## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2014-10-01/UA_Che_Uma_1_2014-10-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2014-10-01/UA_Che_Uma_1_2014-10-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2014-10-01/UA_Che_Uma_1_2014-10-01.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 08:45:42 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	3229153	22592416	0	0	738824	689587	0	0.043748	362519344

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20965968	20965968
2.0	1.939582	485033	485033
3.0	2.822395	9982	9982
4.0	3.651871	875	875
5.0	4.431231	412	412
6.0	5.163503	306	306
7.0	5.851532	238	238
8.0	6.497992	195	195
9.0	7.105394	137	137
10.0	7.676098	134	134
11.0	8.212321	112	112
12.0	8.716145	113	113
13.0	9.18953	94	94
14.0	9.634314	81	81
15.0	10.052224	82	82
16.0	10.444885	81	81
17.0	10.813822	66	66
18.0	11.160469	63	63
19.0	11.486171	61	61
20.0	11.792195	52	52
21.0	12.07973	58	58
22.0	12.349893	39	39
23.0	12.603732	50	50
24.0	12.842235	51	51
25.0	13.066328	31	31
26.0	13.276882	37	37
27.0	13.474714	29	29
28.0	13.660594	28	28
29.0	13.835243	33	33
30.0	13.99934	32	32
31.0	14.153523	30	30
32.0	14.29839	25	25
33.0	14.434505	29	29
34.0	14.562395	21	21
35.0	14.682559	21	21
36.0	14.795463	23	23
37.0	14.901545	20	20
38.0	15.001218	27	27
39.0	15.094869	19	19
40.0	15.182861	22	22
41.0	15.265537	16	16
42.0	15.343219	27	27
43.0	15.416206	20	20
44.0	15.484784	12	12
45.0	15.549219	16	16
46.0	15.60976	15	15
47.0	15.666644	17	17
48.0	15.720091	16	16
49.0	15.770308	10	10
50.0	15.817492	22	22
51.0	15.861825	19	19
52.0	15.903479	10	10
53.0	15.942617	8	8
54.0	15.97939	10	10
55.0	16.013941	16	16
56.0	16.046405	11	11
57.0	16.076907	9	9
58.0	16.105567	8	8
59.0	16.132495	15	15
60.0	16.157795	11	11
61.0	16.181568	8	8
62.0	16.203904	6	6
63.0	16.22489	13	13
64.0	16.244609	7	7
65.0	16.263136	8	8
66.0	16.280544	10	10
67.0	16.2969	5	5
68.0	16.312268	11	11
69.0	16.326707	15	15
70.0	16.340274	15	15
71.0	16.353021	13	13
72.0	16.364998	8	8
73.0	16.376252	11	11
74.0	16.386825	7	7
75.0	16.39676	7	7
76.0	16.406094	9	9
77.0	16.414865	3	3
78.0	16.423105	8	8
79.0	16.430848	6	6
80.0	16.438123	7	7
81.0	16.444958	5	5
82.0	16.451381	4	4
83.0	16.457415	4	4
84.0	16.463085	7	7
85.0	16.468412	4	4
86.0	16.473417	6	6
87.0	16.47812	6	6
88.0	16.482539	6	6
89.0	16.486691	0	0
90.0	16.490592	5	5
91.0	16.494257	9	9
92.0	16.497701	3	3
93.0	16.500937	3	3
94.0	16.503977	6	6
95.0	16.506833	8	8
96.0	16.509517	4	4
97.0	16.512039	4	4
98.0	16.514409	2	2
99.0	16.516635	1	1
100.0	16.518727	4	4
101.0	0	5	5
102.0	0	3	3
103.0	0	3	3
104.0	0	7	7
105.0	0	6	6
106.0	0	2	2
107.0	0	7	7
108.0	0	5	5
109.0	0	2	2
110.0	0	5	5
111.0	0	5	5
112.0	0	3	3
113.0	0	6	6
114.0	0	4	4
115.0	0	2	2
116.0	0	5	5
117.0	0	3	3
118.0	0	6	6
119.0	0	2	2
120.0	0	5	5
121.0	0	3	3
122.0	0	3	3
123.0	0	3	3
124.0	0	2	2
125.0	0	4	4
126.0	0	7	7
127.0	0	5	5
128.0	0	4	4
129.0	0	5	5
130.0	0	4	4
131.0	0	4	4
132.0	0	5	5
133.0	0	4	4
135.0	0	3	3
136.0	0	3	3
137.0	0	4	4
138.0	0	2	2
139.0	0	2	2
140.0	0	4	4
141.0	0	3	3
142.0	0	1	1
143.0	0	4	4
144.0	0	3	3
145.0	0	1	1
146.0	0	3	3
147.0	0	3	3
148.0	0	1	1
149.0	0	1	1
150.0	0	2	2
151.0	0	3	3
152.0	0	1	1
153.0	0	5	5
154.0	0	3	3
156.0	0	1	1
158.0	0	5	5
159.0	0	4	4
160.0	0	1	1
161.0	0	3	3
163.0	0	1	1
164.0	0	5	5
165.0	0	4	4
166.0	0	2	2
167.0	0	1	1
168.0	0	4	4
169.0	0	2	2
172.0	0	1	1
173.0	0	2	2
175.0	0	2	2
176.0	0	3	3
177.0	0	1	1
178.0	0	4	4
179.0	0	3	3
180.0	0	4	4
182.0	0	1	1
183.0	0	4	4
184.0	0	2	2
185.0	0	3	3
187.0	0	2	2
189.0	0	1	1
191.0	0	3	3
192.0	0	1	1
194.0	0	1	1
195.0	0	3	3
196.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	1	1
200.0	0	2	2
201.0	0	4	4
203.0	0	1	1
205.0	0	3	3
206.0	0	2	2
207.0	0	3	3
208.0	0	1	1
212.0	0	3	3
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	3	3
217.0	0	2	2
219.0	0	2	2
220.0	0	1	1
221.0	0	1	1
224.0	0	1	1
226.0	0	2	2
227.0	0	2	2
229.0	0	1	1
232.0	0	4	4
233.0	0	1	1
234.0	0	1	1
236.0	0	1	1
237.0	0	1	1
238.0	0	2	2
240.0	0	1	1
241.0	0	1	1
243.0	0	1	1
244.0	0	2	2
245.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	3	3
250.0	0	2	2
252.0	0	1	1
253.0	0	1	1
257.0	0	1	1
260.0	0	2	2
262.0	0	1	1
263.0	0	2	2
265.0	0	1	1
266.0	0	1	1
267.0	0	4	4
269.0	0	1	1
270.0	0	2	2
273.0	0	3	3
275.0	0	1	1
276.0	0	1	1
277.0	0	2	2
280.0	0	1	1
281.0	0	1	1
283.0	0	1	1
284.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	2	2
290.0	0	1	1
292.0	0	3	3
293.0	0	2	2
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
304.0	0	1	1
306.0	0	1	1
310.0	0	3	3
313.0	0	2	2
315.0	0	1	1
318.0	0	2	2
319.0	0	1	1
320.0	0	1	1
328.0	0	2	2
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	1	1
339.0	0	2	2
340.0	0	1	1
343.0	0	1	1
349.0	0	1	1
353.0	0	1	1
355.0	0	2	2
359.0	0	2	2
361.0	0	1	1
362.0	0	1	1
365.0	0	1	1
367.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	2	2
373.0	0	1	1
377.0	0	1	1
379.0	0	1	1
381.0	0	1	1
390.0	0	1	1
392.0	0	1	1
395.0	0	1	1
396.0	0	1	1
400.0	0	1	1
405.0	0	1	1
407.0	0	1	1
412.0	0	1	1
414.0	0	1	1
417.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	1	1
426.0	0	1	1
428.0	0	1	1
430.0	0	1	1
434.0	0	1	1
457.0	0	1	1
458.0	0	1	1
461.0	0	1	1
462.0	0	1	1
465.0	0	1	1
469.0	0	1	1
489.0	0	1	1
505.0	0	1	1
508.0	0	1	1
513.0	0	1	1
515.0	0	1	1
517.0	0	1	1
521.0	0	1	1
526.0	0	1	1
536.0	0	1	1
542.0	0	1	1
543.0	0	1	1
546.0	0	1	1
554.0	0	1	1
564.0	0	1	1
565.0	0	1	1
568.0	0	1	1
570.0	0	1	1
571.0	0	1	1
583.0	0	1	1
608.0	0	1	1
609.0	0	1	1
618.0	0	1	1
638.0	0	1	1
644.0	0	1	1
650.0	0	1	1
655.0	0	2	2
668.0	0	1	1
686.0	0	1	1
697.0	0	1	1
707.0	0	1	1
708.0	0	1	1
711.0	0	1	1
765.0	0	1	1
796.0	0	1	1
846.0	0	1	1
926.0	0	1	1
948.0	0	1	1
1033.0	0	1	1