## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-10-20/US_Mas_Lan_1_2014-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-10-20/US_Mas_Lan_1_2014-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2014-10-20/US_Mas_Lan_1_2014-10-20.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 20:23:10 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	1690415	55037540	0	0	846342	5750790	0	0.110481	244682011

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	43174403	43174403
2.0	1.798568	4484731	4484731
3.0	2.436279	422865	422865
4.0	2.945535	45777	45777
5.0	3.35221	9327	9327
6.0	3.676968	4056	4056
7.0	3.93631	2289	2289
8.0	4.143412	1543	1543
9.0	4.308797	1123	1123
10.0	4.440868	777	777
11.0	4.546336	635	635
12.0	4.630559	504	504
13.0	4.697817	388	388
14.0	4.751527	313	313
15.0	4.794418	272	272
16.0	4.82867	221	221
17.0	4.856022	180	180
18.0	4.877864	165	165
19.0	4.895307	147	147
20.0	4.909236	136	136
21.0	4.92036	116	116
22.0	4.929243	108	108
23.0	4.936336	104	104
24.0	4.942001	99	99
25.0	4.946524	82	82
26.0	4.950137	90	90
27.0	4.953022	59	59
28.0	4.955325	81	81
29.0	4.957165	70	70
30.0	4.958634	64	64
31.0	4.959807	51	51
32.0	4.960744	37	37
33.0	4.961492	53	53
34.0	4.96209	56	56
35.0	4.962567	36	36
36.0	4.962948	44	44
37.0	4.963252	43	43
38.0	4.963495	42	42
39.0	4.963689	39	39
40.0	4.963844	23	23
41.0	4.963968	30	30
42.0	4.964066	24	24
43.0	4.964145	21	21
44.0	4.964208	30	30
45.0	4.964259	24	24
46.0	4.964299	24	24
47.0	4.964331	30	30
48.0	4.964357	19	19
49.0	4.964377	18	18
50.0	4.964393	12	12
51.0	4.964406	23	23
52.0	4.964417	22	22
53.0	4.964425	22	22
54.0	4.964432	18	18
55.0	4.964437	25	25
56.0	4.964441	14	14
57.0	4.964445	14	14
58.0	4.964448	20	20
59.0	4.96445	20	20
60.0	4.964451	13	13
61.0	4.964453	15	15
62.0	4.964454	8	8
63.0	4.964455	19	19
64.0	4.964455	10	10
65.0	4.964456	17	17
66.0	4.964456	15	15
67.0	4.964457	18	18
68.0	4.964457	12	12
69.0	4.964457	13	13
70.0	4.964457	8	8
71.0	4.964458	6	6
72.0	4.964458	11	11
73.0	4.964458	8	8
74.0	4.964458	13	13
75.0	4.964458	7	7
76.0	4.964458	7	7
77.0	4.964458	9	9
78.0	4.964458	7	7
79.0	4.964458	2	2
80.0	4.964458	3	3
81.0	4.964458	5	5
82.0	4.964458	7	7
83.0	4.964458	6	6
84.0	4.964458	8	8
85.0	4.964458	6	6
86.0	4.964458	7	7
87.0	4.964458	7	7
88.0	4.964458	9	9
89.0	4.964458	7	7
90.0	4.964458	5	5
91.0	4.964458	3	3
92.0	4.964458	4	4
93.0	4.964458	9	9
94.0	4.964458	7	7
95.0	4.964458	7	7
96.0	4.964458	2	2
97.0	4.964458	1	1
98.0	4.964458	3	3
99.0	4.964458	6	6
100.0	4.964458	5	5
101.0	0	5	5
102.0	0	4	4
103.0	0	6	6
104.0	0	4	4
105.0	0	5	5
106.0	0	2	2
107.0	0	6	6
108.0	0	6	6
109.0	0	5	5
110.0	0	5	5
111.0	0	4	4
112.0	0	3	3
114.0	0	2	2
115.0	0	6	6
116.0	0	3	3
117.0	0	6	6
118.0	0	4	4
119.0	0	3	3
120.0	0	6	6
121.0	0	3	3
122.0	0	3	3
123.0	0	3	3
125.0	0	1	1
126.0	0	3	3
129.0	0	3	3
130.0	0	3	3
131.0	0	2	2
132.0	0	3	3
133.0	0	4	4
134.0	0	4	4
135.0	0	4	4
136.0	0	2	2
137.0	0	4	4
138.0	0	3	3
139.0	0	2	2
141.0	0	3	3
142.0	0	4	4
143.0	0	2	2
144.0	0	2	2
145.0	0	3	3
146.0	0	2	2
147.0	0	2	2
148.0	0	2	2
151.0	0	1	1
152.0	0	5	5
153.0	0	1	1
154.0	0	2	2
156.0	0	1	1
157.0	0	3	3
159.0	0	1	1
160.0	0	2	2
163.0	0	4	4
164.0	0	1	1
165.0	0	2	2
166.0	0	2	2
168.0	0	2	2
169.0	0	1	1
170.0	0	1	1
171.0	0	1	1
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	3	3
178.0	0	2	2
179.0	0	4	4
180.0	0	2	2
181.0	0	1	1
182.0	0	1	1
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
193.0	0	2	2
194.0	0	1	1
196.0	0	1	1
198.0	0	4	4
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
205.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
213.0	0	2	2
214.0	0	2	2
216.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	3	3
223.0	0	2	2
225.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	3	3
230.0	0	1	1
231.0	0	1	1
233.0	0	2	2
234.0	0	3	3
237.0	0	2	2
238.0	0	1	1
239.0	0	2	2
240.0	0	1	1
241.0	0	1	1
243.0	0	3	3
244.0	0	1	1
245.0	0	2	2
246.0	0	1	1
250.0	0	2	2
252.0	0	2	2
253.0	0	1	1
256.0	0	2	2
262.0	0	1	1
268.0	0	1	1
269.0	0	1	1
273.0	0	1	1
278.0	0	2	2
279.0	0	1	1
281.0	0	1	1
291.0	0	1	1
295.0	0	2	2
296.0	0	2	2
297.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	1	1
308.0	0	1	1
310.0	0	1	1
313.0	0	1	1
314.0	0	3	3
319.0	0	1	1
321.0	0	1	1
328.0	0	1	1
330.0	0	1	1
332.0	0	2	2
336.0	0	1	1
338.0	0	1	1
342.0	0	1	1
346.0	0	1	1
353.0	0	1	1
355.0	0	1	1
356.0	0	2	2
358.0	0	1	1
361.0	0	1	1
362.0	0	1	1
363.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	1	1
380.0	0	1	1
384.0	0	1	1
391.0	0	1	1
395.0	0	2	2
408.0	0	1	1
416.0	0	1	1
424.0	0	1	1
432.0	0	1	1
435.0	0	1	1
437.0	0	1	1
443.0	0	1	1
444.0	0	1	1
463.0	0	1	1
464.0	0	1	1
482.0	0	1	1
494.0	0	1	1
497.0	0	1	1
506.0	0	1	1
508.0	0	1	1
582.0	0	1	1