## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Sou_Eut_1_2010-07-15/US_Sou_Eut_1_2010-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Sou_Eut_1_2010-07-15/US_Sou_Eut_1_2010-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Sou_Eut_1_2010-07-15/US_Sou_Eut_1_2010-07-15.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: Fri Jan 20 18:46:01 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	5630582	51530268	0	0	2475257	266045	0	0.027669	4973258384

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	50808256	50808256
2.0	1.989692	71321	71321
3.0	2.969182	2890	2890
4.0	3.938576	713	713
5.0	4.897977	310	310
6.0	5.847489	185	185
7.0	6.787213	130	130
8.0	7.717251	109	109
9.0	8.637702	65	65
10.0	9.548664	58	58
11.0	10.450237	49	49
12.0	11.342516	55	55
13.0	12.225598	46	46
14.0	13.099577	37	37
15.0	13.964547	33	33
16.0	14.8206	28	28
17.0	15.66783	42	42
18.0	16.506326	25	25
19.0	17.33618	28	28
20.0	18.157479	27	27
21.0	18.970312	13	13
22.0	19.774766	20	20
23.0	20.570929	15	15
24.0	21.358884	19	19
25.0	22.138717	21	21
26.0	22.910512	18	18
27.0	23.674351	11	11
28.0	24.430316	14	14
29.0	25.178489	11	11
30.0	25.91895	15	15
31.0	26.651778	18	18
32.0	27.377052	6	6
33.0	28.09485	12	12
34.0	28.805249	13	13
35.0	29.508325	11	11
36.0	30.204154	12	12
37.0	30.892811	3	3
38.0	31.574368	10	10
39.0	32.248901	4	4
40.0	32.91648	5	5
41.0	33.577177	10	10
42.0	34.231065	10	10
43.0	34.878212	15	15
44.0	35.518688	5	5
45.0	36.152562	10	10
46.0	36.779903	9	9
47.0	37.400776	9	9
48.0	38.01525	8	8
49.0	38.62339	6	6
50.0	39.225261	3	3
51.0	39.820928	10	10
52.0	40.410455	10	10
53.0	40.993905	8	8
54.0	41.571341	7	7
55.0	42.142824	5	5
56.0	42.708417	5	5
57.0	43.26818	5	5
58.0	43.822172	8	8
59.0	44.370455	8	8
60.0	44.913085	9	9
61.0	45.450122	5	5
62.0	45.981623	8	8
63.0	46.507646	5	5
64.0	47.028246	5	5
65.0	47.54348	7	7
66.0	48.053403	5	5
67.0	48.55807	8	8
68.0	49.057535	3	3
69.0	49.551851	4	4
70.0	50.041072	4	4
71.0	50.525249	7	7
72.0	51.004436	3	3
73.0	51.478684	3	3
74.0	51.948043	2	2
75.0	52.412564	9	9
76.0	52.872296	4	4
77.0	53.32729	9	9
78.0	53.777594	9	9
79.0	54.223256	3	3
80.0	54.664324	3	3
81.0	55.100845	3	3
82.0	55.532867	2	2
83.0	55.960436	10	10
84.0	56.383597	9	9
85.0	56.802396	5	5
86.0	57.216879	3	3
87.0	57.627088	3	3
88.0	58.03307	3	3
89.0	58.434866	2	2
90.0	58.832521	6	6
91.0	59.226077	1	1
92.0	59.615576	4	4
93.0	60.00106	4	4
94.0	60.382571	4	4
95.0	60.760149	3	3
96.0	61.133835	6	6
97.0	61.503669	3	3
98.0	61.86969	5	5
99.0	62.231939	2	2
100.0	62.590454	2	2
101.0	0	2	2
102.0	0	1	1
103.0	0	3	3
104.0	0	3	3
105.0	0	2	2
106.0	0	5	5
107.0	0	6	6
108.0	0	1	1
109.0	0	1	1
110.0	0	3	3
111.0	0	1	1
112.0	0	2	2
113.0	0	3	3
114.0	0	6	6
115.0	0	4	4
116.0	0	3	3
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
120.0	0	2	2
121.0	0	1	1
122.0	0	2	2
124.0	0	3	3
125.0	0	2	2
126.0	0	5	5
127.0	0	7	7
129.0	0	1	1
130.0	0	1	1
132.0	0	1	1
133.0	0	3	3
134.0	0	2	2
135.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	4	4
139.0	0	1	1
140.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	2	2
145.0	0	2	2
148.0	0	2	2
149.0	0	2	2
150.0	0	2	2
151.0	0	1	1
152.0	0	1	1
153.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	2	2
165.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	1	1
171.0	0	3	3
172.0	0	1	1
173.0	0	3	3
174.0	0	2	2
175.0	0	1	1
178.0	0	1	1
179.0	0	1	1
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
191.0	0	1	1
193.0	0	3	3
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	2	2
199.0	0	1	1
201.0	0	3	3
204.0	0	1	1
207.0	0	1	1
210.0	0	1	1
216.0	0	1	1
217.0	0	1	1
220.0	0	1	1
223.0	0	1	1
232.0	0	1	1
243.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
262.0	0	1	1
263.0	0	1	1
275.0	0	1	1
277.0	0	1	1
285.0	0	1	1
291.0	0	1	1
337.0	0	1	1
338.0	0	1	1
378.0	0	1	1
412.0	0	1	1
441.0	0	1	1
484.0	0	1	1
1319.0	0	1	1
2403.0	0	1	1
2884.0	0	1	1
3164.0	0	1	1
3374.0	0	1	1
3445.0	0	1	1
3621.0	0	1	1
3636.0	0	1	1
3747.0	0	1	1
3867.0	0	1	1
3950.0	0	1	1
4135.0	0	1	1
4218.0	0	1	1
4284.0	0	1	1
4570.0	0	1	1
4607.0	0	1	1
4668.0	0	1	1
4693.0	0	1	1
4802.0	0	1	1
5099.0	0	1	1
5732.0	0	1	1
5818.0	0	1	1
6088.0	0	1	1
6276.0	0	1	1
8751.0	0	1	1
9347.0	0	1	1