## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-11-05/US_Vir_Cha_1_2012-11-05.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-11-05/US_Vir_Cha_1_2012-11-05.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-11-05/US_Vir_Cha_1_2012-11-05.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 17:58:07 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	2540593	27622385	0	0	507766	107507	0	0.012508	3539374799

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	27155521	27155521
2.0	1.992226	59117	59117
3.0	2.976739	3973	3973
4.0	3.953598	799	799
5.0	4.922863	355	355
6.0	5.884593	199	199
7.0	6.838846	165	165
8.0	7.785681	85	85
9.0	8.725156	87	87
10.0	9.657327	60	60
11.0	10.582252	47	47
12.0	11.499986	34	34
13.0	12.410586	28	28
14.0	13.314107	20	20
15.0	14.210604	24	24
16.0	15.100131	15	15
17.0	15.982744	16	16
18.0	16.858495	11	11
19.0	17.727438	5	5
20.0	18.589626	8	8
21.0	19.445111	9	9
22.0	20.293946	7	7
23.0	21.136183	12	12
24.0	21.971871	7	7
25.0	22.801063	7	7
26.0	23.623809	10	10
27.0	24.440159	3	3
28.0	25.250163	6	6
29.0	26.05387	9	9
30.0	26.851329	5	5
31.0	27.642588	6	6
32.0	28.427696	7	7
33.0	29.206701	7	7
34.0	29.97965	5	5
35.0	30.74659	5	5
36.0	31.507568	3	3
37.0	32.26263	1	1
38.0	33.011823	3	3
39.0	33.755191	1	1
40.0	34.49278	4	4
41.0	35.224635	2	2
42.0	35.950801	2	2
43.0	36.671322	3	3
44.0	37.386241	2	2
45.0	38.095603	2	2
46.0	38.79945	1	1
47.0	39.497826	3	3
48.0	40.190772	2	2
49.0	40.878332	2	2
50.0	41.560546	0	0
51.0	42.237457	1	1
52.0	42.909106	1	1
53.0	43.575533	3	3
54.0	44.236779	1	1
55.0	44.892885	5	5
56.0	45.543891	4	4
57.0	46.189836	1	1
58.0	46.830759	1	1
59.0	47.466699	2	2
60.0	48.097696	1	1
61.0	48.723788	0	0
62.0	49.345012	1	1
63.0	49.961407	0	0
64.0	50.57301	3	3
65.0	51.179859	0	0
66.0	51.78199	4	4
67.0	52.37944	2	2
68.0	52.972245	2	2
69.0	53.560442	1	1
70.0	54.144067	1	1
71.0	54.723154	1	1
72.0	55.29774	2	2
73.0	55.867859	2	2
74.0	56.433545	3	3
75.0	56.994835	2	2
76.0	57.55176	0	0
77.0	58.104357	0	0
78.0	58.652657	1	1
79.0	59.196695	1	1
80.0	59.736503	2	2
81.0	60.272116	0	0
82.0	60.803564	0	0
83.0	61.330881	0	0
84.0	61.854098	1	1
85.0	62.373249	0	0
86.0	62.888363	0	0
87.0	63.399473	0	0
88.0	63.906609	0	0
89.0	64.409803	0	0
90.0	64.909085	1	1
91.0	65.404486	0	0
92.0	65.896036	1	1
93.0	66.383764	0	0
94.0	66.867701	1	1
95.0	67.347876	1	1
96.0	67.824317	0	0
97.0	68.297055	0	0
98.0	68.766118	0	0
99.0	69.231535	0	0
100.0	69.693333	0	0
101.0	0	2	2
111.0	0	1	1
113.0	0	1	1
115.0	0	1	1
116.0	0	2	2
117.0	0	1	1
119.0	0	1	1
122.0	0	1	1
125.0	0	2	2
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
132.0	0	1	1
133.0	0	2	2
136.0	0	2	2
138.0	0	2	2
139.0	0	1	1
141.0	0	1	1
143.0	0	1	1
147.0	0	1	1
148.0	0	1	1
154.0	0	1	1
159.0	0	1	1
160.0	0	1	1
165.0	0	1	1
166.0	0	1	1
174.0	0	1	1
175.0	0	2	2
176.0	0	2	2
178.0	0	1	1
182.0	0	1	1
184.0	0	1	1
196.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	1	1
212.0	0	1	1
225.0	0	1	1
230.0	0	1	1
240.0	0	1	1
245.0	0	1	1
246.0	0	1	1
250.0	0	1	1
257.0	0	1	1
276.0	0	1	1
279.0	0	1	1
344.0	0	1	1
658.0	0	1	1
719.0	0	1	1
843.0	0	1	1
859.0	0	1	1
962.0	0	1	1
990.0	0	1	1
1564.0	0	1	1
6815.0	0	1	1