## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/CY_Nic_Nic_1_2014-08-10/CY_Nic_Nic_1_2014-08-10.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/CY_Nic_Nic_1_2014-08-10/CY_Nic_Nic_1_2014-08-10.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/CY_Nic_Nic_1_2014-08-10/CY_Nic_Nic_1_2014-08-10.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 08:52:44 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	5923720	31889316	0	0	1753449	942557	0	0.052201	528768999

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	29688415	29688415
2.0	1.941474	710330	710330
3.0	2.827847	13785	13785
4.0	3.662344	1109	1109
5.0	4.448002	549	549
6.0	5.187678	337	337
7.0	5.884064	276	276
8.0	6.539693	224	224
9.0	7.15695	149	149
10.0	7.738082	150	150
11.0	8.285203	146	146
12.0	8.800303	127	127
13.0	9.285256	128	128
14.0	9.741827	112	112
15.0	10.171676	85	85
16.0	10.576368	118	118
17.0	10.957375	98	98
18.0	11.316083	86	86
19.0	11.653798	84	84
20.0	11.971747	88	88
21.0	12.271088	78	78
22.0	12.55291	60	60
23.0	12.818237	63	63
24.0	13.068037	54	54
25.0	13.303216	50	50
26.0	13.524631	50	50
27.0	13.733088	44	44
28.0	13.929345	57	57
29.0	14.114115	45	45
30.0	14.288072	34	34
31.0	14.451848	35	35
32.0	14.606038	42	42
33.0	14.751204	37	37
34.0	14.887875	38	38
35.0	15.016546	34	34
36.0	15.137687	48	48
37.0	15.251738	27	27
38.0	15.359114	30	30
39.0	15.460206	26	26
40.0	15.555381	25	25
41.0	15.644986	28	28
42.0	15.729347	24	24
43.0	15.808771	23	23
44.0	15.883546	24	24
45.0	15.953945	21	21
46.0	16.020223	12	12
47.0	16.082623	24	24
48.0	16.141371	18	18
49.0	16.19668	17	17
50.0	16.248752	15	15
51.0	16.297777	16	16
52.0	16.343933	14	14
53.0	16.387387	15	15
54.0	16.428298	15	15
55.0	16.466815	17	17
56.0	16.503077	19	19
57.0	16.537217	20	20
58.0	16.569359	25	25
59.0	16.59962	15	15
60.0	16.62811	9	9
61.0	16.654933	19	19
62.0	16.680185	5	5
63.0	16.70396	15	15
64.0	16.726343	9	9
65.0	16.747416	15	15
66.0	16.767256	16	16
67.0	16.785935	9	9
68.0	16.803521	10	10
69.0	16.820077	11	11
70.0	16.835664	11	11
71.0	16.85034	11	11
72.0	16.864156	5	5
73.0	16.877163	13	13
74.0	16.88941	3	3
75.0	16.900939	12	12
76.0	16.911794	9	9
77.0	16.922014	8	8
78.0	16.931635	4	4
79.0	16.940694	9	9
80.0	16.949222	5	5
81.0	16.957251	7	7
82.0	16.96481	3	3
83.0	16.971927	5	5
84.0	16.978627	3	3
85.0	16.984935	15	15
86.0	16.990874	13	13
87.0	16.996465	4	4
88.0	17.001729	8	8
89.0	17.006685	2	2
90.0	17.011351	3	3
91.0	17.015744	11	11
92.0	17.01988	4	4
93.0	17.023774	3	3
94.0	17.027439	5	5
95.0	17.030891	5	5
96.0	17.03414	6	6
97.0	17.037199	4	4
98.0	17.040079	10	10
99.0	17.042791	6	6
100.0	17.045344	6	6
101.0	0	5	5
102.0	0	4	4
103.0	0	7	7
104.0	0	1	1
105.0	0	4	4
106.0	0	7	7
107.0	0	7	7
108.0	0	4	4
109.0	0	1	1
111.0	0	4	4
112.0	0	4	4
113.0	0	5	5
114.0	0	4	4
115.0	0	2	2
116.0	0	6	6
117.0	0	6	6
118.0	0	5	5
119.0	0	6	6
120.0	0	5	5
121.0	0	4	4
122.0	0	2	2
123.0	0	4	4
124.0	0	1	1
125.0	0	1	1
126.0	0	5	5
127.0	0	5	5
128.0	0	9	9
129.0	0	1	1
130.0	0	1	1
131.0	0	2	2
132.0	0	1	1
133.0	0	7	7
135.0	0	2	2
136.0	0	2	2
137.0	0	5	5
138.0	0	4	4
139.0	0	1	1
140.0	0	4	4
141.0	0	4	4
142.0	0	3	3
143.0	0	1	1
144.0	0	1	1
145.0	0	4	4
146.0	0	2	2
147.0	0	2	2
148.0	0	2	2
149.0	0	3	3
151.0	0	7	7
154.0	0	1	1
155.0	0	5	5
156.0	0	2	2
157.0	0	2	2
158.0	0	6	6
159.0	0	2	2
160.0	0	7	7
161.0	0	3	3
162.0	0	3	3
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	3	3
169.0	0	3	3
171.0	0	1	1
173.0	0	2	2
174.0	0	3	3
175.0	0	3	3
176.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
183.0	0	3	3
185.0	0	2	2
186.0	0	2	2
188.0	0	2	2
190.0	0	1	1
191.0	0	1	1
193.0	0	2	2
195.0	0	1	1
196.0	0	4	4
197.0	0	1	1
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	2	2
204.0	0	1	1
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
211.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	3	3
217.0	0	2	2
218.0	0	1	1
221.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	3	3
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	2	2
233.0	0	2	2
235.0	0	2	2
236.0	0	1	1
238.0	0	2	2
240.0	0	3	3
241.0	0	1	1
242.0	0	1	1
243.0	0	2	2
244.0	0	1	1
248.0	0	2	2
250.0	0	2	2
253.0	0	1	1
254.0	0	4	4
257.0	0	1	1
259.0	0	3	3
261.0	0	2	2
263.0	0	1	1
264.0	0	2	2
266.0	0	2	2
270.0	0	2	2
271.0	0	4	4
272.0	0	1	1
273.0	0	2	2
275.0	0	1	1
276.0	0	3	3
277.0	0	1	1
278.0	0	1	1
281.0	0	1	1
283.0	0	1	1
284.0	0	1	1
286.0	0	1	1
290.0	0	1	1
293.0	0	1	1
295.0	0	2	2
297.0	0	1	1
299.0	0	1	1
300.0	0	1	1
302.0	0	3	3
304.0	0	2	2
305.0	0	2	2
306.0	0	1	1
311.0	0	1	1
312.0	0	2	2
313.0	0	2	2
314.0	0	1	1
317.0	0	1	1
321.0	0	2	2
323.0	0	1	1
325.0	0	1	1
326.0	0	1	1
327.0	0	1	1
331.0	0	1	1
335.0	0	2	2
337.0	0	2	2
338.0	0	2	2
344.0	0	1	1
347.0	0	1	1
351.0	0	1	1
354.0	0	1	1
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
361.0	0	1	1
366.0	0	1	1
369.0	0	2	2
371.0	0	2	2
373.0	0	1	1
376.0	0	3	3
384.0	0	2	2
387.0	0	1	1
394.0	0	1	1
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
402.0	0	1	1
403.0	0	1	1
406.0	0	1	1
408.0	0	1	1
409.0	0	1	1
414.0	0	2	2
415.0	0	1	1
422.0	0	1	1
425.0	0	2	2
427.0	0	1	1
438.0	0	1	1
445.0	0	1	1
446.0	0	1	1
448.0	0	1	1
449.0	0	1	1
458.0	0	1	1
460.0	0	1	1
466.0	0	2	2
467.0	0	1	1
470.0	0	2	2
479.0	0	1	1
480.0	0	1	1
501.0	0	1	1
508.0	0	1	1
514.0	0	1	1
515.0	0	1	1
516.0	0	1	1
535.0	0	1	1
542.0	0	1	1
544.0	0	1	1
547.0	0	1	1
550.0	0	1	1
567.0	0	1	1
582.0	0	1	1
589.0	0	1	1
602.0	0	1	1
604.0	0	1	1
608.0	0	1	1
632.0	0	1	1
635.0	0	1	1
647.0	0	1	1
650.0	0	1	1
658.0	0	1	1
671.0	0	1	1
674.0	0	1	1
685.0	0	1	1
696.0	0	1	1
713.0	0	1	1
734.0	0	1	1
745.0	0	1	1
749.0	0	1	1
753.0	0	1	1
839.0	0	1	1
859.0	0	1	1
881.0	0	1	1
930.0	0	1	1