## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-10-15/US_Pen_Lin_1_2011-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-10-15/US_Pen_Lin_1_2011-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2011-10-15/US_Pen_Lin_1_2011-10-15.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 18:28:44 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	18586265	33041530	0	0	6207391	301951	0	0.080446	1796783654

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	32329208	32329208
2.0	1.981779	39277	39277
3.0	2.945668	2127	2127
4.0	3.891995	848	848
5.0	4.821078	450	450
6.0	5.733232	327	327
7.0	6.628766	220	220
8.0	7.507981	152	152
9.0	8.371177	110	110
10.0	9.218644	106	106
11.0	10.050669	84	84
12.0	10.867534	69	69
13.0	11.669514	62	62
14.0	12.456881	47	47
15.0	13.229902	45	45
16.0	13.988837	39	39
17.0	14.733943	34	34
18.0	15.465473	45	45
19.0	16.183673	29	29
20.0	16.888787	36	36
21.0	17.581053	32	32
22.0	18.260705	27	27
23.0	18.927973	20	20
24.0	19.583082	26	26
25.0	20.226254	19	19
26.0	20.857707	15	15
27.0	21.477655	16	16
28.0	22.086306	24	24
29.0	22.683867	24	24
30.0	23.270539	20	20
31.0	23.846521	17	17
32.0	24.412009	19	19
33.0	24.967192	19	19
34.0	25.51226	20	20
35.0	26.047396	17	17
36.0	26.57278	19	19
37.0	27.088592	14	14
38.0	27.595005	12	12
39.0	28.092191	10	10
40.0	28.580317	19	19
41.0	29.059549	17	17
42.0	29.530048	4	4
43.0	29.991975	13	13
44.0	30.445485	13	13
45.0	30.890731	11	11
46.0	31.327865	5	5
47.0	31.757033	5	5
48.0	32.178381	14	14
49.0	32.592052	13	13
50.0	32.998185	12	12
51.0	33.396918	7	7
52.0	33.788386	7	7
53.0	34.172721	7	7
54.0	34.550052	9	9
55.0	34.920508	8	8
56.0	35.284214	7	7
57.0	35.641293	11	11
58.0	35.991865	10	10
59.0	36.33605	9	9
60.0	36.673963	7	7
61.0	37.005719	12	12
62.0	37.33143	4	4
63.0	37.651206	12	12
64.0	37.965155	12	12
65.0	38.273384	5	5
66.0	38.575996	18	18
67.0	38.873095	8	8
68.0	39.16478	8	8
69.0	39.45115	14	14
70.0	39.732302	13	13
71.0	40.008332	15	15
72.0	40.279331	9	9
73.0	40.545393	5	5
74.0	40.806607	11	11
75.0	41.063061	5	5
76.0	41.314842	8	8
77.0	41.562035	10	10
78.0	41.804725	10	10
79.0	42.042992	3	3
80.0	42.276917	6	6
81.0	42.506581	6	6
82.0	42.732059	8	8
83.0	42.953429	9	9
84.0	43.170766	7	7
85.0	43.384142	6	6
86.0	43.59363	2	2
87.0	43.799301	7	7
88.0	44.001225	8	8
89.0	44.199469	5	5
90.0	44.394101	8	8
91.0	44.585187	5	5
92.0	44.772791	1	1
93.0	44.956976	4	4
94.0	45.137805	6	6
95.0	45.31534	6	6
96.0	45.489639	5	5
97.0	45.660763	4	4
98.0	45.828768	3	3
99.0	45.993712	7	7
100.0	46.155651	6	6
101.0	0	2	2
102.0	0	4	4
103.0	0	3	3
104.0	0	5	5
105.0	0	2	2
106.0	0	3	3
107.0	0	4	4
108.0	0	2	2
109.0	0	3	3
110.0	0	7	7
111.0	0	2	2
112.0	0	6	6
113.0	0	3	3
114.0	0	4	4
115.0	0	3	3
116.0	0	5	5
117.0	0	4	4
119.0	0	2	2
120.0	0	4	4
122.0	0	5	5
123.0	0	1	1
124.0	0	2	2
125.0	0	6	6
126.0	0	4	4
127.0	0	1	1
128.0	0	2	2
129.0	0	3	3
130.0	0	6	6
131.0	0	3	3
132.0	0	1	1
133.0	0	5	5
134.0	0	4	4
135.0	0	3	3
136.0	0	2	2
139.0	0	4	4
140.0	0	5	5
141.0	0	1	1
142.0	0	4	4
143.0	0	5	5
144.0	0	7	7
145.0	0	2	2
146.0	0	4	4
148.0	0	2	2
149.0	0	2	2
150.0	0	2	2
151.0	0	2	2
152.0	0	4	4
153.0	0	3	3
154.0	0	1	1
155.0	0	1	1
156.0	0	4	4
157.0	0	3	3
158.0	0	2	2
159.0	0	2	2
160.0	0	2	2
161.0	0	2	2
162.0	0	4	4
164.0	0	2	2
165.0	0	3	3
166.0	0	3	3
167.0	0	2	2
168.0	0	4	4
169.0	0	2	2
170.0	0	2	2
171.0	0	3	3
172.0	0	1	1
173.0	0	2	2
175.0	0	2	2
176.0	0	4	4
177.0	0	1	1
178.0	0	4	4
179.0	0	3	3
180.0	0	5	5
181.0	0	5	5
182.0	0	3	3
185.0	0	3	3
186.0	0	2	2
187.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	4	4
191.0	0	1	1
193.0	0	4	4
194.0	0	3	3
195.0	0	4	4
196.0	0	2	2
197.0	0	2	2
200.0	0	6	6
201.0	0	2	2
203.0	0	1	1
204.0	0	4	4
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	2	2
210.0	0	1	1
211.0	0	1	1
212.0	0	2	2
213.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
217.0	0	3	3
218.0	0	1	1
219.0	0	1	1
220.0	0	2	2
221.0	0	2	2
223.0	0	2	2
224.0	0	4	4
225.0	0	1	1
227.0	0	1	1
228.0	0	3	3
229.0	0	2	2
230.0	0	1	1
231.0	0	1	1
232.0	0	3	3
234.0	0	1	1
235.0	0	5	5
236.0	0	3	3
237.0	0	3	3
238.0	0	2	2
239.0	0	1	1
240.0	0	1	1
241.0	0	2	2
243.0	0	1	1
244.0	0	3	3
245.0	0	3	3
246.0	0	2	2
248.0	0	2	2
250.0	0	1	1
251.0	0	3	3
252.0	0	2	2
254.0	0	1	1
255.0	0	2	2
257.0	0	1	1
259.0	0	1	1
260.0	0	2	2
262.0	0	1	1
263.0	0	2	2
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
270.0	0	2	2
271.0	0	2	2
272.0	0	1	1
274.0	0	1	1
277.0	0	1	1
278.0	0	2	2
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
283.0	0	1	1
285.0	0	1	1
286.0	0	1	1
288.0	0	1	1
289.0	0	1	1
290.0	0	1	1
291.0	0	2	2
292.0	0	5	5
295.0	0	2	2
296.0	0	3	3
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
301.0	0	2	2
302.0	0	2	2
303.0	0	3	3
306.0	0	1	1
307.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	3	3
313.0	0	3	3
317.0	0	2	2
318.0	0	1	1
319.0	0	2	2
322.0	0	1	1
324.0	0	1	1
325.0	0	1	1
326.0	0	1	1
331.0	0	1	1
332.0	0	2	2
333.0	0	1	1
334.0	0	2	2
337.0	0	2	2
338.0	0	1	1
339.0	0	2	2
340.0	0	2	2
344.0	0	1	1
348.0	0	1	1
354.0	0	1	1
360.0	0	1	1
367.0	0	1	1
368.0	0	1	1
369.0	0	1	1
371.0	0	2	2
373.0	0	1	1
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
389.0	0	1	1
395.0	0	1	1
396.0	0	1	1
397.0	0	1	1
400.0	0	1	1
401.0	0	1	1
403.0	0	1	1
404.0	0	1	1
408.0	0	1	1
409.0	0	1	1
413.0	0	1	1
416.0	0	2	2
418.0	0	1	1
421.0	0	1	1
424.0	0	1	1
429.0	0	1	1
439.0	0	1	1
449.0	0	1	1
451.0	0	1	1
455.0	0	1	1
458.0	0	1	1
462.0	0	1	1
472.0	0	1	1
477.0	0	1	1
489.0	0	1	1
495.0	0	1	1
496.0	0	1	1
498.0	0	1	1
500.0	0	1	1
502.0	0	2	2
508.0	0	1	1
509.0	0	1	1
510.0	0	1	1
512.0	0	1	1
513.0	0	1	1
516.0	0	1	1
517.0	0	1	1
521.0	0	1	1
522.0	0	1	1
529.0	0	1	1
531.0	0	1	1
537.0	0	1	1
541.0	0	1	1
553.0	0	1	1
568.0	0	1	1
571.0	0	1	1
576.0	0	1	1
578.0	0	2	2
579.0	0	1	1
581.0	0	1	1
587.0	0	1	1
589.0	0	1	1
591.0	0	1	1
598.0	0	1	1
612.0	0	1	1
629.0	0	1	1
637.0	0	1	1
644.0	0	1	1
647.0	0	1	1
649.0	0	1	1
653.0	0	1	1
668.0	0	3	3
695.0	0	1	1
696.0	0	1	1
697.0	0	1	1
702.0	0	1	1
706.0	0	1	1
709.0	0	1	1
714.0	0	1	1
716.0	0	1	1
717.0	0	1	1
724.0	0	1	1
736.0	0	1	1
737.0	0	1	1
741.0	0	1	1
744.0	0	1	1
764.0	0	1	1
769.0	0	1	1
770.0	0	1	1
779.0	0	1	1
792.0	0	1	1
811.0	0	2	2
823.0	0	1	1
837.0	0	1	1
852.0	0	1	1
855.0	0	1	1
858.0	0	1	1
859.0	0	1	1
879.0	0	1	1
899.0	0	1	1
906.0	0	1	1
918.0	0	1	1
938.0	0	1	1
994.0	0	1	1
1028.0	0	1	1
1037.0	0	1	1
1046.0	0	1	1
1099.0	0	1	1
1108.0	0	1	1
1126.0	0	1	1
1129.0	0	1	1
1151.0	0	1	1
1257.0	0	1	1
1281.0	0	1	1
1349.0	0	1	1
1379.0	0	1	1
1398.0	0	1	1
1399.0	0	1	1
1421.0	0	1	1
1477.0	0	1	1
1492.0	0	1	1
1565.0	0	1	1
1611.0	0	1	1
1825.0	0	1	1
2014.0	0	1	1
2121.0	0	1	1
2154.0	0	1	1
2206.0	0	1	1
2217.0	0	1	1
2407.0	0	1	1
2408.0	0	1	1
2436.0	0	1	1
2576.0	0	1	1
2754.0	0	1	1