## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2014-10-17/US_Pen_Lin_1_2014-10-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2014-10-17/US_Pen_Lin_1_2014-10-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2014-10-17/US_Pen_Lin_1_2014-10-17.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 21:53:43 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	1657638	70707640	0	0	885832	21758219	0	0.310347	89859947

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	31966256	31966256
2.0	1.45527	10624905	10624905
3.0	1.662541	3343684	3343684
4.0	1.756905	933921	933921
5.0	1.799866	237909	237909
6.0	1.819425	58704	58704
7.0	1.828329	15549	15549
8.0	1.832383	4982	4982
9.0	1.834229	2404	2404
10.0	1.835069	1298	1298
11.0	1.835452	930	930
12.0	1.835626	698	698
13.0	1.835705	524	524
14.0	1.835741	444	444
15.0	1.835758	336	336
16.0	1.835765	317	317
17.0	1.835769	241	241
18.0	1.83577	197	197
19.0	1.835771	168	168
20.0	1.835771	132	132
21.0	1.835771	140	140
22.0	1.835771	114	114
23.0	1.835771	108	108
24.0	1.835771	117	117
25.0	1.835771	86	86
26.0	1.835771	64	64
27.0	1.835771	76	76
28.0	1.835771	68	68
29.0	1.835771	73	73
30.0	1.835771	55	55
31.0	1.835771	52	52
32.0	1.835771	47	47
33.0	1.835771	48	48
34.0	1.835771	38	38
35.0	1.835771	43	43
36.0	1.835771	31	31
37.0	1.835771	43	43
38.0	1.835771	32	32
39.0	1.835771	28	28
40.0	1.835771	30	30
41.0	1.835771	19	19
42.0	1.835771	19	19
43.0	1.835771	28	28
44.0	1.835771	18	18
45.0	1.835771	16	16
46.0	1.835771	24	24
47.0	1.835771	22	22
48.0	1.835771	27	27
49.0	1.835771	25	25
50.0	1.835771	22	22
51.0	1.835771	20	20
52.0	1.835771	20	20
53.0	1.835771	21	21
54.0	1.835771	23	23
55.0	1.835771	18	18
56.0	1.835771	24	24
57.0	1.835771	14	14
58.0	1.835771	14	14
59.0	1.835771	15	15
60.0	1.835771	18	18
61.0	1.835771	11	11
62.0	1.835771	9	9
63.0	1.835771	15	15
64.0	1.835771	11	11
65.0	1.835771	15	15
66.0	1.835771	12	12
67.0	1.835771	13	13
68.0	1.835771	9	9
69.0	1.835771	18	18
70.0	1.835771	11	11
71.0	1.835771	7	7
72.0	1.835771	12	12
73.0	1.835771	7	7
74.0	1.835771	4	4
75.0	1.835771	6	6
76.0	1.835771	8	8
77.0	1.835771	5	5
78.0	1.835771	9	9
79.0	1.835771	10	10
80.0	1.835771	11	11
81.0	1.835771	8	8
82.0	1.835771	7	7
83.0	1.835771	6	6
84.0	1.835771	7	7
85.0	1.835771	2	2
86.0	1.835771	3	3
87.0	1.835771	7	7
88.0	1.835771	5	5
89.0	1.835771	7	7
90.0	1.835771	3	3
91.0	1.835771	4	4
92.0	1.835771	5	5
93.0	1.835771	3	3
94.0	1.835771	8	8
95.0	1.835771	4	4
96.0	1.835771	6	6
97.0	1.835771	3	3
98.0	1.835771	7	7
99.0	1.835771	4	4
100.0	1.835771	6	6
101.0	0	6	6
102.0	0	3	3
103.0	0	11	11
104.0	0	5	5
105.0	0	2	2
106.0	0	2	2
108.0	0	2	2
109.0	0	4	4
110.0	0	2	2
111.0	0	4	4
112.0	0	3	3
113.0	0	4	4
114.0	0	2	2
115.0	0	2	2
116.0	0	3	3
118.0	0	1	1
119.0	0	2	2
120.0	0	2	2
121.0	0	1	1
122.0	0	1	1
123.0	0	5	5
124.0	0	2	2
125.0	0	2	2
126.0	0	1	1
128.0	0	2	2
129.0	0	2	2
130.0	0	1	1
131.0	0	5	5
132.0	0	2	2
133.0	0	2	2
134.0	0	2	2
135.0	0	4	4
136.0	0	4	4
137.0	0	1	1
138.0	0	5	5
139.0	0	2	2
140.0	0	3	3
141.0	0	4	4
142.0	0	1	1
143.0	0	3	3
144.0	0	2	2
145.0	0	3	3
147.0	0	1	1
148.0	0	1	1
149.0	0	2	2
151.0	0	1	1
152.0	0	2	2
155.0	0	1	1
157.0	0	1	1
158.0	0	2	2
159.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	1	1
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
169.0	0	1	1
170.0	0	4	4
171.0	0	3	3
172.0	0	3	3
173.0	0	3	3
174.0	0	2	2
175.0	0	1	1
177.0	0	1	1
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
182.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
190.0	0	4	4
191.0	0	1	1
192.0	0	1	1
193.0	0	2	2
194.0	0	2	2
196.0	0	1	1
197.0	0	2	2
199.0	0	2	2
201.0	0	1	1
203.0	0	1	1
205.0	0	2	2
206.0	0	2	2
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	1	1
216.0	0	1	1
218.0	0	2	2
221.0	0	1	1
223.0	0	1	1
230.0	0	1	1
233.0	0	2	2
234.0	0	2	2
235.0	0	1	1
236.0	0	2	2
237.0	0	1	1
238.0	0	2	2
241.0	0	3	3
242.0	0	3	3
246.0	0	2	2
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	2	2
252.0	0	1	1
261.0	0	1	1
262.0	0	1	1
265.0	0	1	1
269.0	0	1	1
271.0	0	1	1
274.0	0	1	1
277.0	0	1	1
280.0	0	2	2
281.0	0	1	1
282.0	0	1	1
284.0	0	1	1
286.0	0	1	1
300.0	0	2	2
301.0	0	1	1
303.0	0	1	1
307.0	0	1	1
310.0	0	1	1
313.0	0	1	1
333.0	0	1	1
334.0	0	1	1
335.0	0	1	1
339.0	0	1	1
341.0	0	1	1
345.0	0	1	1
347.0	0	1	1
356.0	0	1	1
358.0	0	2	2
366.0	0	2	2
370.0	0	1	1
372.0	0	2	2
376.0	0	1	1
377.0	0	1	1
381.0	0	1	1
388.0	0	1	1
389.0	0	1	1
393.0	0	2	2
397.0	0	1	1
398.0	0	1	1
413.0	0	1	1
417.0	0	1	1
421.0	0	1	1
425.0	0	1	1
428.0	0	1	1
431.0	0	1	1
448.0	0	2	2
451.0	0	1	1
452.0	0	1	1
458.0	0	1	1
466.0	0	2	2
467.0	0	1	1
468.0	0	1	1
475.0	0	1	1
478.0	0	1	1
482.0	0	1	1
492.0	0	1	1
502.0	0	1	1
511.0	0	1	1
515.0	0	1	1
531.0	0	1	1
584.0	0	1	1
595.0	0	1	1
610.0	0	1	1
616.0	0	1	1
642.0	0	1	1
656.0	0	1	1
662.0	0	1	1
695.0	0	1	1
720.0	0	1	1
736.0	0	1	1
753.0	0	1	1
762.0	0	1	1
764.0	0	1	1
774.0	0	1	1
787.0	0	1	1
795.0	0	1	1
807.0	0	1	1
834.0	0	1	1
845.0	0	1	1
904.0	0	1	1
961.0	0	1	1
1005.0	0	1	1
1010.0	0	1	1
1014.0	0	1	1
1119.0	0	1	1
1147.0	0	1	1
1207.0	0	1	1
1385.0	0	1	1
1476.0	0	1	1
1484.0	0	1	1
1501.0	0	1	1
1576.0	0	1	1
1589.0	0	1	1
2006.0	0	1	1
2129.0	0	1	1
2201.0	0	1	1
2227.0	0	1	1
2247.0	0	1	1
3703.0	0	1	1
4106.0	0	1	1