## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-10-08/ES_Ciu_Tom_1_2015-10-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-10-08/ES_Ciu_Tom_1_2015-10-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ciu_Tom_1_2015-10-08/ES_Ciu_Tom_1_2015-10-08.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 08:52:16 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	6648929	27387237	0	0	3105070	3502894	0	0.164609	97724800

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20350819	20350819
2.0	1.755596	2526225	2526225
3.0	2.326521	304656	304656
4.0	2.75791	41324	41324
5.0	3.083865	7836	7836
6.0	3.330156	2499	2499
7.0	3.516252	1260	1260
8.0	3.656866	807	807
9.0	3.763113	548	548
10.0	3.843392	422	422
11.0	3.904052	357	357
12.0	3.949885	332	332
13.0	3.984517	226	226
14.0	4.010685	200	200
15.0	4.030457	171	171
16.0	4.045397	146	146
17.0	4.056685	129	129
18.0	4.065215	141	141
19.0	4.071659	108	108
20.0	4.076529	124	124
21.0	4.080209	71	71
22.0	4.082989	100	100
23.0	4.08509	80	80
24.0	4.086677	78	78
25.0	4.087876	69	69
26.0	4.088782	67	67
27.0	4.089467	66	66
28.0	4.089985	61	61
29.0	4.090376	54	54
30.0	4.090671	54	54
31.0	4.090894	47	47
32.0	4.091063	45	45
33.0	4.09119	50	50
34.0	4.091287	46	46
35.0	4.091359	52	52
36.0	4.091414	27	27
37.0	4.091456	45	45
38.0	4.091487	32	32
39.0	4.091511	37	37
40.0	4.091529	36	36
41.0	4.091542	31	31
42.0	4.091553	20	20
43.0	4.09156	27	27
44.0	4.091566	23	23
45.0	4.091571	24	24
46.0	4.091574	19	19
47.0	4.091576	25	25
48.0	4.091578	28	28
49.0	4.09158	28	28
50.0	4.091581	15	15
51.0	4.091582	25	25
52.0	4.091582	20	20
53.0	4.091583	19	19
54.0	4.091583	26	26
55.0	4.091583	14	14
56.0	4.091584	27	27
57.0	4.091584	23	23
58.0	4.091584	16	16
59.0	4.091584	16	16
60.0	4.091584	12	12
61.0	4.091584	16	16
62.0	4.091584	20	20
63.0	4.091584	13	13
64.0	4.091584	12	12
65.0	4.091584	10	10
66.0	4.091584	23	23
67.0	4.091584	13	13
68.0	4.091584	12	12
69.0	4.091584	19	19
70.0	4.091584	11	11
71.0	4.091584	10	10
72.0	4.091584	7	7
73.0	4.091584	12	12
74.0	4.091584	13	13
75.0	4.091584	8	8
76.0	4.091584	9	9
77.0	4.091584	12	12
78.0	4.091584	11	11
79.0	4.091584	9	9
80.0	4.091584	3	3
81.0	4.091584	9	9
82.0	4.091584	11	11
83.0	4.091584	15	15
84.0	4.091584	6	6
85.0	4.091584	9	9
86.0	4.091584	8	8
87.0	4.091584	8	8
88.0	4.091584	5	5
89.0	4.091584	6	6
90.0	4.091584	9	9
91.0	4.091584	6	6
92.0	4.091584	7	7
93.0	4.091584	7	7
94.0	4.091584	6	6
95.0	4.091584	10	10
96.0	4.091584	6	6
97.0	4.091584	6	6
98.0	4.091584	6	6
99.0	4.091584	2	2
100.0	4.091584	4	4
101.0	0	6	6
102.0	0	6	6
103.0	0	3	3
104.0	0	5	5
105.0	0	2	2
106.0	0	8	8
107.0	0	4	4
108.0	0	6	6
109.0	0	7	7
110.0	0	6	6
111.0	0	7	7
112.0	0	2	2
113.0	0	5	5
114.0	0	5	5
115.0	0	7	7
116.0	0	1	1
117.0	0	4	4
118.0	0	5	5
119.0	0	4	4
120.0	0	7	7
121.0	0	4	4
122.0	0	3	3
123.0	0	4	4
124.0	0	6	6
125.0	0	1	1
126.0	0	3	3
127.0	0	5	5
128.0	0	6	6
130.0	0	5	5
131.0	0	1	1
132.0	0	6	6
133.0	0	3	3
134.0	0	4	4
135.0	0	1	1
136.0	0	3	3
137.0	0	3	3
138.0	0	4	4
139.0	0	5	5
140.0	0	1	1
141.0	0	2	2
142.0	0	3	3
143.0	0	6	6
144.0	0	7	7
145.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	4	4
149.0	0	2	2
150.0	0	3	3
151.0	0	4	4
152.0	0	1	1
153.0	0	2	2
154.0	0	2	2
155.0	0	1	1
156.0	0	1	1
157.0	0	4	4
158.0	0	1	1
159.0	0	2	2
161.0	0	2	2
162.0	0	3	3
163.0	0	2	2
164.0	0	3	3
165.0	0	3	3
166.0	0	3	3
167.0	0	1	1
168.0	0	2	2
169.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	3	3
174.0	0	2	2
175.0	0	2	2
176.0	0	2	2
177.0	0	2	2
179.0	0	2	2
180.0	0	3	3
181.0	0	2	2
182.0	0	1	1
183.0	0	5	5
184.0	0	2	2
188.0	0	1	1
189.0	0	2	2
190.0	0	2	2
191.0	0	3	3
192.0	0	1	1
194.0	0	3	3
195.0	0	1	1
196.0	0	1	1
197.0	0	2	2
200.0	0	2	2
201.0	0	1	1
203.0	0	2	2
204.0	0	1	1
205.0	0	2	2
206.0	0	2	2
207.0	0	3	3
209.0	0	1	1
210.0	0	1	1
211.0	0	2	2
212.0	0	2	2
214.0	0	2	2
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
220.0	0	1	1
221.0	0	4	4
224.0	0	1	1
226.0	0	1	1
228.0	0	2	2
231.0	0	1	1
232.0	0	2	2
235.0	0	1	1
236.0	0	2	2
239.0	0	1	1
240.0	0	2	2
245.0	0	1	1
248.0	0	1	1
260.0	0	2	2
261.0	0	1	1
262.0	0	2	2
264.0	0	4	4
266.0	0	1	1
270.0	0	1	1
274.0	0	2	2
275.0	0	1	1
276.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	1	1
289.0	0	2	2
292.0	0	1	1
294.0	0	1	1
296.0	0	1	1
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
303.0	0	1	1
305.0	0	1	1
307.0	0	1	1
308.0	0	1	1
311.0	0	2	2
313.0	0	1	1
316.0	0	1	1
317.0	0	1	1
319.0	0	1	1
329.0	0	1	1
332.0	0	1	1
335.0	0	1	1
338.0	0	1	1
344.0	0	1	1
359.0	0	1	1
365.0	0	2	2
369.0	0	1	1
382.0	0	1	1
403.0	0	2	2
404.0	0	1	1
423.0	0	1	1
433.0	0	1	1
448.0	0	1	1
453.0	0	1	1
462.0	0	1	1
485.0	0	1	1
501.0	0	1	1
503.0	0	1	1
535.0	0	1	1
548.0	0	1	1
587.0	0	1	1
619.0	0	1	1
672.0	0	1	1