## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/scratch/aob2x/tempOut/ES_ba_12_fall/ES_ba_12_fall.sorted_merged.bam] OUTPUT=/scratch/aob2x/tempOut/ES_ba_12_fall/ES_ba_12_fall.dedup.bam METRICS_FILE=/scratch/aob2x/tempOut/ES_ba_12_fall/ES_ba_12_fall.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: Tue Nov 10 00:32:39 UTC 2020

## 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	4983446	46164806	0	0	1788664	199515	0	0.022481	5325525647

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	45461815	45461815
2.0	1.991369	87216	87216
3.0	2.974181	7992	7992
4.0	3.948511	1970	1970
5.0	4.91443	716	716
6.0	5.872013	356	356
7.0	6.821331	223	223
8.0	7.762456	152	152
9.0	8.695457	147	147
10.0	9.620405	98	98
11.0	10.53737	112	112
12.0	11.446421	89	89
13.0	12.347625	50	50
14.0	13.241051	70	70
15.0	14.126766	44	44
16.0	15.004836	53	53
17.0	15.875328	47	47
18.0	16.738306	41	41
19.0	17.593835	39	39
20.0	18.441981	33	33
21.0	19.282805	33	33
22.0	20.116373	24	24
23.0	20.942746	27	27
24.0	21.761987	20	20
25.0	22.574156	17	17
26.0	23.379316	19	19
27.0	24.177526	11	11
28.0	24.968847	11	11
29.0	25.753337	17	17
30.0	26.531057	16	16
31.0	27.302064	13	13
32.0	28.066416	9	9
33.0	28.824172	7	7
34.0	29.575386	9	9
35.0	30.320118	10	10
36.0	31.058421	8	8
37.0	31.790352	7	7
38.0	32.515965	3	3
39.0	33.235316	7	7
40.0	33.948457	3	3
41.0	34.655444	6	6
42.0	35.356328	6	6
43.0	36.051163	5	5
44.0	36.740001	1	1
45.0	37.422893	2	2
46.0	38.099892	10	10
47.0	38.771047	1	1
48.0	39.436409	3	3
49.0	40.096028	3	3
50.0	40.749954	3	3
51.0	41.398236	1	1
52.0	42.040923	1	1
53.0	42.678062	6	6
54.0	43.309702	5	5
55.0	43.935891	3	3
56.0	44.556675	5	5
57.0	45.1721	4	4
58.0	45.782214	2	2
59.0	46.387062	4	4
60.0	46.986689	2	2
61.0	47.581141	1	1
62.0	48.170462	2	2
63.0	48.754697	4	4
64.0	49.333889	2	2
65.0	49.908082	3	3
66.0	50.477319	2	2
67.0	51.041643	4	4
68.0	51.601096	4	4
69.0	52.15572	1	1
70.0	52.705557	2	2
71.0	53.250649	5	5
72.0	53.791036	2	2
73.0	54.326758	1	1
74.0	54.857857	4	4
75.0	55.384372	2	2
76.0	55.906343	2	2
77.0	56.423808	2	2
78.0	56.936807	1	1
79.0	57.445378	1	1
80.0	57.94956	0	0
81.0	58.449389	2	2
82.0	58.944905	3	3
83.0	59.436144	1	1
84.0	59.923143	0	0
85.0	60.405939	0	0
86.0	60.884568	2	2
87.0	61.359065	2	2
88.0	61.829467	1	1
89.0	62.295809	2	2
90.0	62.758126	1	1
91.0	63.216453	1	1
92.0	63.670824	1	1
93.0	64.121273	2	2
94.0	64.567834	0	0
95.0	65.010541	1	1
96.0	65.449426	4	4
97.0	65.884524	0	0
98.0	66.315866	0	0
99.0	66.743485	0	0
100.0	67.167414	2	2
101.0	0	1	1
102.0	0	2	2
103.0	0	1	1
104.0	0	1	1
105.0	0	2	2
107.0	0	1	1
109.0	0	5	5
111.0	0	1	1
112.0	0	1	1
114.0	0	1	1
117.0	0	2	2
118.0	0	1	1
119.0	0	2	2
121.0	0	1	1
122.0	0	1	1
127.0	0	4	4
130.0	0	1	1
132.0	0	1	1
133.0	0	2	2
134.0	0	1	1
140.0	0	1	1
142.0	0	2	2
143.0	0	2	2
146.0	0	1	1
150.0	0	2	2
151.0	0	2	2
152.0	0	1	1
155.0	0	1	1
160.0	0	1	1
162.0	0	2	2
163.0	0	1	1
164.0	0	1	1
169.0	0	2	2
170.0	0	1	1
172.0	0	1	1
174.0	0	1	1
177.0	0	1	1
179.0	0	2	2
189.0	0	1	1
191.0	0	1	1
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
197.0	0	2	2
198.0	0	2	2
199.0	0	2	2
204.0	0	1	1
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
215.0	0	1	1
217.0	0	1	1
219.0	0	1	1
221.0	0	2	2
235.0	0	1	1
237.0	0	1	1
241.0	0	1	1
245.0	0	1	1
257.0	0	1	1
265.0	0	1	1
270.0	0	1	1
282.0	0	1	1
285.0	0	1	1
286.0	0	1	1
312.0	0	1	1
321.0	0	2	2
322.0	0	1	1
333.0	0	1	1
334.0	0	2	2
335.0	0	1	1
336.0	0	1	1
375.0	0	1	1
396.0	0	1	1
406.0	0	1	1
417.0	0	1	1
423.0	0	1	1
425.0	0	1	1
434.0	0	1	1
478.0	0	1	1
485.0	0	1	1
486.0	0	2	2
512.0	0	1	1
513.0	0	1	1
543.0	0	1	1
549.0	0	1	1
579.0	0	1	1
581.0	0	1	1
616.0	0	1	1
624.0	0	1	1
633.0	0	1	1
634.0	0	1	1
681.0	0	1	1
683.0	0	1	1
688.0	0	1	1
728.0	0	1	1
785.0	0	2	2
788.0	0	1	1
841.0	0	1	1
1104.0	0	1	1
1225.0	0	1	1
1430.0	0	1	1
1450.0	0	1	1
1798.0	0	1	1
1836.0	0	1	1
2761.0	0	1	1
12114.0	0	1	1