## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Rho_Pro_6_2015-06-11/US_Rho_Pro_6_2015-06-11.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Rho_Pro_6_2015-06-11/US_Rho_Pro_6_2015-06-11.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Rho_Pro_6_2015-06-11/US_Rho_Pro_6_2015-06-11.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 01:18:23 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	300040	10293336	0	0	33763	95749	0	0.010785	549847471

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	9875279	9875279
2.0	1.981454	85029	85029
3.0	2.944705	473	473
4.0	3.890092	102	102
5.0	4.817946	60	60
6.0	5.728591	61	61
7.0	6.622347	35	35
8.0	7.499528	33	33
9.0	8.36044	33	33
10.0	9.205386	23	23
11.0	10.034661	28	28
12.0	10.848556	19	19
13.0	11.647356	15	15
14.0	12.431342	20	20
15.0	13.200788	18	18
16.0	13.955963	14	14
17.0	14.697133	16	16
18.0	15.424557	13	13
19.0	16.13849	9	9
20.0	16.839182	7	7
21.0	17.526879	6	6
22.0	18.201822	14	14
23.0	18.864247	5	5
24.0	19.514386	10	10
25.0	20.152468	3	3
26.0	20.778717	6	6
27.0	21.39335	8	8
28.0	21.996585	8	8
29.0	22.588631	3	3
30.0	23.169698	3	3
31.0	23.739988	6	6
32.0	24.299701	10	10
33.0	24.849033	0	0
34.0	25.388178	1	1
35.0	25.917324	4	4
36.0	26.436655	3	3
37.0	26.946356	2	2
38.0	27.446603	2	2
39.0	27.937572	0	0
40.0	28.419436	1	1
41.0	28.892363	3	3
42.0	29.35652	2	2
43.0	29.812067	3	3
44.0	30.259166	0	0
45.0	30.697974	2	2
46.0	31.128643	1	1
47.0	31.551324	1	1
48.0	31.966167	1	1
49.0	32.373315	0	0
50.0	32.772913	0	0
51.0	33.1651	0	0
52.0	33.550013	1	1
53.0	33.927787	0	0
54.0	34.298555	1	1
55.0	34.662447	0	0
56.0	35.01959	1	1
57.0	35.370109	0	0
58.0	35.714128	1	1
59.0	36.051766	0	0
60.0	36.383142	0	0
61.0	36.708373	1	1
62.0	37.027572	0	0
63.0	37.340851	0	0
64.0	37.648319	1	1
65.0	37.950086	1	1
66.0	38.246255	1	1
67.0	38.536932	0	0
68.0	38.822218	1	1
69.0	39.102213	0	0
70.0	39.377015	2	2
71.0	39.646721	0	0
72.0	39.911425	0	0
73.0	40.171219	0	0
74.0	40.426195	0	0
75.0	40.676442	1	1
76.0	40.922048	0	0
77.0	41.163099	0	0
78.0	41.39968	1	1
79.0	41.631873	0	0
80.0	41.859759	0	0
81.0	42.083419	0	0
82.0	42.302931	0	0
83.0	42.518372	1	1
84.0	42.729818	0	0
85.0	42.937341	0	0
86.0	43.141016	1	1
87.0	43.340914	0	0
88.0	43.537104	0	0
89.0	43.729656	0	0
90.0	43.918637	0	0
91.0	44.104112	0	0
92.0	44.286148	0	0
93.0	44.464808	0	0
94.0	44.640154	0	0
95.0	44.812249	2	2
96.0	44.981151	0	0
97.0	45.146921	0	0
98.0	45.309617	0	0
99.0	45.469295	0	0
100.0	45.626012	0	0
123.0	0	1	1
187.0	0	1	1
311.0	0	1	1
428.0	0	1	1
551.0	0	1	1