## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-07-16/US_Pen_Lin_1_2012-07-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-07-16/US_Pen_Lin_1_2012-07-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2012-07-16/US_Pen_Lin_1_2012-07-16.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: Fri Jan 20 17:54:43 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	3346597	41251817	0	0	1328628	158759	0	0.019175	5345660827

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	40700652	40700652
2.0	1.992313	15786	15786
3.0	2.976998	945	945
4.0	3.954113	281	281
5.0	4.923717	228	228
6.0	5.885867	164	164
7.0	6.840622	152	152
8.0	7.788037	113	113
9.0	8.728169	77	77
10.0	9.661074	81	81
11.0	10.586807	62	62
12.0	11.505424	44	44
13.0	12.41698	33	33
14.0	13.321529	33	33
15.0	14.219124	33	33
16.0	15.109819	27	27
17.0	15.993667	18	18
18.0	16.870721	15	15
19.0	17.741032	20	20
20.0	18.604654	21	21
21.0	19.461636	13	13
22.0	20.312031	8	8
23.0	21.155889	10	10
24.0	21.99326	14	14
25.0	22.824194	11	11
26.0	23.64874	9	9
27.0	24.466948	8	8
28.0	25.278866	13	13
29.0	26.084543	12	12
30.0	26.884026	9	9
31.0	27.677364	7	7
32.0	28.464603	9	9
33.0	29.245791	9	9
34.0	30.020973	6	6
35.0	30.790196	6	6
36.0	31.553506	6	6
37.0	32.310949	6	6
38.0	33.062569	5	5
39.0	33.808411	5	5
40.0	34.54852	8	8
41.0	35.282939	4	4
42.0	36.011713	5	5
43.0	36.734884	3	3
44.0	37.452496	4	4
45.0	38.164592	3	3
46.0	38.871214	2	2
47.0	39.572404	6	6
48.0	40.268204	1	1
49.0	40.958655	1	1
50.0	41.643799	5	5
51.0	42.323675	4	4
52.0	42.998325	4	4
53.0	43.66779	2	2
54.0	44.332107	5	5
55.0	44.991318	3	3
56.0	45.645462	4	4
57.0	46.294577	1	1
58.0	46.938702	3	3
59.0	47.577876	0	0
60.0	48.212136	2	2
61.0	48.841521	3	3
62.0	49.466068	2	2
63.0	50.085813	2	2
64.0	50.700794	3	3
65.0	51.311048	3	3
66.0	51.916611	1	1
67.0	52.517519	8	8
68.0	53.113807	1	1
69.0	53.705512	2	2
70.0	54.292668	2	2
71.0	54.87531	3	3
72.0	55.453474	1	1
73.0	56.027193	4	4
74.0	56.596502	1	1
75.0	57.161434	3	3
76.0	57.722024	2	2
77.0	58.278304	0	0
78.0	58.830308	1	1
79.0	59.378069	2	2
80.0	59.921619	1	1
81.0	60.460991	2	2
82.0	60.996217	1	1
83.0	61.527328	2	2
84.0	62.054356	0	0
85.0	62.577333	2	2
86.0	63.09629	2	2
87.0	63.611257	3	3
88.0	64.122266	1	1
89.0	64.629347	2	2
90.0	65.132529	1	1
91.0	65.631844	1	1
92.0	66.12732	1	1
93.0	66.618987	0	0
94.0	67.106875	0	0
95.0	67.591012	1	1
96.0	68.071428	0	0
97.0	68.548151	1	1
98.0	69.021209	1	1
99.0	69.49063	3	3
100.0	69.956443	0	0
101.0	0	2	2
102.0	0	3	3
103.0	0	1	1
104.0	0	1	1
105.0	0	1	1
106.0	0	1	1
107.0	0	1	1
108.0	0	1	1
109.0	0	3	3
110.0	0	2	2
111.0	0	2	2
113.0	0	2	2
115.0	0	1	1
116.0	0	3	3
120.0	0	1	1
123.0	0	1	1
124.0	0	1	1
127.0	0	2	2
130.0	0	1	1
131.0	0	1	1
137.0	0	1	1
139.0	0	1	1
141.0	0	1	1
151.0	0	2	2
155.0	0	1	1
158.0	0	1	1
165.0	0	1	1
167.0	0	1	1
170.0	0	1	1
173.0	0	1	1
176.0	0	2	2
178.0	0	1	1
179.0	0	1	1
188.0	0	1	1
193.0	0	2	2
195.0	0	1	1
208.0	0	1	1
210.0	0	1	1
212.0	0	1	1
229.0	0	1	1
230.0	0	1	1
236.0	0	1	1
241.0	0	1	1
243.0	0	1	1
247.0	0	1	1
265.0	0	1	1
276.0	0	1	1
287.0	0	1	1
291.0	0	1	1
322.0	0	1	1
356.0	0	1	1
382.0	0	1	1
393.0	0	1	1
419.0	0	1	1
522.0	0	1	1
564.0	0	1	1
594.0	0	1	1
610.0	0	1	1
720.0	0	1	1
733.0	0	1	1
800.0	0	1	1
931.0	0	1	1
971.0	0	1	1
998.0	0	1	1
1087.0	0	1	1
1143.0	0	1	1
1286.0	0	1	1
1328.0	0	1	1
1565.0	0	1	1
1625.0	0	1	1
1974.0	0	1	1
2051.0	0	1	1
2283.0	0	1	1
2501.0	0	1	1
3005.0	0	1	1
3580.0	0	1	1
3782.0	0	1	1
8387.0	0	1	1
10330.0	0	1	1
11603.0	0	1	1
12520.0	0	1	1
29162.0	0	1	1