## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-10-02/US_Mas_Lan_1_2012-10-02.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-10-02/US_Mas_Lan_1_2012-10-02.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-10-02/US_Mas_Lan_1_2012-10-02.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 17:28:22 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	2599413	29441497	0	0	832093	92667	0	0.016548	4667152023

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	29012880	29012880
2.0	1.993712	21752	21752
3.0	2.981174	1784	1784
4.0	3.962428	557	557
5.0	4.93751	289	289
6.0	5.906461	177	177
7.0	6.869319	126	126
8.0	7.826122	108	108
9.0	8.776909	82	82
10.0	9.721716	66	66
11.0	10.660582	63	63
12.0	11.593545	52	52
13.0	12.52064	47	47
14.0	13.441905	41	41
15.0	14.357378	43	43
16.0	15.267093	35	35
17.0	16.171088	27	27
18.0	17.069398	27	27
19.0	17.962059	30	30
20.0	18.849107	23	23
21.0	19.730576	10	10
22.0	20.606503	18	18
23.0	21.476921	10	10
24.0	22.341866	9	9
25.0	23.201372	14	14
26.0	24.055473	15	15
27.0	24.904203	14	14
28.0	25.747596	11	11
29.0	26.585685	5	5
30.0	27.418504	9	9
31.0	28.246086	8	8
32.0	29.068464	3	3
33.0	29.885671	4	4
34.0	30.697738	4	4
35.0	31.504699	5	5
36.0	32.306585	6	6
37.0	33.103429	4	4
38.0	33.895262	3	3
39.0	34.682116	1	1
40.0	35.464022	5	5
41.0	36.24101	4	4
42.0	37.013113	0	0
43.0	37.780361	4	4
44.0	38.542783	2	2
45.0	39.300412	4	4
46.0	40.053276	4	4
47.0	40.801405	1	1
48.0	41.544831	5	5
49.0	42.283581	6	6
50.0	43.017686	2	2
51.0	43.747174	2	2
52.0	44.472075	5	5
53.0	45.192418	2	2
54.0	45.908231	4	4
55.0	46.619542	5	5
56.0	47.326381	4	4
57.0	48.028774	5	5
58.0	48.726751	1	1
59.0	49.420339	2	2
60.0	50.109565	3	3
61.0	50.794457	3	3
62.0	51.475042	3	3
63.0	52.151347	3	3
64.0	52.8234	1	1
65.0	53.491226	2	2
66.0	54.154853	2	2
67.0	54.814306	4	4
68.0	55.469613	2	2
69.0	56.120799	2	2
70.0	56.76789	0	0
71.0	57.410912	1	1
72.0	58.04989	2	2
73.0	58.684851	2	2
74.0	59.315818	1	1
75.0	59.942817	1	1
76.0	60.565874	1	1
77.0	61.185013	1	1
78.0	61.800258	0	0
79.0	62.411635	1	1
80.0	63.019166	1	1
81.0	63.622878	1	1
82.0	64.222793	3	3
83.0	64.818936	1	1
84.0	65.41133	0	0
85.0	65.999998	1	1
86.0	66.584965	2	2
87.0	67.166253	2	2
88.0	67.743886	3	3
89.0	68.317887	0	0
90.0	68.888278	1	1
91.0	69.455082	1	1
92.0	70.018322	4	4
93.0	70.57802	1	1
94.0	71.134199	0	0
95.0	71.68688	1	1
96.0	72.236086	2	2
97.0	72.781838	1	1
98.0	73.324158	0	0
99.0	73.863067	0	0
100.0	74.398588	0	0
101.0	0	2	2
102.0	0	1	1
106.0	0	1	1
109.0	0	1	1
111.0	0	1	1
112.0	0	1	1
115.0	0	1	1
116.0	0	2	2
117.0	0	3	3
120.0	0	2	2
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
124.0	0	2	2
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	2	2
131.0	0	1	1
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	2	2
137.0	0	1	1
140.0	0	1	1
143.0	0	2	2
145.0	0	1	1
149.0	0	1	1
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
162.0	0	1	1
163.0	0	2	2
165.0	0	2	2
166.0	0	1	1
168.0	0	2	2
169.0	0	2	2
176.0	0	1	1
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
183.0	0	1	1
187.0	0	1	1
189.0	0	1	1
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
195.0	0	2	2
199.0	0	1	1
202.0	0	1	1
203.0	0	1	1
205.0	0	1	1
209.0	0	1	1
213.0	0	1	1
214.0	0	1	1
217.0	0	1	1
219.0	0	1	1
233.0	0	1	1
243.0	0	1	1
247.0	0	2	2
250.0	0	1	1
253.0	0	1	1
255.0	0	1	1
259.0	0	1	1
269.0	0	1	1
273.0	0	1	1
279.0	0	1	1
285.0	0	1	1
290.0	0	1	1
297.0	0	1	1
302.0	0	1	1
307.0	0	1	1
325.0	0	1	1
346.0	0	1	1
347.0	0	1	1
352.0	0	1	1
355.0	0	1	1
357.0	0	1	1
367.0	0	1	1
381.0	0	1	1
401.0	0	1	1
406.0	0	1	1
523.0	0	1	1
593.0	0	1	1
786.0	0	1	1
1146.0	0	1	1
1248.0	0	1	1
1394.0	0	1	1
1406.0	0	1	1
1638.0	0	1	1
1746.0	0	1	1
2639.0	0	1	1
11608.0	0	1	1