## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Nor_Ral_2_2003-07-01/US_Nor_Ral_2_2003-07-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Nor_Ral_2_2003-07-01/US_Nor_Ral_2_2003-07-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Nor_Ral_2_2003-07-01/US_Nor_Ral_2_2003-07-01.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 17:12:29 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	569377	17088274	0	0	115015	143566	0	0.011574	1011281493

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	16379554	16379554
2.0	1.983244	67848	67848
3.0	2.950014	5594	5594
4.0	3.900584	1482	1482
5.0	4.835227	724	724
6.0	5.75421	401	401
7.0	6.657794	234	234
8.0	7.546238	172	172
9.0	8.419796	145	145
10.0	9.278716	107	107
11.0	10.123245	78	78
12.0	10.953623	59	59
13.0	11.770088	65	65
14.0	12.572872	49	49
15.0	13.362205	48	48
16.0	14.138312	43	43
17.0	14.901415	27	27
18.0	15.651732	22	22
19.0	16.389477	28	28
20.0	17.11486	20	20
21.0	17.828089	15	15
22.0	18.529367	20	20
23.0	19.218895	14	14
24.0	19.896869	19	19
25.0	20.563484	12	12
26.0	21.218929	8	8
27.0	21.863391	9	9
28.0	22.497055	5	5
29.0	23.120102	2	2
30.0	23.732709	2	2
31.0	24.335051	5	5
32.0	24.927301	4	4
33.0	25.509627	4	4
34.0	26.082196	2	2
35.0	26.645171	5	5
36.0	27.198713	3	3
37.0	27.74298	1	1
38.0	28.278128	7	7
39.0	28.804308	2	2
40.0	29.321673	0	0
41.0	29.830368	2	2
42.0	30.33054	2	2
43.0	30.822331	1	1
44.0	31.305882	1	1
45.0	31.781331	2	2
46.0	32.248813	1	1
47.0	32.708462	0	0
48.0	33.16041	1	1
49.0	33.604785	4	4
50.0	34.041714	4	4
51.0	34.471322	1	1
52.0	34.893731	1	1
53.0	35.309063	0	0
54.0	35.717436	0	0
55.0	36.118966	0	0
56.0	36.513768	2	2
57.0	36.901955	0	0
58.0	37.283638	1	1
59.0	37.658925	1	1
60.0	38.027924	2	2
61.0	38.390741	0	0
62.0	38.747478	2	2
63.0	39.098237	0	0
64.0	39.44312	0	0
65.0	39.782224	1	1
66.0	40.115645	1	1
67.0	40.443481	1	1
68.0	40.765823	1	1
69.0	41.082764	2	2
70.0	41.394394	0	0
71.0	41.700803	0	0
72.0	42.002077	1	1
73.0	42.298304	4	4
74.0	42.589567	0	0
75.0	42.87595	1	1
76.0	43.157535	1	1
77.0	43.434401	0	0
78.0	43.706628	0	0
79.0	43.974294	0	0
80.0	44.237475	1	1
81.0	44.496246	3	3
82.0	44.750681	1	1
83.0	45.000853	1	1
84.0	45.246833	1	1
85.0	45.488692	0	0
86.0	45.726498	0	0
87.0	45.960319	1	1
88.0	46.190223	2	2
89.0	46.416274	1	1
90.0	46.638538	0	0
91.0	46.857078	2	2
92.0	47.071956	0	0
93.0	47.283233	0	0
94.0	47.49097	0	0
95.0	47.695227	1	1
96.0	47.896061	1	1
97.0	48.09353	1	1
98.0	48.28769	0	0
99.0	48.478597	0	0
100.0	48.666305	2	2
101.0	0	1	1
103.0	0	4	4
104.0	0	2	2
105.0	0	1	1
110.0	0	1	1
112.0	0	1	1
113.0	0	1	1
115.0	0	1	1
116.0	0	1	1
117.0	0	1	1
120.0	0	1	1
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
124.0	0	1	1
125.0	0	1	1
126.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
134.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
141.0	0	1	1
145.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
155.0	0	1	1
158.0	0	1	1
163.0	0	1	1
165.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
171.0	0	1	1
175.0	0	1	1
177.0	0	1	1
178.0	0	1	1
181.0	0	1	1
182.0	0	1	1
184.0	0	1	1
188.0	0	1	1
196.0	0	1	1
208.0	0	1	1
210.0	0	1	1
212.0	0	1	1
220.0	0	1	1
221.0	0	1	1
227.0	0	1	1
232.0	0	1	1
238.0	0	1	1
257.0	0	1	1
260.0	0	1	1
265.0	0	1	1
266.0	0	1	1
270.0	0	1	1
285.0	0	1	1
322.0	0	1	1
325.0	0	1	1
348.0	0	1	1
368.0	0	1	1
410.0	0	1	1
434.0	0	1	1
446.0	0	1	1
455.0	0	1	1
467.0	0	1	1
489.0	0	1	1
504.0	0	1	1
512.0	0	1	1
527.0	0	1	1
531.0	0	1	1
532.0	0	1	1
560.0	0	1	1
567.0	0	1	1
609.0	0	1	1
611.0	0	1	1
614.0	0	1	1
637.0	0	1	1
671.0	0	1	1
675.0	0	1	1
685.0	0	1	1
693.0	0	1	1
694.0	0	1	1
721.0	0	1	1
734.0	0	1	1
738.0	0	1	1
759.0	0	2	2
792.0	0	1	1
800.0	0	1	1
802.0	0	1	1
900.0	0	1	1
933.0	0	1	1
998.0	0	1	1
1019.0	0	1	1
1077.0	0	1	1
1240.0	0	1	1