## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-09-02/ES_Ciu_Tom_1_2016-09-02.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-09-02/ES_Ciu_Tom_1_2016-09-02.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2016-09-02/ES_Ciu_Tom_1_2016-09-02.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 09:35:52 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	35625293	14070328	0	0	9658042	1173453	0	0.188266	79596999

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11671548	11671548
2.0	1.837973	770111	770111
3.0	2.540171	57767	57767
4.0	3.128595	7060	7060
5.0	3.621677	2325	2325
6.0	4.034867	1464	1464
7.0	4.381109	974	974
8.0	4.671251	755	755
9.0	4.914381	523	523
10.0	5.118118	439	439
11.0	5.288844	353	353
12.0	5.431908	279	279
13.0	5.551791	254	254
14.0	5.65225	212	212
15.0	5.736432	170	170
16.0	5.806974	166	166
17.0	5.866087	156	156
18.0	5.915622	129	129
19.0	5.95713	105	105
20.0	5.991913	115	115
21.0	6.021061	101	101
22.0	6.045485	110	110
23.0	6.065953	101	101
24.0	6.083104	102	102
25.0	6.097476	83	83
26.0	6.109519	73	73
27.0	6.119611	93	93
28.0	6.128068	76	76
29.0	6.135155	71	71
30.0	6.141093	71	71
31.0	6.146069	68	68
32.0	6.150239	60	60
33.0	6.153733	52	52
34.0	6.156661	56	56
35.0	6.159115	53	53
36.0	6.161171	52	52
37.0	6.162894	43	43
38.0	6.164338	47	47
39.0	6.165548	39	39
40.0	6.166562	41	41
41.0	6.167411	43	43
42.0	6.168123	41	41
43.0	6.16872	34	34
44.0	6.16922	34	34
45.0	6.169639	37	37
46.0	6.16999	33	33
47.0	6.170284	26	26
48.0	6.17053	24	24
49.0	6.170737	36	36
50.0	6.17091	20	20
51.0	6.171055	30	30
52.0	6.171177	25	25
53.0	6.171278	26	26
54.0	6.171364	27	27
55.0	6.171435	17	17
56.0	6.171495	21	21
57.0	6.171545	7	7
58.0	6.171587	13	13
59.0	6.171623	16	16
60.0	6.171652	15	15
61.0	6.171677	11	11
62.0	6.171698	15	15
63.0	6.171715	15	15
64.0	6.17173	12	12
65.0	6.171742	17	17
66.0	6.171752	14	14
67.0	6.171761	13	13
68.0	6.171768	14	14
69.0	6.171774	16	16
70.0	6.171779	8	8
71.0	6.171783	14	14
72.0	6.171787	17	17
73.0	6.17179	14	14
74.0	6.171792	13	13
75.0	6.171794	12	12
76.0	6.171796	11	11
77.0	6.171798	11	11
78.0	6.171799	12	12
79.0	6.1718	9	9
80.0	6.171801	13	13
81.0	6.171801	6	6
82.0	6.171802	12	12
83.0	6.171802	15	15
84.0	6.171803	10	10
85.0	6.171803	8	8
86.0	6.171804	14	14
87.0	6.171804	8	8
88.0	6.171804	8	8
89.0	6.171804	11	11
90.0	6.171804	9	9
91.0	6.171804	7	7
92.0	6.171805	9	9
93.0	6.171805	10	10
94.0	6.171805	8	8
95.0	6.171805	13	13
96.0	6.171805	7	7
97.0	6.171805	14	14
98.0	6.171805	5	5
99.0	6.171805	7	7
100.0	6.171805	7	7
101.0	0	5	5
102.0	0	7	7
103.0	0	7	7
104.0	0	8	8
105.0	0	11	11
106.0	0	9	9
107.0	0	8	8
108.0	0	8	8
109.0	0	12	12
110.0	0	8	8
111.0	0	6	6
112.0	0	9	9
113.0	0	4	4
114.0	0	4	4
115.0	0	5	5
116.0	0	11	11
117.0	0	10	10
118.0	0	9	9
119.0	0	6	6
120.0	0	5	5
121.0	0	4	4
122.0	0	6	6
123.0	0	6	6
124.0	0	2	2
125.0	0	7	7
126.0	0	4	4
127.0	0	6	6
128.0	0	5	5
129.0	0	7	7
130.0	0	4	4
131.0	0	5	5
132.0	0	3	3
133.0	0	3	3
134.0	0	6	6
135.0	0	3	3
136.0	0	6	6
137.0	0	8	8
138.0	0	1	1
139.0	0	9	9
140.0	0	5	5
141.0	0	2	2
142.0	0	4	4
143.0	0	1	1
144.0	0	4	4
145.0	0	4	4
146.0	0	1	1
147.0	0	3	3
148.0	0	1	1
149.0	0	4	4
150.0	0	5	5
151.0	0	3	3
152.0	0	6	6
153.0	0	5	5
154.0	0	2	2
155.0	0	1	1
156.0	0	3	3
157.0	0	1	1
158.0	0	5	5
159.0	0	2	2
160.0	0	2	2
162.0	0	2	2
163.0	0	2	2
164.0	0	2	2
165.0	0	2	2
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	3	3
171.0	0	2	2
172.0	0	3	3
173.0	0	2	2
174.0	0	4	4
175.0	0	3	3
176.0	0	2	2
177.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
183.0	0	1	1
185.0	0	4	4
186.0	0	3	3
187.0	0	1	1
188.0	0	1	1
190.0	0	4	4
191.0	0	1	1
192.0	0	3	3
193.0	0	1	1
194.0	0	1	1
196.0	0	3	3
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
203.0	0	2	2
206.0	0	2	2
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
211.0	0	3	3
212.0	0	1	1
213.0	0	2	2
214.0	0	2	2
216.0	0	3	3
217.0	0	2	2
218.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	3	3
226.0	0	2	2
230.0	0	1	1
236.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	3	3
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
248.0	0	1	1
250.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	2	2
257.0	0	1	1
258.0	0	2	2
260.0	0	2	2
261.0	0	1	1
265.0	0	1	1
268.0	0	1	1
269.0	0	1	1
272.0	0	1	1
274.0	0	1	1
276.0	0	2	2
280.0	0	1	1
281.0	0	1	1
283.0	0	1	1
288.0	0	1	1
289.0	0	2	2
290.0	0	2	2
291.0	0	1	1
292.0	0	1	1
294.0	0	1	1
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
301.0	0	2	2
305.0	0	2	2
308.0	0	1	1
315.0	0	1	1
319.0	0	1	1
321.0	0	1	1
323.0	0	1	1
326.0	0	1	1
335.0	0	1	1
336.0	0	1	1
340.0	0	1	1
349.0	0	2	2
354.0	0	1	1
361.0	0	1	1
364.0	0	1	1
368.0	0	1	1
369.0	0	1	1
371.0	0	1	1
372.0	0	1	1
379.0	0	1	1
380.0	0	1	1
400.0	0	1	1
403.0	0	1	1
412.0	0	1	1
414.0	0	1	1
416.0	0	1	1
419.0	0	1	1
422.0	0	1	1
423.0	0	1	1
430.0	0	1	1
431.0	0	1	1
434.0	0	1	1
435.0	0	1	1
436.0	0	1	1
439.0	0	1	1
442.0	0	2	2
458.0	0	1	1
468.0	0	1	1
476.0	0	1	1
480.0	0	1	1
481.0	0	1	1
495.0	0	2	2
501.0	0	1	1
502.0	0	1	1
507.0	0	1	1
526.0	0	1	1
548.0	0	1	1
564.0	0	1	1
578.0	0	1	1
592.0	0	1	1
593.0	0	1	1
609.0	0	1	1
655.0	0	1	1
718.0	0	1	1
721.0	0	1	1
748.0	0	1	1
779.0	0	1	1
829.0	0	1	1
890.0	0	1	1
1104.0	0	1	1
1124.0	0	1	1
1235.0	0	1	1
2051.0	0	1	1
4050.0	0	1	1