## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-09-17/FI_Pir_Aka_1_2016-09-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-09-17/FI_Pir_Aka_1_2016-09-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2016-09-17/FI_Pir_Aka_1_2016-09-17.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 09:08:23 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	34951979	12136279	0	0	8667911	1004025	0	0.180262	69245591

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	10105090	10105090
2.0	1.839235	663634	663634
3.0	2.543551	51044	51044
4.0	3.134637	6190	6190
5.0	3.630698	1990	1990
6.0	4.04701	1134	1134
7.0	4.396393	771	771
8.0	4.689608	536	536
9.0	4.935684	351	351
10.0	5.1422	311	311
11.0	5.315515	228	228
12.0	5.460967	222	222
13.0	5.583036	179	179
14.0	5.68548	161	161
15.0	5.771455	149	149
16.0	5.843608	133	133
17.0	5.904162	120	120
18.0	5.95498	118	118
19.0	5.997629	114	114
20.0	6.033421	92	92
21.0	6.06346	82	82
22.0	6.088669	97	97
23.0	6.109825	84	84
24.0	6.12758	96	96
25.0	6.142481	90	90
26.0	6.154986	84	84
27.0	6.165481	70	70
28.0	6.174289	60	60
29.0	6.18168	62	62
30.0	6.187884	62	62
31.0	6.19309	44	44
32.0	6.197459	61	61
33.0	6.201126	62	62
34.0	6.204203	55	55
35.0	6.206785	53	53
36.0	6.208953	45	45
37.0	6.210772	42	42
38.0	6.212298	43	43
39.0	6.213579	37	37
40.0	6.214654	41	41
41.0	6.215557	31	31
42.0	6.216314	39	39
43.0	6.216949	34	34
44.0	6.217483	31	31
45.0	6.21793	27	27
46.0	6.218306	22	22
47.0	6.218621	28	28
48.0	6.218886	26	26
49.0	6.219108	25	25
50.0	6.219294	22	22
51.0	6.219451	26	26
52.0	6.219582	21	21
53.0	6.219692	16	16
54.0	6.219784	8	8
55.0	6.219862	16	16
56.0	6.219927	17	17
57.0	6.219982	21	21
58.0	6.220028	12	12
59.0	6.220066	13	13
60.0	6.220098	15	15
61.0	6.220125	15	15
62.0	6.220148	18	18
63.0	6.220167	15	15
64.0	6.220183	10	10
65.0	6.220197	15	15
66.0	6.220208	17	17
67.0	6.220217	13	13
68.0	6.220225	13	13
69.0	6.220232	6	6
70.0	6.220238	11	11
71.0	6.220242	7	7
72.0	6.220246	16	16
73.0	6.22025	12	12
74.0	6.220252	13	13
75.0	6.220255	12	12
76.0	6.220257	9	9
77.0	6.220258	8	8
78.0	6.22026	9	9
79.0	6.220261	10	10
80.0	6.220262	11	11
81.0	6.220263	5	5
82.0	6.220263	8	8
83.0	6.220264	11	11
84.0	6.220264	13	13
85.0	6.220265	8	8
86.0	6.220265	4	4
87.0	6.220265	7	7
88.0	6.220266	5	5
89.0	6.220266	10	10
90.0	6.220266	12	12
91.0	6.220266	9	9
92.0	6.220266	6	6
93.0	6.220266	11	11
94.0	6.220266	7	7
95.0	6.220267	5	5
96.0	6.220267	9	9
97.0	6.220267	7	7
98.0	6.220267	3	3
99.0	6.220267	10	10
100.0	6.220267	13	13
101.0	0	7	7
102.0	0	6	6
103.0	0	7	7
104.0	0	2	2
105.0	0	8	8
106.0	0	5	5
107.0	0	8	8
108.0	0	7	7
109.0	0	7	7
110.0	0	9	9
111.0	0	5	5
112.0	0	6	6
113.0	0	6	6
114.0	0	6	6
115.0	0	6	6
116.0	0	5	5
117.0	0	2	2
118.0	0	6	6
119.0	0	6	6
120.0	0	9	9
121.0	0	6	6
122.0	0	4	4
123.0	0	5	5
124.0	0	2	2
125.0	0	5	5
126.0	0	7	7
127.0	0	5	5
128.0	0	6	6
129.0	0	9	9
130.0	0	4	4
131.0	0	7	7
132.0	0	5	5
133.0	0	4	4
134.0	0	3	3
135.0	0	2	2
136.0	0	3	3
137.0	0	3	3
138.0	0	2	2
139.0	0	4	4
140.0	0	2	2
141.0	0	4	4
142.0	0	2	2
143.0	0	1	1
145.0	0	2	2
146.0	0	4	4
147.0	0	7	7
148.0	0	2	2
149.0	0	1	1
150.0	0	4	4
151.0	0	1	1
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
158.0	0	4	4
159.0	0	1	1
160.0	0	3	3
161.0	0	1	1
162.0	0	3	3
163.0	0	4	4
164.0	0	2	2
165.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
170.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
178.0	0	1	1
179.0	0	3	3
180.0	0	1	1
182.0	0	4	4
183.0	0	2	2
184.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
189.0	0	2	2
190.0	0	1	1
192.0	0	1	1
193.0	0	2	2
194.0	0	3	3
196.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	3	3
205.0	0	2	2
206.0	0	3	3
208.0	0	2	2
209.0	0	1	1
210.0	0	1	1
213.0	0	1	1
214.0	0	2	2
215.0	0	1	1
216.0	0	3	3
218.0	0	1	1
220.0	0	1	1
222.0	0	2	2
224.0	0	2	2
226.0	0	2	2
227.0	0	1	1
229.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
238.0	0	1	1
240.0	0	1	1
242.0	0	1	1
243.0	0	2	2
253.0	0	2	2
255.0	0	2	2
256.0	0	1	1
257.0	0	1	1
258.0	0	1	1
262.0	0	1	1
263.0	0	1	1
266.0	0	3	3
270.0	0	1	1
271.0	0	1	1
273.0	0	1	1
278.0	0	2	2
283.0	0	1	1
287.0	0	1	1
300.0	0	1	1
301.0	0	1	1
302.0	0	1	1
305.0	0	1	1
306.0	0	1	1
307.0	0	2	2
308.0	0	1	1
309.0	0	1	1
312.0	0	1	1
323.0	0	1	1
328.0	0	1	1
334.0	0	1	1
336.0	0	1	1
347.0	0	1	1
350.0	0	1	1
352.0	0	1	1
353.0	0	1	1
357.0	0	1	1
361.0	0	1	1
373.0	0	1	1
375.0	0	1	1
377.0	0	1	1
386.0	0	1	1
392.0	0	1	1
399.0	0	1	1
400.0	0	1	1
411.0	0	1	1
425.0	0	1	1
430.0	0	1	1
434.0	0	1	1
439.0	0	1	1
453.0	0	1	1
490.0	0	1	1
498.0	0	1	1
501.0	0	1	1
507.0	0	1	1
512.0	0	1	1
513.0	0	2	2
527.0	0	1	1
539.0	0	1	1
542.0	0	1	1
558.0	0	1	1
567.0	0	1	1
605.0	0	1	1
705.0	0	1	1
719.0	0	1	1
757.0	0	1	1
936.0	0	1	1
975.0	0	1	1
1050.0	0	1	1
1156.0	0	1	1
1478.0	0	1	1
2625.0	0	1	1