## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-22/UA_Ode_Ode_1_2014-07-22.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-22/UA_Ode_Ode_1_2014-07-22.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2014-07-22/UA_Ode_Ode_1_2014-07-22.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 16:53:13 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	2968684	20082362	0	0	680916	684076	0	0.047505	288045280

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18517222	18517222
2.0	1.932655	440882	440882
3.0	2.802502	8725	8725
4.0	3.613768	943	943
5.0	4.370401	492	492
6.0	5.076078	342	342
7.0	5.734232	259	259
8.0	6.348062	178	178
9.0	6.920555	176	176
10.0	7.454493	133	133
11.0	7.952473	140	140
12.0	8.416917	127	127
13.0	8.850084	128	128
14.0	9.254079	128	128
15.0	9.630867	96	96
16.0	9.98228	100	100
17.0	10.310028	94	94
18.0	10.615703	84	84
19.0	10.900793	73	73
20.0	11.166684	86	86
21.0	11.414668	67	67
22.0	11.645953	67	67
23.0	11.861661	60	60
24.0	12.062842	49	49
25.0	12.250475	39	39
26.0	12.425472	51	51
27.0	12.588684	49	49
28.0	12.740905	49	49
29.0	12.882874	48	48
30.0	13.015282	37	37
31.0	13.138774	43	43
32.0	13.253949	46	46
33.0	13.361367	36	36
34.0	13.461552	26	26
35.0	13.554989	28	28
36.0	13.642134	25	25
37.0	13.723411	26	26
38.0	13.799213	25	25
39.0	13.869911	27	27
40.0	13.935848	30	30
41.0	13.997344	21	21
42.0	14.054699	23	23
43.0	14.108191	23	23
44.0	14.158081	21	21
45.0	14.204611	12	12
46.0	14.248008	16	16
47.0	14.288482	22	22
48.0	14.32623	27	27
49.0	14.361436	22	22
50.0	14.394272	15	15
51.0	14.424896	19	19
52.0	14.453457	18	18
53.0	14.480095	22	22
54.0	14.504939	15	15
55.0	14.528111	20	20
56.0	14.549721	14	14
57.0	14.569876	15	15
58.0	14.588674	18	18
59.0	14.606206	12	12
60.0	14.622558	13	13
61.0	14.637808	12	12
62.0	14.652031	13	13
63.0	14.665296	8	8
64.0	14.677668	10	10
65.0	14.689207	13	13
66.0	14.699968	9	9
67.0	14.710005	10	10
68.0	14.719366	11	11
69.0	14.728097	13	13
70.0	14.73624	13	13
71.0	14.743834	12	12
72.0	14.750917	11	11
73.0	14.757522	5	5
74.0	14.763683	10	10
75.0	14.769429	6	6
76.0	14.774789	8	8
77.0	14.779787	5	5
78.0	14.784448	4	4
79.0	14.788796	9	9
80.0	14.792851	12	12
81.0	14.796633	13	13
82.0	14.80016	4	4
83.0	14.803449	10	10
84.0	14.806517	7	7
85.0	14.809379	9	9
86.0	14.812048	7	7
87.0	14.814537	6	6
88.0	14.816858	5	5
89.0	14.819023	8	8
90.0	14.821042	6	6
91.0	14.822925	8	8
92.0	14.824682	4	4
93.0	14.82632	5	5
94.0	14.827848	5	5
95.0	14.829273	5	5
96.0	14.830602	8	8
97.0	14.831841	5	5
98.0	14.832997	5	5
99.0	14.834075	4	4
100.0	14.835081	1	1
101.0	0	7	7
102.0	0	6	6
103.0	0	3	3
104.0	0	2	2
105.0	0	5	5
106.0	0	5	5
107.0	0	4	4
108.0	0	2	2
109.0	0	9	9
110.0	0	4	4
111.0	0	2	2
112.0	0	4	4
113.0	0	4	4
114.0	0	2	2
115.0	0	4	4
116.0	0	5	5
117.0	0	6	6
118.0	0	5	5
119.0	0	4	4
120.0	0	5	5
121.0	0	3	3
122.0	0	2	2
123.0	0	2	2
124.0	0	1	1
125.0	0	5	5
126.0	0	2	2
127.0	0	2	2
128.0	0	1	1
129.0	0	4	4
130.0	0	8	8
131.0	0	3	3
132.0	0	3	3
133.0	0	4	4
134.0	0	3	3
135.0	0	3	3
136.0	0	3	3
137.0	0	6	6
138.0	0	2	2
139.0	0	2	2
140.0	0	2	2
141.0	0	3	3
142.0	0	1	1
143.0	0	5	5
146.0	0	2	2
147.0	0	3	3
148.0	0	2	2
149.0	0	2	2
150.0	0	5	5
151.0	0	3	3
152.0	0	3	3
153.0	0	4	4
154.0	0	3	3
155.0	0	3	3
156.0	0	2	2
157.0	0	1	1
158.0	0	2	2
159.0	0	1	1
161.0	0	4	4
162.0	0	5	5
163.0	0	3	3
164.0	0	1	1
165.0	0	4	4
166.0	0	4	4
167.0	0	4	4
168.0	0	2	2
169.0	0	4	4
170.0	0	3	3
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	2	2
175.0	0	3	3
176.0	0	2	2
177.0	0	1	1
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
181.0	0	3	3
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
187.0	0	1	1
188.0	0	3	3
190.0	0	2	2
191.0	0	1	1
192.0	0	2	2
193.0	0	1	1
194.0	0	6	6
197.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	3	3
205.0	0	2	2
206.0	0	2	2
207.0	0	2	2
209.0	0	1	1
211.0	0	2	2
212.0	0	2	2
213.0	0	1	1
214.0	0	1	1
215.0	0	3	3
216.0	0	1	1
219.0	0	1	1
221.0	0	4	4
222.0	0	2	2
226.0	0	2	2
232.0	0	1	1
233.0	0	1	1
234.0	0	2	2
235.0	0	3	3
236.0	0	1	1
237.0	0	2	2
239.0	0	1	1
240.0	0	1	1
244.0	0	2	2
246.0	0	2	2
249.0	0	1	1
251.0	0	3	3
252.0	0	2	2
255.0	0	1	1
256.0	0	2	2
258.0	0	1	1
260.0	0	2	2
263.0	0	1	1
264.0	0	2	2
265.0	0	2	2
267.0	0	1	1
269.0	0	3	3
272.0	0	1	1
273.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	1	1
282.0	0	1	1
283.0	0	3	3
286.0	0	2	2
289.0	0	1	1
291.0	0	1	1
292.0	0	2	2
294.0	0	2	2
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
300.0	0	3	3
301.0	0	1	1
302.0	0	2	2
303.0	0	1	1
304.0	0	1	1
306.0	0	1	1
308.0	0	1	1
309.0	0	2	2
310.0	0	1	1
312.0	0	1	1
313.0	0	3	3
315.0	0	1	1
317.0	0	2	2
318.0	0	1	1
321.0	0	1	1
324.0	0	2	2
328.0	0	1	1
330.0	0	3	3
331.0	0	1	1
334.0	0	1	1
335.0	0	2	2
344.0	0	3	3
346.0	0	1	1
350.0	0	1	1
355.0	0	1	1
361.0	0	1	1
362.0	0	2	2
363.0	0	1	1
364.0	0	1	1
367.0	0	1	1
373.0	0	1	1
374.0	0	1	1
375.0	0	1	1
377.0	0	1	1
378.0	0	1	1
379.0	0	2	2
381.0	0	1	1
385.0	0	1	1
386.0	0	2	2
391.0	0	1	1
393.0	0	1	1
397.0	0	3	3
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
403.0	0	1	1
405.0	0	1	1
406.0	0	1	1
414.0	0	1	1
415.0	0	1	1
419.0	0	1	1
421.0	0	1	1
422.0	0	1	1
424.0	0	1	1
429.0	0	1	1
435.0	0	1	1
438.0	0	2	2
439.0	0	1	1
441.0	0	2	2
448.0	0	1	1
451.0	0	1	1
459.0	0	1	1
461.0	0	1	1
462.0	0	2	2
463.0	0	1	1
471.0	0	1	1
480.0	0	1	1
481.0	0	1	1
483.0	0	1	1
486.0	0	1	1
488.0	0	1	1
492.0	0	1	1
493.0	0	1	1
503.0	0	1	1
507.0	0	1	1
511.0	0	2	2
516.0	0	2	2
522.0	0	1	1
530.0	0	1	1
533.0	0	1	1
536.0	0	1	1
543.0	0	1	1
549.0	0	1	1
551.0	0	1	1
565.0	0	1	1
575.0	0	1	1
594.0	0	1	1
603.0	0	1	1
605.0	0	1	1
614.0	0	1	1
618.0	0	1	1
619.0	0	1	1
622.0	0	1	1
634.0	0	1	1
638.0	0	1	1
641.0	0	1	1
649.0	0	1	1
659.0	0	2	2
668.0	0	1	1
682.0	0	1	1
692.0	0	1	1
693.0	0	1	1
704.0	0	1	1
726.0	0	1	1
729.0	0	1	1
731.0	0	1	1
741.0	0	1	1
742.0	0	1	1
777.0	0	1	1
787.0	0	1	1
799.0	0	1	1
806.0	0	1	1
836.0	0	1	1
838.0	0	1	1
854.0	0	1	1
885.0	0	1	1
893.0	0	1	1
927.0	0	1	1
944.0	0	1	1
954.0	0	1	1
996.0	0	1	1
1128.0	0	1	1
1344.0	0	1	1
1410.0	0	1	1