.0	0	5	5
201.0	0	5	5
203.0	0	5	5
204.0	0	1	1
205.0	0	2	2
206.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	5	5
214.0	0	1	1
215.0	0	2	2
216.0	0	3	3
217.0	0	2	2
218.0	0	1	1
219.0	0	3	3
220.0	0	3	3
221.0	0	5	5
222.0	0	2	2
224.0	0	3	3
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
228.0	0	2	2
229.0	0	3	3
230.0	0	1	1
232.0	0	2	2
234.0	0	2	2
235.0	0	1	1
236.0	0	2	2
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	2	2
243.0	0	1	1
244.0	0	1	1
245.0	0	2	2
246.0	0	3	3
248.0	0	1	1
249.0	0	1	1
250.0	0	2	2
251.0	0	1	1
253.0	0	3	3
255.0	0	2	2
256.0	0	2	2
257.0	0	5	5
258.0	0	1	1
259.0	0	2	2
260.0	0	5	5
261.0	0	1	1
262.0	0	2	2
263.0	0	2	2
265.0	0	1	1
266.0	0	1	1
268.0	0	2	2
270.0	0	3	3
271.0	0	2	2
272.0	0	1	1
273.0	0	1	1
275.0	0	1	1
276.0	0	1	1
278.0	0	2	2
280.0	0	2	2
281.0	0	1	1
282.0	0	1	1
284.0	0	1	1
285.0	0	4	4
287.0	0	1	1
288.0	0	2	2
290.0	0	1	1
291.0	0	1	1
292.0	0	2	2
293.0	0	1	1
294.0	0	2	2
296.0	0	2	2
297.0	0	1	1
298.0	0	1	1
300.0	0	2	2
302.0	0	1	1
303.0	0	2	2
304.0	0	1	1
306.0	0	1	1
307.0	0	1	1
308.0	0	3	3
310.0	0	3	3
311.0	0	1	1
318.0	0	2	2
319.0	0	2	2
320.0	0	2	2
322.0	0	1	1
323.0	0	1	1
324.0	0	1	1
327.0	0	2	2
328.0	0	2	2
329.0	0	2	2
330.0	0	1	1
331.0	0	4	4
333.0	0	1	1
335.0	0	1	1
336.0	0	2	2
337.0	0	2	2
338.0	0	2	2
340.0	0	1	1
344.0	0	1	1
347.0	0	2	2
348.0	0	2	2
351.0	0	1	1
353.0	0	3	3
354.0	0	1	1
356.0	0	1	1
358.0	0	1	1
360.0	0	1	1
366.0	0	5	5
367.0	0	1	1
368.0	0	1	1
369.0	0	1	1
370.0	0	1	1
374.0	0	3	3
377.0	0	1	1
381.0	0	2	2
383.0	0	2	2
384.0	0	1	1
388.0	0	1	1
391.0	0	1	1
394.0	0	1	1
398.0	0	1	1
400.0	0	1	1
403.0	0	1	1
405.0	0	1	1
406.0	0	1	1
410.0	0	1	1
414.0	0	1	1
422.0	0	1	1
423.0	0	1	1
424.0	0	2	2
425.0	0	2	2
427.0	0	1	1
428.0	0	1	1
429.0	0	1	1
431.0	0	1	1
432.0	0	1	1
446.0	0	1	1
447.0	0	1	1
448.0	0	1	1
450.0	0	1	1
452.0	0	1	1
453.0	0	1	1
456.0	0	2	2
457.0	0	1	1
461.0	0	2	2
465.0	0	1	1
469.0	0	3	3
474.0	0	1	1
479.0	0	1	1
483.0	0	2	2
484.0	0	1	1
485.0	0	2	2
489.0	0	2	2
494.0	0	1	1
495.0	0	2	2
499.0	0	1	1
500.0	0	3	3
502.0	0	1	1
511.0	0	1	1
519.0	0	1	1
522.0	0	1	1
524.0	0	3	3
529.0	0	1	1
530.0	0	1	1
532.0	0	1	1
533.0	0	1	1
535.0	0	1	1
537.0	0	1	1
538.0	0	1	1
540.0	0	1	1
542.0	0	1	1
550.0	0	1	1
551.0	0	1	1
561.0	0	1	1
562.0	0	1	1
567.0	0	1	1
571.0	0	1	1
572.0	0	1	1
577.0	0	1	1
580.0	0	1	1
589.0	0	1	1
591.0	0	1	1
600.0	0	1	1
601.0	0	1	1
603.0	0	1	1
604.0	0	1	1
607.0	0	1	1
608.0	0	1	1
610.0	0	1	1
616.0	0	1	1
617.0	0	1	1
621.0	0	1	1
627.0	0	1	1
632.0	0	1	1
636.0	0	1	1
640.0	0	2	2
641.0	0	1	1
652.0	0	1	1
662.0	0	1	1
670.0	0	2	2
671.0	0	1	1
674.0	0	1	1
691.0	0	1	1
697.0	0	1	1
698.0	0	1	1
704.0	0	1	1
718.0	0	1	1
721.0	0	1	1
723.0	0	1	1
731.0	0	1	1
732.0	0	1	1
735.0	0	1	1
757.0	0	1	1
764.0	0	1	1
775.0	0	1	1
781.0	0	1	1
794.0	0	1	1
807.0	0	1	1
812.0	0	1	1
819.0	0	1	1
823.0	0	1	1
826.0	0	1	1
834.0	0	1	1
840.0	0	1	1
855.0	0	1	1
865.0	0	1	1
894.0	0	1	1
912.0	0	1	1
917.0	0	1	1
935.0	0	1	1
941.0	0	1	1
1007.0	0	1	1
1009.0	0	1	1
1029.0	0	1	1
1044.0	0	1	1
1047.0	0	1	1
1060.0	0	1	1
1067.0	0	1	1
1077.0	0	1	1
1084.0	0	1	1
1092.0	0	1	1
1131.0	0	1	1
1144.0	0	1	1
1159.0	0	1	1
1179.0	0	1	1
1212.0	0	1	1
1261.0	0	1	1
1332.0	0	1	1
1547.0	0	1	1
1581.0	0	1	1
1773.0	0	1	1
1865.0	0	1	1