## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Lou_Bat_0_2013-09-15/US_Lou_Bat_0_2013-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Lou_Bat_0_2013-09-15/US_Lou_Bat_0_2013-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Lou_Bat_0_2013-09-15/US_Lou_Bat_0_2013-09-15.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: Tue Apr 25 06:16:17 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	3454844	62667999	0	0	2047799	993521	0	0.031329	1955499432

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	60128305	60128305
2.0	1.968461	811945	811945
3.0	2.906378	45155	45155
4.0	3.814714	9953	9953
5.0	4.694401	3789	3789
6.0	5.546345	1825	1825
7.0	6.371419	1063	1063
8.0	7.17047	637	637
9.0	7.944321	451	451
10.0	8.693765	297	297
11.0	9.419573	222	222
12.0	10.122489	139	139
13.0	10.803236	122	122
14.0	11.462513	88	88
15.0	12.100996	56	56
16.0	12.719343	64	64
17.0	13.318188	53	53
18.0	13.898146	37	37
19.0	14.459812	29	29
20.0	15.003764	23	23
21.0	15.530561	23	23
22.0	16.040743	26	26
23.0	16.534834	14	14
24.0	17.013342	12	12
25.0	17.476758	18	18
26.0	17.925559	14	14
27.0	18.360205	15	15
28.0	18.781143	8	8
29.0	19.188804	13	13
30.0	19.583609	8	8
31.0	19.965961	11	11
32.0	20.336255	10	10
33.0	20.69487	3	3
34.0	21.042175	8	8
35.0	21.378526	7	7
36.0	21.704269	4	4
37.0	22.019738	2	2
38.0	22.325258	1	1
39.0	22.621142	4	4
40.0	22.907694	6	6
41.0	23.185208	0	0
42.0	23.45397	3	3
43.0	23.714256	1	1
44.0	23.966332	2	2
45.0	24.210458	4	4
46.0	24.446885	1	1
47.0	24.675855	4	4
48.0	24.897603	3	3
49.0	25.112358	1	1
50.0	25.320339	1	1
51.0	25.521761	0	0
52.0	25.716831	3	3
53.0	25.905748	1	1
54.0	26.088707	1	1
55.0	26.265895	1	1
56.0	26.437495	1	1
57.0	26.603684	2	2
58.0	26.76463	0	0
59.0	26.920501	0	0
60.0	27.071455	2	2
61.0	27.217649	2	2
62.0	27.359232	1	1
63.0	27.496349	0	0
64.0	27.629142	1	1
65.0	27.757747	0	0
66.0	27.882296	1	1
67.0	28.002916	0	0
68.0	28.119732	2	2
69.0	28.232864	0	0
70.0	28.342428	2	2
71.0	28.448537	0	0
72.0	28.551299	0	0
73.0	28.65082	0	0
74.0	28.747202	0	0
75.0	28.840544	2	2
76.0	28.930942	0	0
77.0	29.01849	0	0
78.0	29.103276	0	0
79.0	29.185388	0	0
80.0	29.26491	0	0
81.0	29.341924	1	1
82.0	29.41651	2	2
83.0	29.488743	0	0
84.0	29.558698	1	1
85.0	29.626446	0	0
86.0	29.692058	0	0
87.0	29.7556	0	0
88.0	29.817139	0	0
89.0	29.876736	0	0
90.0	29.934454	0	0
91.0	29.990352	0	0
92.0	30.044486	0	0
93.0	30.096914	0	0
94.0	30.147687	0	0
95.0	30.19686	0	0
96.0	30.244481	0	0
97.0	30.290601	1	1
98.0	30.335266	1	1
99.0	30.378522	0	0
100.0	30.420414	0	0
105.0	0	1	1
106.0	0	1	1
112.0	0	1	1
124.0	0	1	1
126.0	0	1	1
133.0	0	2	2
142.0	0	1	1
157.0	0	1	1
158.0	0	1	1