## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-07-15/US_Flo_Hom_1_2010-07-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-07-15/US_Flo_Hom_1_2010-07-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Flo_Hom_1_2010-07-15/US_Flo_Hom_1_2010-07-15.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 17:39:06 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	3729571	38182947	0	0	1237800	644136	0	0.031538	1118936254

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	36566595	36566595
2.0	1.966451	233272	233272
3.0	2.90048	18560	18560
4.0	3.803172	4908	4908
5.0	4.675581	2085	2085
6.0	5.518722	1109	1109
7.0	6.333576	709	709
8.0	7.121093	464	464
9.0	7.88219	303	303
10.0	8.617753	264	264
11.0	9.328639	179	179
12.0	10.015675	166	166
13.0	10.679663	111	111
14.0	11.321375	77	77
15.0	11.941558	100	100
16.0	12.540934	67	67
17.0	13.120203	61	61
18.0	13.680038	61	61
19.0	14.221091	53	53
20.0	14.743992	48	48
21.0	15.249351	49	49
22.0	15.737756	36	36
23.0	16.209775	34	34
24.0	16.665959	31	31
25.0	17.106838	28	28
26.0	17.532927	34	34
27.0	17.944721	26	26
28.0	18.342699	28	28
29.0	18.727326	29	29
30.0	19.09905	19	19
31.0	19.458302	25	25
32.0	19.805502	15	15
33.0	20.141054	17	17
34.0	20.465349	7	7
35.0	20.778764	5	5
36.0	21.081664	11	11
37.0	21.374403	10	10
38.0	21.65732	14	14
39.0	21.930746	15	15
40.0	22.194999	10	10
41.0	22.450386	10	10
42.0	22.697206	12	12
43.0	22.935745	9	9
44.0	23.166282	12	12
45.0	23.389084	9	9
46.0	23.604412	12	12
47.0	23.812515	3	3
48.0	24.013637	7	7
49.0	24.208012	11	11
50.0	24.395866	14	14
51.0	24.577417	9	9
52.0	24.752878	7	7
53.0	24.922452	9	9
54.0	25.086337	6	6
55.0	25.244724	5	5
56.0	25.397797	12	12
57.0	25.545735	3	3
58.0	25.68871	7	7
59.0	25.826888	4	4
60.0	25.960431	7	7
61.0	26.089493	7	7
62.0	26.214226	6	6
63.0	26.334774	6	6
64.0	26.451277	4	4
65.0	26.563872	5	5
66.0	26.67269	2	2
67.0	26.777857	7	7
68.0	26.879496	5	5
69.0	26.977725	5	5
70.0	27.072658	15	15
71.0	27.164407	5	5
72.0	27.253078	9	9
73.0	27.338773	9	9
74.0	27.421594	11	11
75.0	27.501636	4	4
76.0	27.578993	5	5
77.0	27.653755	1	1
78.0	27.726009	4	4
79.0	27.795838	6	6
80.0	27.863325	7	7
81.0	27.928548	4	4
82.0	27.991583	2	2
83.0	28.052503	7	7
84.0	28.111379	5	5
85.0	28.16828	2	2
86.0	28.223272	3	3
87.0	28.276419	4	4
88.0	28.327783	3	3
89.0	28.377424	6	6
90.0	28.425399	2	2
91.0	28.471765	2	2
92.0	28.516576	3	3
93.0	28.559883	4	4
94.0	28.601737	5	5
95.0	28.642187	4	4
96.0	28.68128	3	3
97.0	28.719062	7	7
98.0	28.755576	2	2
99.0	28.790865	5	5
100.0	28.82497	3	3
101.0	0	4	4
102.0	0	4	4
103.0	0	3	3
104.0	0	3	3
105.0	0	5	5
106.0	0	4	4
107.0	0	3	3
108.0	0	2	2
109.0	0	9	9
110.0	0	5	5
111.0	0	3	3
112.0	0	3	3
113.0	0	2	2
114.0	0	3	3
115.0	0	7	7
116.0	0	1	1
117.0	0	2	2
118.0	0	1	1
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	6	6
125.0	0	4	4
127.0	0	2	2
128.0	0	4	4
129.0	0	3	3
130.0	0	6	6
131.0	0	4	4
132.0	0	2	2
133.0	0	1	1
135.0	0	2	2
136.0	0	4	4
137.0	0	1	1
138.0	0	3	3
139.0	0	3	3
140.0	0	2	2
141.0	0	4	4
142.0	0	4	4
143.0	0	5	5
144.0	0	1	1
145.0	0	3	3
146.0	0	2	2
147.0	0	1	1
148.0	0	2	2
149.0	0	1	1
150.0	0	2	2
151.0	0	3	3
152.0	0	2	2
153.0	0	4	4
154.0	0	3	3
155.0	0	1	1
156.0	0	1	1
157.0	0	3	3
158.0	0	7	7
159.0	0	2	2
160.0	0	1	1
161.0	0	3	3
162.0	0	2	2
163.0	0	3	3
164.0	0	3	3
165.0	0	3	3
166.0	0	2	2
167.0	0	2	2
168.0	0	2	2
170.0	0	3	3
171.0	0	1	1
172.0	0	2	2
173.0	0	4	4
174.0	0	3	3
175.0	0	2	2
176.0	0	4	4
177.0	0	2	2
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
182.0	0	4	4
183.0	0	2	2
184.0	0	3	3
185.0	0	3	3
188.0	0	1	1
189.0	0	1	1
191.0	0	1	1
192.0	0	3	3
193.0	0	2	2
195.0	0	2	2
196.0	0	2	2
198.0	0	1	1
199.0	0	3	3
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	2	2
205.0	0	1	1
206.0	0	3	3
207.0	0	3	3
208.0	0	3	3
209.0	0	1	1
210.0	0	1	1
212.0	0	4	4
214.0	0	1	1
215.0	0	2	2
216.0	0	3	3
217.0	0	1	1
218.0	0	3	3
219.0	0	1	1
220.0	0	1	1
221.0	0	3	3
222.0	0	1	1
225.0	0	2	2
227.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
234.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
242.0	0	3	3
244.0	0	2	2
245.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	2	2
252.0	0	1	1
253.0	0	3	3
255.0	0	2	2
257.0	0	3	3
258.0	0	2	2
260.0	0	3	3
261.0	0	1	1
262.0	0	1	1
263.0	0	2	2
264.0	0	3	3
265.0	0	2	2
267.0	0	3	3
268.0	0	1	1
269.0	0	3	3
270.0	0	3	3
272.0	0	1	1
273.0	0	1	1
276.0	0	2	2
281.0	0	2	2
282.0	0	3	3
283.0	0	1	1
285.0	0	4	4
286.0	0	1	1
288.0	0	1	1
289.0	0	2	2
290.0	0	1	1
291.0	0	2	2
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
299.0	0	1	1
300.0	0	1	1
301.0	0	2	2
303.0	0	3	3
304.0	0	1	1
305.0	0	3	3
306.0	0	3	3
307.0	0	1	1
309.0	0	1	1
311.0	0	2	2
312.0	0	3	3
314.0	0	1	1
316.0	0	1	1
317.0	0	2	2
319.0	0	2	2
320.0	0	1	1
322.0	0	3	3
324.0	0	2	2
325.0	0	2	2
327.0	0	1	1
329.0	0	1	1
333.0	0	4	4
334.0	0	1	1
335.0	0	2	2
336.0	0	1	1
337.0	0	1	1
338.0	0	1	1
340.0	0	1	1
341.0	0	1	1
342.0	0	1	1
344.0	0	1	1
345.0	0	1	1
346.0	0	1	1
347.0	0	1	1
350.0	0	2	2
351.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	1	1
355.0	0	1	1
367.0	0	2	2
370.0	0	3	3
371.0	0	1	1
372.0	0	1	1
373.0	0	1	1
375.0	0	1	1
376.0	0	1	1
377.0	0	3	3
384.0	0	2	2
385.0	0	2	2
386.0	0	2	2
388.0	0	3	3
390.0	0	1	1
391.0	0	2	2
392.0	0	1	1
397.0	0	2	2
398.0	0	3	3
399.0	0	1	1
402.0	0	3	3
405.0	0	2	2
406.0	0	3	3
408.0	0	1	1
409.0	0	1	1
410.0	0	1	1
412.0	0	2	2
413.0	0	3	3
414.0	0	3	3
415.0	0	1	1
416.0	0	1	1
418.0	0	3	3
424.0	0	2	2
425.0	0	1	1
429.0	0	1	1
432.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
438.0	0	2	2
439.0	0	1	1
444.0	0	1	1
446.0	0	1	1
449.0	0	1	1
450.0	0	2	2
452.0	0	1	1
455.0	0	1	1
465.0	0	1	1
471.0	0	1	1
473.0	0	1	1
475.0	0	1	1
476.0	0	1	1
478.0	0	2	2
479.0	0	1	1
481.0	0	2	2
482.0	0	1	1
484.0	0	3	3
489.0	0	2	2
491.0	0	1	1
494.0	0	1	1
496.0	0	2	2
499.0	0	1	1
500.0	0	1	1
502.0	0	1	1
504.0	0	1	1
507.0	0	1	1
508.0	0	3	3
510.0	0	1	1
511.0	0	1	1
519.0	0	1	1
525.0	0	1	1
527.0	0	2	2
529.0	0	1	1
533.0	0	3	3
538.0	0	2	2
541.0	0	2	2
543.0	0	1	1
546.0	0	2	2
547.0	0	1	1
548.0	0	1	1
549.0	0	1	1
552.0	0	1	1
553.0	0	1	1
554.0	0	1	1
560.0	0	2	2
562.0	0	1	1
565.0	0	1	1
567.0	0	1	1
568.0	0	1	1
570.0	0	1	1
575.0	0	1	1
576.0	0	1	1
584.0	0	1	1
585.0	0	2	2
586.0	0	1	1
587.0	0	1	1
592.0	0	1	1
593.0	0	1	1
596.0	0	1	1
597.0	0	1	1
599.0	0	1	1
602.0	0	1	1
603.0	0	1	1
604.0	0	1	1
607.0	0	1	1
614.0	0	1	1
615.0	0	1	1
620.0	0	1	1
621.0	0	1	1
622.0	0	1	1
623.0	0	1	1
626.0	0	1	1
627.0	0	2	2
628.0	0	1	1
629.0	0	1	1
631.0	0	1	1
637.0	0	1	1
639.0	0	1	1
656.0	0	1	1
660.0	0	1	1
661.0	0	1	1
666.0	0	2	2
668.0	0	1	1
669.0	0	1	1
672.0	0	1	1
674.0	0	1	1
675.0	0	1	1
679.0	0	1	1
689.0	0	3	3
698.0	0	1	1
706.0	0	1	1
708.0	0	1	1
712.0	0	1	1
713.0	0	1	1
716.0	0	1	1
717.0	0	1	1
719.0	0	1	1
720.0	0	1	1
724.0	0	1	1
726.0	0	2	2
728.0	0	1	1
731.0	0	1	1
739.0	0	1	1
740.0	0	1	1
750.0	0	1	1
758.0	0	1	1
764.0	0	1	1
767.0	0	1	1
774.0	0	1	1
790.0	0	1	1
792.0	0	1	1
797.0	0	1	1
803.0	0	1	1
807.0	0	1	1
817.0	0	1	1
823.0	0	1	1
834.0	0	1	1
839.0	0	1	1
852.0	0	1	1
857.0	0	1	1
858.0	0	1	1
872.0	0	3	3
873.0	0	1	1
904.0	0	1	1
907.0	0	1	1
910.0	0	1	1
944.0	0	1	1
947.0	0	1	1
955.0	0	1	1
978.0	0	1	1
986.0	0	1	1
988.0	0	1	1
1020.0	0	1	1
1030.0	0	1	1
1040.0	0	1	1
1046.0	0	1	1
1070.0	0	1	1
1073.0	0	1	1
1106.0	0	1	1
1115.0	0	1	1
1124.0	0	1	1
1132.0	0	1	1
1160.0	0	1	1
1178.0	0	1	1
1299.0	0	1	1
1317.0	0	1	1
1372.0	0	1	1
1419.0	0	1	1
1446.0	0	1	1
1465.0	0	1	1
1481.0	0	1	1
1486.0	0	1	1
1567.0	0	1	1
1574.0	0	1	1
1585.0	0	1	1
1606.0	0	1	1
1641.0	0	1	1
1642.0	0	1	1
1647.0	0	1	1
1714.0	0	1	1
1838.0	0	1	1
1868.0	0	1	1
1986.0	0	1	1
2077.0	0	1	1
2150.0	0	1	1
2173.0	0	1	1
2365.0	0	1	1
2519.0	0	1	1
2606.0	0	1	1
2640.0	0	1	1
2703.0	0	1	1
2829.0	0	1	1
2989.0	0	1	1
3357.0	0	1	1
5040.0	0	1	1