## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-07-25/US_New_Ith_1_2012-07-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-07-25/US_New_Ith_1_2012-07-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_New_Ith_1_2012-07-25/US_New_Ith_1_2012-07-25.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 18:09:32 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	1929990	44211871	0	0	642206	229957	0	0.012198	4235369567

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	43541257	43541257
2.0	1.989616	62442	62442
3.0	2.968955	4693	4693
4.0	3.938124	1009	1009
5.0	4.897228	401	401
6.0	5.846373	265	265
7.0	6.785662	170	170
8.0	7.715197	150	150
9.0	8.635079	117	117
10.0	9.545409	88	88
11.0	10.446285	87	87
12.0	11.337806	64	64
13.0	12.220069	69	69
14.0	13.093171	55	55
15.0	13.957206	55	55
16.0	14.812268	41	41
17.0	15.658451	37	37
18.0	16.495847	43	43
19.0	17.324547	39	39
20.0	18.144641	23	23
21.0	18.95622	17	17
22.0	19.75937	21	21
23.0	20.55418	16	16
24.0	21.340737	16	16
25.0	22.119125	15	15
26.0	22.889431	10	10
27.0	23.651737	12	12
28.0	24.406127	14	14
29.0	25.152683	12	12
30.0	25.891487	9	9
31.0	26.622618	8	8
32.0	27.346157	7	7
33.0	28.062183	7	7
34.0	28.770773	5	5
35.0	29.472005	6	6
36.0	30.165955	3	3
37.0	30.852699	1	1
38.0	31.532311	5	5
39.0	32.204866	4	4
40.0	32.870436	3	3
41.0	33.529095	4	4
42.0	34.180915	5	5
43.0	34.825965	2	2
44.0	35.464317	2	2
45.0	36.096041	3	3
46.0	36.721204	9	9
47.0	37.339875	3	3
48.0	37.952121	2	2
49.0	38.55801	1	1
50.0	39.157607	7	7
51.0	39.750977	5	5
52.0	40.338186	1	1
53.0	40.919297	6	6
54.0	41.494373	3	3
55.0	42.063477	6	6
56.0	42.626672	1	1
57.0	43.184018	2	2
58.0	43.735577	2	2
59.0	44.281407	2	2
60.0	44.82157	3	3
61.0	45.356124	2	2
62.0	45.885126	2	2
63.0	46.408635	1	1
64.0	46.926707	2	2
65.0	47.4394	3	3
66.0	47.946769	2	2
67.0	48.448869	1	1
68.0	48.945755	1	1
69.0	49.437481	3	3
70.0	49.924101	4	4
71.0	50.405667	3	3
72.0	50.882233	2	2
73.0	51.35385	1	1
74.0	51.820569	3	3
75.0	52.282442	3	3
76.0	52.739518	1	1
77.0	53.191848	1	1
78.0	53.639481	1	1
79.0	54.082465	2	2
80.0	54.52085	2	2
81.0	54.954681	4	4
82.0	55.384008	1	1
83.0	55.808877	0	0
84.0	56.229333	0	0
85.0	56.645423	1	1
86.0	57.057193	3	3
87.0	57.464686	2	2
88.0	57.867948	1	1
89.0	58.267022	0	0
90.0	58.661952	2	2
91.0	59.052781	1	1
92.0	59.439551	2	2
93.0	59.822305	0	0
94.0	60.201084	0	0
95.0	60.57593	2	2
96.0	60.946883	1	1
97.0	61.313984	2	2
98.0	61.677273	0	0
99.0	62.03679	2	2
100.0	62.392573	1	1
101.0	0	2	2
103.0	0	2	2
105.0	0	1	1
107.0	0	1	1
109.0	0	1	1
111.0	0	1	1
113.0	0	2	2
117.0	0	1	1
119.0	0	1	1
120.0	0	3	3
123.0	0	2	2
125.0	0	1	1
126.0	0	2	2
127.0	0	1	1
128.0	0	1	1
129.0	0	2	2
130.0	0	1	1
131.0	0	1	1
133.0	0	2	2
136.0	0	2	2
137.0	0	2	2
139.0	0	3	3
144.0	0	1	1
146.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	2	2
151.0	0	1	1
153.0	0	1	1
157.0	0	1	1
159.0	0	1	1
165.0	0	1	1
166.0	0	1	1
168.0	0	1	1
171.0	0	1	1
175.0	0	1	1
176.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
183.0	0	1	1
184.0	0	1	1
186.0	0	1	1
187.0	0	1	1
193.0	0	2	2
199.0	0	1	1
205.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
228.0	0	1	1
230.0	0	1	1
232.0	0	1	1
238.0	0	1	1
241.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
255.0	0	1	1
256.0	0	1	1
258.0	0	1	1
262.0	0	1	1
267.0	0	1	1
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
285.0	0	1	1
288.0	0	1	1
291.0	0	1	1
293.0	0	1	1
298.0	0	1	1
299.0	0	1	1
301.0	0	1	1
308.0	0	1	1
310.0	0	1	1
315.0	0	2	2
333.0	0	1	1
336.0	0	1	1
338.0	0	1	1
339.0	0	1	1
341.0	0	1	1
344.0	0	2	2
352.0	0	1	1
361.0	0	1	1
370.0	0	1	1
372.0	0	1	1
382.0	0	1	1
384.0	0	1	1
387.0	0	1	1
480.0	0	1	1
527.0	0	1	1
541.0	0	1	1
595.0	0	1	1
602.0	0	1	1
634.0	0	1	1
648.0	0	1	1
755.0	0	1	1
857.0	0	1	1
955.0	0	1	1
1000.0	0	1	1
1034.0	0	1	1
1057.0	0	1	1
1241.0	0	1	1
1253.0	0	1	1
1562.0	0	1	1
1762.0	0	1	1
1945.0	0	1	1
2066.0	0	1	1
2129.0	0	1	1
2711.0	0	1	1
3023.0	0	1	1
3690.0	0	1	1
3954.0	0	1	1
8142.0	0	1	1
10722.0	0	1	1
11315.0	0	1	1
12153.0	0	1	1
28294.0	0	1	1