## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-12-16/US_Cal_Pla_1_2013-12-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-12-16/US_Cal_Pla_1_2013-12-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-12-16/US_Cal_Pla_1_2013-12-16.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 17:38:31 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	3390865	31021875	0	0	1059903	1652778	0	0.066715	280697937

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	27765707	27765707
2.0	1.895371	1104319	1104319
3.0	2.697061	39666	39666
4.0	3.41487	3067	3067
5.0	4.057576	1155	1155
6.0	4.633037	763	763
7.0	5.148288	604	604
8.0	5.609628	413	413
9.0	6.0227	322	322
10.0	6.392552	275	275
11.0	6.723706	236	236
12.0	7.020213	183	183
13.0	7.285696	150	150
14.0	7.523402	136	136
15.0	7.736238	131	131
16.0	7.926804	95	95
17.0	8.097432	101	101
18.0	8.250207	93	93
19.0	8.386997	69	69
20.0	8.509476	79	79
21.0	8.619139	72	72
22.0	8.717329	67	67
23.0	8.805245	54	54
24.0	8.883962	61	61
25.0	8.954444	50	50
26.0	9.017551	73	73
27.0	9.074055	62	62
28.0	9.124647	51	51
29.0	9.169946	43	43
30.0	9.210505	45	45
31.0	9.246821	31	31
32.0	9.279337	33	33
33.0	9.308451	32	32
34.0	9.334518	37	37
35.0	9.357859	23	23
36.0	9.378757	30	30
37.0	9.397468	28	28
38.0	9.414222	24	24
39.0	9.429223	26	26
40.0	9.442655	23	23
41.0	9.454681	24	24
42.0	9.465449	29	29
43.0	9.47509	27	27
44.0	9.483722	20	20
45.0	9.491451	21	21
46.0	9.498372	24	24
47.0	9.504568	18	18
48.0	9.510117	21	21
49.0	9.515084	21	21
50.0	9.519532	20	20
51.0	9.523514	13	13
52.0	9.52708	19	19
53.0	9.530273	25	25
54.0	9.533132	20	20
55.0	9.535691	12	12
56.0	9.537983	12	12
57.0	9.540035	19	19
58.0	9.541872	15	15
59.0	9.543517	12	12
60.0	9.54499	11	11
61.0	9.546309	13	13
62.0	9.54749	10	10
63.0	9.548547	11	11
64.0	9.549494	10	10
65.0	9.550342	11	11
66.0	9.5511	12	12
67.0	9.55178	10	10
68.0	9.552388	12	12
69.0	9.552933	6	6
70.0	9.553421	11	11
71.0	9.553858	9	9
72.0	9.554249	10	10
73.0	9.554599	9	9
74.0	9.554912	11	11
75.0	9.555193	3	3
76.0	9.555444	3	3
77.0	9.555669	8	8
78.0	9.555871	7	7
79.0	9.556051	11	11
80.0	9.556213	14	14
81.0	9.556357	7	7
82.0	9.556487	10	10
83.0	9.556603	10	10
84.0	9.556707	6	6
85.0	9.5568	14	14
86.0	9.556883	8	8
87.0	9.556957	8	8
88.0	9.557024	3	3
89.0	9.557084	6	6
90.0	9.557137	8	8
91.0	9.557185	5	5
92.0	9.557228	3	3
93.0	9.557267	5	5
94.0	9.557301	9	9
95.0	9.557332	5	5
96.0	9.557359	7	7
97.0	9.557384	6	6
98.0	9.557406	3	3
99.0	9.557426	8	8
100.0	9.557443	3	3
101.0	0	7	7
102.0	0	5	5
103.0	0	8	8
104.0	0	8	8
105.0	0	6	6
106.0	0	7	7
107.0	0	5	5
108.0	0	7	7
109.0	0	6	6
110.0	0	3	3
111.0	0	6	6
112.0	0	5	5
113.0	0	3	3
114.0	0	8	8
115.0	0	3	3
116.0	0	3	3
117.0	0	8	8
118.0	0	3	3
119.0	0	4	4
120.0	0	3	3
121.0	0	5	5
122.0	0	8	8
123.0	0	3	3
124.0	0	7	7
125.0	0	7	7
126.0	0	8	8
127.0	0	2	2
128.0	0	3	3
129.0	0	6	6
130.0	0	2	2
131.0	0	5	5
132.0	0	4	4
133.0	0	2	2
134.0	0	3	3
135.0	0	5	5
136.0	0	3	3
137.0	0	6	6
138.0	0	1	1
139.0	0	7	7
140.0	0	5	5
141.0	0	6	6
142.0	0	5	5
143.0	0	2	2
144.0	0	3	3
145.0	0	3	3
146.0	0	4	4
147.0	0	6	6
148.0	0	2	2
149.0	0	3	3
150.0	0	5	5
151.0	0	4	4
152.0	0	4	4
153.0	0	5	5
154.0	0	4	4
155.0	0	5	5
156.0	0	2	2
157.0	0	4	4
158.0	0	7	7
159.0	0	4	4
160.0	0	3	3
161.0	0	2	2
162.0	0	5	5
163.0	0	1	1
164.0	0	5	5
165.0	0	1	1
166.0	0	2	2
167.0	0	8	8
168.0	0	3	3
169.0	0	4	4
170.0	0	5	5
171.0	0	4	4
172.0	0	4	4
173.0	0	3	3
174.0	0	3	3
175.0	0	2	2
176.0	0	4	4
177.0	0	3	3
178.0	0	2	2
179.0	0	3	3
180.0	0	2	2
181.0	0	3	3
182.0	0	2	2
183.0	0	6	6
185.0	0	6	6
186.0	0	5	5
187.0	0	2	2
188.0	0	3	3
190.0	0	4	4
191.0	0	1	1
192.0	0	3	3
193.0	0	2	2
194.0	0	3	3
195.0	0	2	2
196.0	0	3	3
197.0	0	3	3
198.0	0	4	4
199.0	0	1	1
200.0	0	3	3
201.0	0	2	2
202.0	0	2	2
203.0	0	2	2
204.0	0	2	2
205.0	0	4	4
206.0	0	2	2
207.0	0	2	2
208.0	0	2	2
209.0	0	3	3
210.0	0	3	3
211.0	0	2	2
212.0	0	2	2
213.0	0	2	2
214.0	0	1	1
215.0	0	3	3
216.0	0	3	3
217.0	0	1	1
218.0	0	6	6
219.0	0	3	3
220.0	0	2	2
222.0	0	3	3
223.0	0	1	1
224.0	0	3	3
225.0	0	1	1
226.0	0	4	4
227.0	0	1	1
228.0	0	2	2
229.0	0	4	4
230.0	0	2	2
231.0	0	2	2
232.0	0	2	2
233.0	0	2	2
234.0	0	2	2
235.0	0	3	3
236.0	0	1	1
237.0	0	1	1
238.0	0	2	2
239.0	0	2	2
241.0	0	2	2
242.0	0	3	3
243.0	0	3	3
244.0	0	5	5
245.0	0	1	1
246.0	0	1	1
247.0	0	4	4
249.0	0	3	3
250.0	0	1	1
251.0	0	1	1
253.0	0	4	4
254.0	0	5	5
255.0	0	2	2
256.0	0	4	4
257.0	0	4	4
259.0	0	3	3
260.0	0	1	1
261.0	0	3	3
262.0	0	1	1
263.0	0	3	3
264.0	0	2	2
265.0	0	3	3
266.0	0	6	6
267.0	0	4	4
268.0	0	1	1
269.0	0	1	1
270.0	0	2	2
271.0	0	1	1
272.0	0	2	2
273.0	0	2	2
274.0	0	3	3
276.0	0	1	1
277.0	0	3	3
278.0	0	1	1
279.0	0	2	2
280.0	0	3	3
281.0	0	1	1
282.0	0	1	1
283.0	0	1	1
285.0	0	1	1
286.0	0	1	1
288.0	0	2	2
289.0	0	2	2
291.0	0	2	2
292.0	0	2	2
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
300.0	0	2	2
301.0	0	3	3
302.0	0	2	2
303.0	0	2	2
305.0	0	1	1
306.0	0	2	2
307.0	0	1	1
310.0	0	3	3
311.0	0	1	1
312.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	3	3
318.0	0	1	1
319.0	0	1	1
321.0	0	3	3
322.0	0	2	2
324.0	0	1	1
325.0	0	3	3
326.0	0	1	1
327.0	0	1	1
328.0	0	1	1
329.0	0	1	1
330.0	0	1	1
331.0	0	2	2
333.0	0	2	2
334.0	0	1	1
335.0	0	1	1
336.0	0	1	1
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
340.0	0	1	1
341.0	0	1	1
342.0	0	2	2
343.0	0	2	2
345.0	0	1	1
346.0	0	1	1
349.0	0	2	2
350.0	0	1	1
351.0	0	1	1
354.0	0	1	1
356.0	0	2	2
358.0	0	1	1
362.0	0	2	2
363.0	0	1	1
364.0	0	1	1
365.0	0	1	1
366.0	0	4	4
367.0	0	3	3
368.0	0	1	1
369.0	0	1	1
371.0	0	1	1
373.0	0	1	1
374.0	0	2	2
376.0	0	1	1
380.0	0	2	2
381.0	0	1	1
382.0	0	1	1
383.0	0	1	1
385.0	0	1	1
386.0	0	1	1
388.0	0	3	3
389.0	0	1	1
391.0	0	1	1
396.0	0	1	1
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
403.0	0	1	1
404.0	0	1	1
405.0	0	1	1
415.0	0	1	1
417.0	0	2	2
418.0	0	1	1
420.0	0	1	1
421.0	0	2	2
425.0	0	2	2
426.0	0	1	1
429.0	0	1	1
431.0	0	1	1
435.0	0	1	1
439.0	0	1	1
440.0	0	1	1
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
447.0	0	2	2
451.0	0	1	1
452.0	0	1	1
455.0	0	1	1
456.0	0	1	1
457.0	0	1	1
458.0	0	2	2
462.0	0	1	1
463.0	0	1	1
464.0	0	2	2
466.0	0	1	1
467.0	0	1	1
468.0	0	1	1
470.0	0	1	1
471.0	0	1	1
472.0	0	2	2
473.0	0	2	2
475.0	0	1	1
479.0	0	1	1
482.0	0	1	1
483.0	0	1	1
485.0	0	1	1
487.0	0	2	2
492.0	0	1	1
493.0	0	1	1
494.0	0	2	2
495.0	0	1	1
496.0	0	1	1
498.0	0	2	2
500.0	0	1	1
502.0	0	1	1
508.0	0	1	1
510.0	0	3	3
511.0	0	1	1
515.0	0	1	1
517.0	0	1	1
520.0	0	1	1
522.0	0	1	1
524.0	0	1	1
527.0	0	1	1
533.0	0	1	1
534.0	0	1	1
535.0	0	1	1
536.0	0	1	1
539.0	0	1	1
541.0	0	1	1
542.0	0	1	1
545.0	0	1	1
548.0	0	1	1
559.0	0	1	1
561.0	0	1	1
564.0	0	1	1
565.0	0	2	2
568.0	0	1	1
572.0	0	1	1
573.0	0	1	1
575.0	0	1	1
576.0	0	1	1
578.0	0	1	1
581.0	0	1	1
589.0	0	2	2
593.0	0	2	2
594.0	0	1	1
598.0	0	1	1
602.0	0	1	1
609.0	0	1	1
615.0	0	1	1
617.0	0	2	2
618.0	0	1	1
621.0	0	1	1
625.0	0	2	2
627.0	0	1	1
631.0	0	1	1
634.0	0	2	2
635.0	0	1	1
643.0	0	1	1
646.0	0	1	1
651.0	0	1	1
653.0	0	1	1
656.0	0	1	1
661.0	0	1	1
663.0	0	1	1
664.0	0	1	1
665.0	0	1	1
670.0	0	1	1
673.0	0	1	1
674.0	0	2	2
675.0	0	1	1
677.0	0	1	1
679.0	0	1	1
680.0	0	2	2
687.0	0	1	1
690.0	0	2	2
693.0	0	1	1
696.0	0	1	1
697.0	0	1	1
705.0	0	1	1
708.0	0	1	1
716.0	0	1	1
724.0	0	2	2
728.0	0	1	1
734.0	0	1	1
737.0	0	1	1
741.0	0	1	1
744.0	0	1	1
745.0	0	1	1
748.0	0	1	1
753.0	0	1	1
756.0	0	1	1
757.0	0	2	2
761.0	0	1	1
764.0	0	1	1
767.0	0	2	2
768.0	0	1	1
772.0	0	1	1
774.0	0	1	1
778.0	0	1	1
794.0	0	1	1
800.0	0	1	1
802.0	0	1	1
806.0	0	1	1
812.0	0	1	1
821.0	0	1	1
825.0	0	2	2
836.0	0	2	2
839.0	0	1	1
862.0	0	1	1
867.0	0	1	1
875.0	0	2	2
876.0	0	1	1
882.0	0	1	1
889.0	0	1	1
897.0	0	1	1
903.0	0	1	1
907.0	0	1	1
911.0	0	1	1
915.0	0	1	1
917.0	0	1	1
923.0	0	1	1
932.0	0	1	1
935.0	0	1	1
948.0	0	1	1
950.0	0	1	1
956.0	0	1	1
958.0	0	1	1
999.0	0	1	1
1001.0	0	1	1
1006.0	0	1	1
1023.0	0	1	1
1040.0	0	1	1
1043.0	0	1	1
1050.0	0	1	1
1053.0	0	1	1
1056.0	0	1	1
1061.0	0	1	1
1095.0	0	1	1
1104.0	0	1	1
1107.0	0	1	1
1114.0	0	2	2
1124.0	0	1	1
1139.0	0	1	1
1163.0	0	1	1
1177.0	0	1	1
1193.0	0	1	1
1216.0	0	1	1
1225.0	0	1	1
1242.0	0	1	1
1245.0	0	1	1
1263.0	0	1	1
1276.0	0	1	1
1287.0	0	1	1
1298.0	0	1	1
1329.0	0	1	1
1343.0	0	1	1
1365.0	0	1	1
1366.0	0	1	1
1381.0	0	1	1
1422.0	0	1	1
1508.0	0	1	1
1522.0	0	1	1
1566.0	0	1	1
1581.0	0	1	1
1612.0	0	1	1
1634.0	0	1	1
1636.0	0	1	1
1658.0	0	1	1
1691.0	0	1	1
1705.0	0	1	1
1737.0	0	1	1
1839.0	0	1	1
1899.0	0	1	1
1918.0	0	1	1
1987.0	0	2	2
2141.0	0	1	1
2200.0	0	1	1
2204.0	0	1	1
2314.0	0	1	1
2337.0	0	1	1
2815.0	0	1	1
2861.0	0	1	1
3054.0	0	1	1
3101.0	0	1	1
3768.0	0	1	1
3860.0	0	1	1