## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/PA_Pan_Pan_1_2012-01-16/PA_Pan_Pan_1_2012-01-16.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/PA_Pan_Pan_1_2012-01-16/PA_Pan_Pan_1_2012-01-16.dedup.bam METRICS_FILE=./pipeline_output_destplus/PA_Pan_Pan_1_2012-01-16/PA_Pan_Pan_1_2012-01-16.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: Sat Jan 14 02:53:03 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	188610	55468754	0	0	76635	1424833	0	0.026333	1061129554

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	52114025	52114025
2.0	1.949069	1214764	1214764
3.0	2.849802	57785	57785
4.0	3.70466	11990	11990
5.0	4.51598	4547	4547
6.0	5.285978	2016	2016
7.0	6.016761	940	940
8.0	6.710324	481	481
9.0	7.368563	286	286
10.0	7.993278	156	156
11.0	8.586176	108	108
12.0	9.148877	56	56
13.0	9.68292	47	47
14.0	10.189763	30	30
15.0	10.670793	29	29
16.0	11.127323	36	36
17.0	11.560603	29	29
18.0	11.971815	20	20
19.0	12.362084	14	14
20.0	12.732476	10	10
21.0	13.084004	7	7
22.0	13.417628	11	11
23.0	13.734261	10	10
24.0	14.034767	8	8
25.0	14.319969	3	3
26.0	14.590645	3	3
27.0	14.847535	2	2
28.0	15.091342	3	3
29.0	15.322731	1	1
30.0	15.542336	7	7
31.0	15.750756	6	6
32.0	15.948561	2	2
33.0	16.136292	2	2
34.0	16.314462	1	1
35.0	16.483557	6	6
36.0	16.64404	4	4
37.0	16.79635	3	3
38.0	16.940903	1	1
39.0	17.078093	1	1
40.0	17.208296	0	0
41.0	17.331868	0	0
42.0	17.449146	3	3
43.0	17.560452	3	3
44.0	17.666088	2	2
45.0	17.766344	0	0
46.0	17.861494	2	2
47.0	17.951798	1	1
48.0	18.037503	2	2
49.0	18.118843	0	0
50.0	18.19604	0	0
51.0	18.269306	0	0
52.0	18.33884	0	0
53.0	18.404833	3	3
54.0	18.467464	2	2
55.0	18.526906	0	0
56.0	18.58332	1	1
57.0	18.636861	0	0
58.0	18.687676	1	1
59.0	18.735902	2	2
60.0	18.781672	1	1
61.0	18.825111	1	1
62.0	18.866337	1	1
63.0	18.905464	0	0
64.0	18.942598	1	1
65.0	18.977841	0	0
66.0	19.011289	1	1
67.0	19.043034	2	2
68.0	19.073161	0	0
69.0	19.101755	0	0
70.0	19.128892	0	0
71.0	19.154646	0	0
72.0	19.17909	0	0
73.0	19.202288	0	0
74.0	19.224305	0	0
75.0	19.2452	0	0
76.0	19.265031	0	0
77.0	19.283852	2	2
78.0	19.301715	0	0
79.0	19.318668	0	0
80.0	19.334757	0	0
81.0	19.350027	0	0
82.0	19.36452	1	1
83.0	19.378274	0	0
84.0	19.391328	0	0
85.0	19.403716	0	0
86.0	19.415474	0	0
87.0	19.426633	1	1
88.0	19.437224	1	1
89.0	19.447275	0	0
90.0	19.456815	0	0
91.0	19.465868	0	0
92.0	19.474461	0	0
93.0	19.482616	1	1
94.0	19.490355	1	1
95.0	19.4977	1	1
96.0	19.504672	0	0
97.0	19.511288	0	0
98.0	19.517567	0	0
99.0	19.523526	0	0
100.0	19.529182	0	0
101.0	0	1	1
105.0	0	1	1
106.0	0	1	1
111.0	0	1	1
112.0	0	2	2
117.0	0	1	1
120.0	0	1	1
121.0	0	1	1
150.0	0	1	1
164.0	0	1	1
168.0	0	1	1
263.0	0	1	1
298.0	0	1	1
306.0	0	1	1
336.0	0	1	1
337.0	0	1	1
339.0	0	1	1
378.0	0	1	1
446.0	0	1	1
455.0	0	1	1
471.0	0	1	1
570.0	0	1	1
595.0	0	1	1
620.0	0	1	1
652.0	0	1	1
862.0	0	1	1