## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mai_Bow_2_2009-10-15/US_Mai_Bow_2_2009-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mai_Bow_2_2009-10-15/US_Mai_Bow_2_2009-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mai_Bow_2_2009-10-15/US_Mai_Bow_2_2009-10-15.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 16:55:46 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	3777192	12325503	0	0	733681	203506	0	0.040125	369132046

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11774769	11774769
2.0	1.967161	102448	102448
3.0	2.902561	6107	6107
4.0	3.807243	1096	1096
5.0	4.682216	431	431
6.0	5.528456	237	237
7.0	6.346906	153	153
8.0	7.138479	105	105
9.0	7.904057	76	76
10.0	8.644494	56	56
11.0	9.360616	54	54
12.0	10.053221	46	46
13.0	10.723081	42	42
14.0	11.370944	36	36
15.0	11.997531	36	36
16.0	12.603542	29	29
17.0	13.189652	30	30
18.0	13.756515	25	25
19.0	14.304762	23	23
20.0	14.835005	34	34
21.0	15.347836	19	19
22.0	15.843825	17	17
23.0	16.323527	24	24
24.0	16.787475	19	19
25.0	17.236188	16	16
26.0	17.670166	23	23
27.0	18.089892	20	20
28.0	18.495835	18	18
29.0	18.888446	12	12
30.0	19.268165	12	12
31.0	19.635414	9	9
32.0	19.990603	11	11
33.0	20.334128	11	11
34.0	20.666372	8	8
35.0	20.987705	11	11
36.0	21.298486	11	11
37.0	21.599061	10	10
38.0	21.889765	5	5
39.0	22.170923	8	8
40.0	22.442848	7	7
41.0	22.705843	3	3
42.0	22.960201	8	8
43.0	23.206207	7	7
44.0	23.444134	6	6
45.0	23.674248	9	9
46.0	23.896804	7	7
47.0	24.112053	5	5
48.0	24.320233	5	5
49.0	24.521576	6	6
50.0	24.716307	7	7
51.0	24.904644	8	8
52.0	25.086795	5	5
53.0	25.262965	4	4
54.0	25.43335	10	10
55.0	25.598139	9	9
56.0	25.757517	3	3
57.0	25.911661	4	4
58.0	26.060743	5	5
59.0	26.20493	7	7
60.0	26.344381	4	4
61.0	26.479253	2	2
62.0	26.609696	4	4
63.0	26.735855	6	6
64.0	26.857871	5	5
65.0	26.97588	7	7
66.0	27.090014	4	4
67.0	27.2004	6	6
68.0	27.307161	3	3
69.0	27.410416	7	7
70.0	27.51028	2	2
71.0	27.606865	2	2
72.0	27.700278	2	2
73.0	27.790623	2	2
74.0	27.878002	8	8
75.0	27.962511	3	3
76.0	28.044245	0	0
77.0	28.123294	6	6
78.0	28.199748	7	7
79.0	28.273691	4	4
80.0	28.345206	3	3
81.0	28.414373	5	5
82.0	28.481268	3	3
83.0	28.545966	3	3
84.0	28.60854	2	2
85.0	28.669058	1	1
86.0	28.72759	2	2
87.0	28.784199	4	4
88.0	28.838949	2	2
89.0	28.891902	1	1
90.0	28.943115	4	4
91.0	28.992647	4	4
92.0	29.040552	1	1
93.0	29.086883	4	4
94.0	29.131694	4	4
95.0	29.175033	2	2
96.0	29.216948	2	2
97.0	29.257487	2	2
98.0	29.296695	2	2
99.0	29.334615	3	3
100.0	29.37129	1	1
101.0	0	2	2
102.0	0	2	2
103.0	0	4	4
104.0	0	2	2
106.0	0	3	3
107.0	0	3	3
108.0	0	2	2
109.0	0	4	4
110.0	0	2	2
111.0	0	4	4
112.0	0	2	2
113.0	0	2	2
114.0	0	1	1
115.0	0	3	3
116.0	0	2	2
117.0	0	5	5
118.0	0	1	1
120.0	0	2	2
121.0	0	1	1
122.0	0	3	3
123.0	0	2	2
125.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	2	2
129.0	0	3	3
131.0	0	2	2
132.0	0	1	1
133.0	0	3	3
134.0	0	2	2
135.0	0	1	1
136.0	0	3	3
137.0	0	2	2
138.0	0	4	4
139.0	0	2	2
142.0	0	3	3
143.0	0	1	1
144.0	0	3	3
145.0	0	2	2
146.0	0	1	1
147.0	0	2	2
148.0	0	2	2
151.0	0	2	2
152.0	0	2	2
154.0	0	3	3
155.0	0	1	1
156.0	0	4	4
157.0	0	2	2
158.0	0	1	1
159.0	0	3	3
160.0	0	1	1
164.0	0	3	3
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	4	4
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
179.0	0	1	1
180.0	0	2	2
181.0	0	1	1
182.0	0	2	2
183.0	0	1	1
185.0	0	2	2
187.0	0	1	1
190.0	0	2	2
192.0	0	2	2
193.0	0	1	1
194.0	0	2	2
196.0	0	2	2
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
201.0	0	2	2
204.0	0	2	2
205.0	0	1	1
207.0	0	1	1
210.0	0	3	3
211.0	0	1	1
213.0	0	1	1
216.0	0	1	1
217.0	0	1	1
219.0	0	2	2
220.0	0	1	1
222.0	0	1	1
226.0	0	2	2
227.0	0	2	2
228.0	0	2	2
231.0	0	1	1
234.0	0	1	1
236.0	0	2	2
238.0	0	1	1
242.0	0	1	1
243.0	0	2	2
247.0	0	2	2
248.0	0	1	1
249.0	0	2	2
251.0	0	2	2
254.0	0	2	2
256.0	0	2	2
258.0	0	1	1
261.0	0	1	1
263.0	0	1	1
270.0	0	1	1
275.0	0	1	1
281.0	0	1	1
287.0	0	1	1
289.0	0	1	1
291.0	0	1	1
301.0	0	1	1
303.0	0	1	1
304.0	0	2	2
305.0	0	1	1
311.0	0	1	1
316.0	0	1	1
323.0	0	1	1
326.0	0	1	1
328.0	0	2	2
331.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
340.0	0	1	1
343.0	0	1	1
351.0	0	1	1
354.0	0	1	1
368.0	0	1	1
370.0	0	1	1
373.0	0	1	1
375.0	0	1	1
385.0	0	1	1
395.0	0	1	1
396.0	0	1	1
397.0	0	1	1
401.0	0	1	1
406.0	0	1	1
425.0	0	1	1
434.0	0	1	1
443.0	0	1	1
462.0	0	1	1
471.0	0	1	1
507.0	0	1	1
510.0	0	1	1
520.0	0	1	1
530.0	0	1	1
533.0	0	1	1
595.0	0	1	1
605.0	0	1	1
789.0	0	1	1