## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/HR_Dub_Her_1_2019-09-19/HR_Dub_Her_1_2019-09-19.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/HR_Dub_Her_1_2019-09-19/HR_Dub_Her_1_2019-09-19.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/HR_Dub_Her_1_2019-09-19/HR_Dub_Her_1_2019-09-19.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 Feb 16 09:25:39 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	4978872	54123954	0	0	3320196	33879062	370120	0.627752	22223423

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.001614	6338411	0	6377572
2.0	1.089314	4228600	353683	4249410
3.0	1.096993	2925296	6766	2929689
4.0	1.097665	1922621	181	1914963
5.0	1.097724	1211459	32	1200543
6.0	1.097729	740693	14	728523
7.0	1.09773	444708	8	434500
8.0	1.09773	261853	9	254142
9.0	1.09773	152076	7	146975
10.0	1.09773	87296	7	83533
11.0	1.09773	50193	4	47508
12.0	1.09773	28009	2	26407
13.0	1.09773	15835	4	14819
14.0	1.09773	8822	3	8222
15.0	1.09773	5054	5	4645
16.0	1.09773	2954	2	2751
17.0	1.09773	1763	2	1686
18.0	1.09773	1096	0	1020
19.0	1.09773	791	1	718
20.0	1.09773	553	0	520
21.0	1.09773	424	1	389
22.0	1.09773	328	0	332
23.0	1.09773	271	2	264
24.0	1.09773	259	1	256
25.0	1.09773	191	0	189
26.0	1.09773	165	2	154
27.0	1.09773	137	0	141
28.0	1.09773	146	0	148
29.0	1.09773	152	0	154
30.0	1.09773	121	0	117
31.0	1.09773	135	1	134
32.0	1.09773	103	0	104
33.0	1.09773	100	0	100
34.0	1.09773	87	0	87
35.0	1.09773	100	1	92
36.0	1.09773	89	0	93
37.0	1.09773	84	1	88
38.0	1.09773	78	1	77
39.0	1.09773	68	0	63
40.0	1.09773	75	1	73
41.0	1.09773	61	0	62
42.0	1.09773	70	0	70
43.0	1.09773	60	0	65
44.0	1.09773	63	0	61
45.0	1.09773	50	0	46
46.0	1.09773	40	0	43
47.0	1.09773	46	0	48
48.0	1.09773	41	0	35
49.0	1.09773	40	0	42
50.0	1.09773	42	0	40
51.0	1.09773	48	0	50
52.0	1.09773	35	0	32
53.0	1.09773	25	0	27
54.0	1.09773	32	0	35
55.0	1.09773	37	0	36
56.0	1.09773	36	0	32
57.0	1.09773	30	0	32
58.0	1.09773	40	0	41
59.0	1.09773	32	0	30
60.0	1.09773	28	0	28
61.0	1.09773	39	0	38
62.0	1.09773	26	0	28
63.0	1.09773	34	0	33
64.0	1.09773	35	0	36
65.0	1.09773	15	0	12
66.0	1.09773	16	0	18
67.0	1.09773	25	0	24
68.0	1.09773	25	0	25
69.0	1.09773	24	0	27
70.0	1.09773	25	0	25
71.0	1.09773	18	0	19
72.0	1.09773	21	0	17
73.0	1.09773	22	0	23
74.0	1.09773	23	1	21
75.0	1.09773	17	0	19
76.0	1.09773	21	0	20
77.0	1.09773	22	0	20
78.0	1.09773	19	0	20
79.0	1.09773	19	0	19
80.0	1.09773	18	0	22
81.0	1.09773	22	0	18
82.0	1.09773	22	0	22
83.0	1.09773	14	0	14
84.0	1.09773	11	0	12
85.0	1.09773	18	0	16
86.0	1.09773	14	0	15
87.0	1.09773	7	0	7
88.0	1.09773	15	0	18
89.0	1.09773	23	0	21
90.0	1.09773	11	0	11
91.0	1.09773	11	0	10
92.0	1.09773	15	0	18
93.0	1.09773	18	0	17
94.0	1.09773	16	0	13
95.0	1.09773	10	0	12
96.0	1.09773	15	0	15
97.0	1.09773	13	0	12
98.0	1.09773	8	0	8
99.0	1.09773	5	0	7
100.0	1.09773	14	0	11
101.0	0	9	0	9
102.0	0	9	0	9
103.0	0	7	0	9
104.0	0	15	0	15
105.0	0	8	0	6
106.0	0	12	0	14
107.0	0	15	0	14
108.0	0	9	0	9
109.0	0	7	0	7
110.0	0	9	0	7
111.0	0	4	0	6
112.0	0	9	0	10
113.0	0	9	0	9
114.0	0	8	0	6
115.0	0	5	0	6
116.0	0	7	0	6
117.0	0	4	0	4
118.0	0	8	0	11
119.0	0	11	0	9
120.0	0	9	1	9
121.0	0	5	0	4
122.0	0	5	0	6
123.0	0	7	0	7
124.0	0	6	0	4
125.0	0	4	0	6
126.0	0	3	0	2
127.0	0	7	0	8
128.0	0	8	0	12
129.0	0	11	0	6
130.0	0	9	0	9
131.0	0	3	0	2
132.0	0	2	0	5
133.0	0	7	0	4
134.0	0	6	0	7
135.0	0	6	0	7
136.0	0	7	0	6
137.0	0	9	0	11
138.0	0	11	0	10
139.0	0	7	0	9
140.0	0	12	0	8
141.0	0	4	0	4
142.0	0	2	0	4
143.0	0	7	0	8
144.0	0	9	0	6
145.0	0	4	0	4
146.0	0	4	0	4
147.0	0	5	0	6
148.0	0	2	0	5
149.0	0	9	0	5
150.0	0	5	0	5
151.0	0	1	0	1
152.0	0	2	0	4
153.0	0	9	0	7
154.0	0	2	0	3
155.0	0	4	0	3
156.0	0	6	0	9
157.0	0	3	0	2
158.0	0	1	0	0
159.0	0	4	0	3
160.0	0	6	0	7
161.0	0	1	0	1
162.0	0	4	0	3
164.0	0	2	0	4
165.0	0	1	0	0
166.0	0	8	0	7
167.0	0	3	0	3
168.0	0	8	0	10
169.0	0	2	0	3
170.0	0	3	0	1
171.0	0	2	0	3
172.0	0	3	0	2
173.0	0	2	0	1
174.0	0	3	0	3
175.0	0	6	0	7
176.0	0	3	0	3
177.0	0	2	0	1
178.0	0	3	0	3
179.0	0	0	0	1
180.0	0	1	0	2
181.0	0	5	0	4
182.0	0	6	0	6
183.0	0	2	0	3
184.0	0	3	0	1
185.0	0	1	0	1
186.0	0	2	0	4
187.0	0	4	0	6
188.0	0	7	0	4
189.0	0	1	0	0
190.0	0	1	0	3
191.0	0	4	0	2
192.0	0	0	0	1
193.0	0	6	0	6
194.0	0	2	0	2
195.0	0	7	0	7
196.0	0	3	0	4
197.0	0	5	0	4
198.0	0	2	0	3
199.0	0	5	0	4
200.0	0	2	0	2
201.0	0	1	0	0
202.0	0	1	0	3
203.0	0	3	0	2
204.0	0	3	0	4
205.0	0	2	0	1
206.0	0	2	0	4
207.0	0	4	0	3
208.0	0	3	0	3
209.0	0	2	0	1
210.0	0	3	0	4
211.0	0	2	0	1
212.0	0	3	0	2
213.0	0	2	0	2
214.0	0	2	0	2
215.0	0	2	0	3
216.0	0	5	0	5
218.0	0	3	0	3
219.0	0	1	0	2
220.0	0	4	0	2
221.0	0	2	0	4
222.0	0	2	0	2
223.0	0	6	0	4
224.0	0	2	0	2
225.0	0	1	0	2
226.0	0	3	0	2
227.0	0	0	0	1
228.0	0	2	0	2
229.0	0	2	0	1
230.0	0	3	0	4
231.0	0	1	0	2
232.0	0	3	0	4
233.0	0	2	0	1
234.0	0	4	0	2
235.0	0	1	0	1
236.0	0	0	0	1
237.0	0	2	0	2
238.0	0	3	0	2
239.0	0	1	0	1
240.0	0	3	0	4
241.0	0	3	0	3
242.0	0	2	0	1
243.0	0	1	0	1
244.0	0	1	0	5
245.0	0	6	0	3
246.0	0	2	0	3
247.0	0	2	0	1
248.0	0	4	0	4
249.0	0	3	0	5
250.0	0	4	0	1
251.0	0	0	0	1
252.0	0	2	1	3
253.0	0	2	0	2
254.0	0	3	0	2
255.0	0	1	0	1
256.0	0	5	0	5
257.0	0	2	0	1
258.0	0	2	0	2
259.0	0	0	0	1
261.0	0	1	0	0
263.0	0	1	0	1
265.0	0	0	0	1
266.0	0	2	0	1
267.0	0	2	0	3
268.0	0	1	0	2
269.0	0	1	0	1
270.0	0	4	0	3
271.0	0	1	0	0
272.0	0	0	0	1
273.0	0	2	0	2
274.0	0	1	0	1
275.0	0	4	0	3
276.0	0	2	0	3
277.0	0	1	0	2
278.0	0	2	0	1
279.0	0	2	0	2
280.0	0	4	0	4
281.0	0	1	0	0
282.0	0	1	0	3
283.0	0	3	0	1
284.0	0	1	0	1
285.0	0	0	0	1
286.0	0	2	0	3
287.0	0	2	0	0
288.0	0	1	0	2
289.0	0	2	0	2
290.0	0	5	0	5
291.0	0	1	0	1
292.0	0	0	0	1
293.0	0	2	0	1
294.0	0	2	0	1
296.0	0	1	0	1
297.0	0	0	0	1
298.0	0	1	0	1
300.0	0	3	0	3
301.0	0	1	0	1
302.0	0	1	0	0
303.0	0	2	0	2
304.0	0	1	0	1
305.0	0	1	0	1
307.0	0	0	0	2
308.0	0	2	0	1
309.0	0	0	0	2
310.0	0	3	0	2
311.0	0	2	0	1
312.0	0	3	0	4
313.0	0	2	0	2
314.0	0	3	0	1
315.0	0	2	0	3
316.0	0	2	0	1
317.0	0	1	0	3
318.0	0	1	0	0
319.0	0	1	0	2
320.0	0	4	0	3
321.0	0	1	0	1
322.0	0	2	0	1
323.0	0	2	0	2
325.0	0	0	0	1
326.0	0	1	0	1
327.0	0	1	0	1
328.0	0	2	0	2
330.0	0	0	0	1
331.0	0	4	0	2
334.0	0	2	0	2
335.0	0	0	0	2
336.0	0	2	0	1
337.0	0	3	0	2
340.0	0	3	0	3
341.0	0	2	0	2
342.0	0	1	0	2
343.0	0	1	0	2
344.0	0	2	0	0
345.0	0	1	0	1
347.0	0	1	0	3
348.0	0	1	0	1
349.0	0	2	0	2
350.0	0	1	0	1
351.0	0	3	0	2
352.0	0	4	0	3
354.0	0	0	0	1
355.0	0	1	0	1
356.0	0	2	0	2
357.0	0	2	0	1
359.0	0	0	0	1
360.0	0	2	0	1
361.0	0	1	0	1
362.0	0	1	0	1
363.0	0	0	0	1
364.0	0	1	0	0
366.0	0	1	0	1
367.0	0	2	0	2
369.0	0	0	0	1
370.0	0	1	0	2
371.0	0	2	0	1
373.0	0	2	0	1
375.0	0	1	0	3
376.0	0	1	0	1
377.0	0	1	0	0
378.0	0	2	0	1
379.0	0	1	0	1
381.0	0	2	0	2
382.0	0	1	0	2
383.0	0	1	0	0
386.0	0	0	0	1
387.0	0	1	0	1
388.0	0	0	0	1
389.0	0	1	0	3
390.0	0	2	0	1
391.0	0	3	0	2
392.0	0	2	0	2
393.0	0	2	0	1
395.0	0	1	0	0
396.0	0	0	0	1
397.0	0	1	0	0
398.0	0	1	0	1
399.0	0	1	0	1
400.0	0	1	0	2
401.0	0	2	0	3
402.0	0	2	0	0
405.0	0	0	0	1
406.0	0	2	0	2
408.0	0	1	0	0
409.0	0	1	0	2
410.0	0	1	0	0
411.0	0	0	0	2
412.0	0	2	0	1
413.0	0	0	0	1
414.0	0	4	0	2
415.0	0	2	0	2
417.0	0	1	0	1
418.0	0	2	0	2
419.0	0	1	0	1
422.0	0	1	0	1
423.0	0	1	0	1
424.0	0	1	0	1
426.0	0	0	0	1
428.0	0	2	0	1
429.0	0	1	0	1
434.0	0	2	0	2
439.0	0	0	0	1
441.0	0	1	0	2
442.0	0	2	0	4
443.0	0	3	0	1
444.0	0	2	0	1
445.0	0	2	0	1
448.0	0	0	0	1
449.0	0	2	0	1
451.0	0	0	0	1
453.0	0	1	0	0
456.0	0	0	0	1
459.0	0	1	0	0
460.0	0	2	0	3
462.0	0	3	0	3
465.0	0	1	0	0
466.0	0	0	0	1
467.0	0	3	0	3
469.0	0	2	0	2
471.0	0	1	0	1
472.0	0	1	0	1
473.0	0	1	0	1
474.0	0	1	0	1
475.0	0	0	0	1
476.0	0	3	0	3
477.0	0	1	0	0
478.0	0	1	0	4
479.0	0	1	0	0
480.0	0	3	0	2
481.0	0	1	0	0
482.0	0	0	0	1
484.0	0	2	0	0
485.0	0	0	0	1
486.0	0	1	0	1
488.0	0	1	0	0
489.0	0	1	0	1
490.0	0	0	0	2
491.0	0	1	0	0
492.0	0	1	0	0
497.0	0	2	0	2
507.0	0	0	0	1
509.0	0	1	0	0
511.0	0	1	0	2
514.0	0	1	0	0
516.0	0	1	0	3
517.0	0	1	0	0
518.0	0	2	0	1
521.0	0	1	0	1
522.0	0	1	0	1
524.0	0	1	0	1
526.0	0	2	0	2
529.0	0	0	0	1
532.0	0	1	0	0
534.0	0	0	0	1
535.0	0	1	0	1
536.0	0	1	0	1
537.0	0	2	0	1
544.0	0	0	0	1
548.0	0	1	0	0
549.0	0	1	0	1
552.0	0	0	0	1
553.0	0	1	0	0
554.0	0	1	0	2
555.0	0	1	0	0
556.0	0	0	0	1
557.0	0	2	0	1
558.0	0	0	0	1
559.0	0	1	0	1
560.0	0	0	0	1
562.0	0	3	0	2
563.0	0	2	0	1
564.0	0	1	0	1
569.0	0	2	0	2
572.0	0	2	0	2
577.0	0	0	0	1
581.0	0	1	0	0
582.0	0	1	0	1
583.0	0	1	0	1
584.0	0	0	0	1
587.0	0	2	0	1
589.0	0	0	0	1
590.0	0	1	0	1
591.0	0	0	0	1
594.0	0	1	0	0
595.0	0	1	0	0
596.0	0	1	0	2
598.0	0	1	0	1
600.0	0	1	0	0
601.0	0	1	0	1
603.0	0	2	0	2
605.0	0	1	0	1
609.0	0	1	0	1
612.0	0	1	0	1
616.0	0	1	0	1
622.0	0	1	0	1
624.0	0	0	0	1
625.0	0	1	0	0
627.0	0	0	0	1
629.0	0	0	0	1
630.0	0	1	0	0
631.0	0	1	0	0
633.0	0	2	0	2
636.0	0	1	0	2
642.0	0	1	0	0
643.0	0	1	0	1
646.0	0	1	0	2
647.0	0	0	0	1
648.0	0	2	0	0
653.0	0	0	0	1
655.0	0	1	0	1
656.0	0	1	0	0
657.0	0	0	0	1
658.0	0	0	0	1
661.0	0	2	0	0
662.0	0	1	0	1
664.0	0	1	0	1
665.0	0	1	0	1
666.0	0	1	0	1
667.0	0	1	0	2
671.0	0	1	0	0
675.0	0	0	0	1
678.0	0	1	0	0
681.0	0	0	0	1
683.0	0	1	0	2
685.0	0	1	0	0
686.0	0	1	0	1
688.0	0	2	0	1
689.0	0	1	0	1
693.0	0	1	0	1
698.0	0	1	0	1
703.0	0	1	0	1
707.0	0	1	0	1
710.0	0	0	0	1
712.0	0	1	0	1
715.0	0	1	0	0
716.0	0	1	0	1
720.0	0	1	0	1
727.0	0	0	0	1
728.0	0	1	0	0
729.0	0	1	0	1
731.0	0	1	0	1
744.0	0	1	0	1
746.0	0	1	0	1
747.0	0	0	0	1
749.0	0	2	0	1
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