## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/RU_Ale_15_Aug_2017/RU_Ale_15_Aug_2017.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/RU_Ale_15_Aug_2017/RU_Ale_15_Aug_2017.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/RU_Ale_15_Aug_2017/RU_Ale_15_Aug_2017.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: Wed Dec 21 04:23:58 UTC 2022

## 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	2595022	21651430	0	0	1401387	6542507	226166	0.315622	28775893

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007082	10240081	0	10351342
2.0	1.481646	3033893	219405	2989606
3.0	1.705273	871122	2884	832896
4.0	1.810652	246637	50	228791
5.0	1.86031	71468	11	64380
6.0	1.883709	21816	8	19410
7.0	1.894736	7863	5	7018
8.0	1.899932	3681	8	3424
9.0	1.902381	2020	7	1890
10.0	1.903535	1402	2	1364
11.0	1.904078	1030	2	980
12.0	1.904334	751	2	753
13.0	1.904455	571	1	552
14.0	1.904512	483	3	478
15.0	1.904539	382	1	377
16.0	1.904552	311	3	302
17.0	1.904558	280	1	264
18.0	1.90456	229	1	225
19.0	1.904562	197	0	191
20.0	1.904562	158	1	154
21.0	1.904563	133	1	128
22.0	1.904563	121	0	118
23.0	1.904563	104	1	110
24.0	1.904563	103	0	105
25.0	1.904563	78	0	72
26.0	1.904563	76	0	73
27.0	1.904563	70	0	70
28.0	1.904563	70	0	65
29.0	1.904563	52	0	52
30.0	1.904563	46	0	47
31.0	1.904563	35	1	33
32.0	1.904563	40	0	38
33.0	1.904563	44	0	47
34.0	1.904563	44	0	40
35.0	1.904563	26	0	31
36.0	1.904563	41	1	35
37.0	1.904563	25	0	28
38.0	1.904563	31	0	30
39.0	1.904563	26	0	27
40.0	1.904563	27	0	24
41.0	1.904563	27	0	28
42.0	1.904563	27	0	25
43.0	1.904563	19	0	20
44.0	1.904563	17	0	18
45.0	1.904563	25	0	24
46.0	1.904563	14	0	12
47.0	1.904563	17	0	18
48.0	1.904563	18	0	19
49.0	1.904563	14	0	12
50.0	1.904563	14	0	16
51.0	1.904563	20	0	19
52.0	1.904563	17	0	17
53.0	1.904563	13	0	15
54.0	1.904563	12	0	10
55.0	1.904563	12	0	12
56.0	1.904563	10	0	10
57.0	1.904563	11	0	9
58.0	1.904563	7	0	10
59.0	1.904563	11	0	9
60.0	1.904563	9	0	9
61.0	1.904563	11	0	11
62.0	1.904563	5	0	6
63.0	1.904563	8	0	8
64.0	1.904563	8	0	7
65.0	1.904563	8	0	8
66.0	1.904563	12	0	14
67.0	1.904563	8	0	6
68.0	1.904563	10	0	9
69.0	1.904563	4	0	8
70.0	1.904563	13	0	10
71.0	1.904563	6	0	5
72.0	1.904563	6	0	11
73.0	1.904563	7	0	4
74.0	1.904563	7	0	8
75.0	1.904563	7	0	8
76.0	1.904563	10	0	8
77.0	1.904563	3	0	4
78.0	1.904563	5	0	4
79.0	1.904563	11	0	10
80.0	1.904563	9	0	11
81.0	1.904563	9	0	8
82.0	1.904563	7	0	6
83.0	1.904563	7	0	6
84.0	1.904563	3	0	3
85.0	1.904563	3	0	5
86.0	1.904563	4	1	3
87.0	1.904563	8	0	8
88.0	1.904563	7	0	8
89.0	1.904563	7	0	5
90.0	1.904563	5	0	5
91.0	1.904563	2	0	3
92.0	1.904563	5	0	4
93.0	1.904563	2	0	3
94.0	1.904563	6	0	6
95.0	1.904563	7	0	7
96.0	1.904563	6	0	6
97.0	1.904563	3	0	6
98.0	1.904563	7	0	6
99.0	1.904563	8	0	7
100.0	1.904563	4	0	4
101.0	0	6	0	4
102.0	0	4	0	6
103.0	0	5	0	4
104.0	0	3	0	4
105.0	0	4	0	5
106.0	0	7	0	4
107.0	0	0	0	1
108.0	0	4	0	4
109.0	0	1	0	0
110.0	0	2	0	3
111.0	0	2	0	1
112.0	0	3	0	3
113.0	0	0	0	1
114.0	0	5	0	5
115.0	0	7	0	7
116.0	0	8	0	10
117.0	0	3	0	1
118.0	0	1	0	1
119.0	0	4	0	5
120.0	0	5	0	3
121.0	0	2	0	2
122.0	0	3	0	4
123.0	0	3	0	4
124.0	0	2	0	1
125.0	0	3	0	2
126.0	0	2	0	3
127.0	0	2	0	1
128.0	0	2	0	2
129.0	0	2	0	2
130.0	0	2	0	3
131.0	0	4	0	3
132.0	0	2	0	4
133.0	0	2	0	2
134.0	0	5	0	7
135.0	0	4	0	2
136.0	0	2	0	1
137.0	0	3	0	4
138.0	0	2	0	0
139.0	0	2	0	2
140.0	0	0	0	1
141.0	0	2	0	2
142.0	0	2	0	3
143.0	0	3	0	3
144.0	0	6	0	5
145.0	0	1	0	1
146.0	0	3	0	2
147.0	0	0	0	1
148.0	0	3	0	3
149.0	0	3	0	6
150.0	0	4	0	0
151.0	0	2	0	2
152.0	0	1	0	1
153.0	0	2	0	4
154.0	0	7	0	6
155.0	0	3	0	2
156.0	0	1	0	1
157.0	0	1	0	1
158.0	0	2	0	4
159.0	0	2	0	3
160.0	0	2	0	1
161.0	0	3	0	2
162.0	0	1	0	1
163.0	0	2	0	2
164.0	0	1	0	1
165.0	0	2	0	1
166.0	0	5	0	5
167.0	0	1	0	1
168.0	0	1	0	1
169.0	0	2	0	2
172.0	0	1	0	1
173.0	0	2	0	4
174.0	0	1	0	0
175.0	0	4	0	4
176.0	0	1	0	0
177.0	0	2	0	2
178.0	0	1	0	1
180.0	0	4	0	4
181.0	0	1	0	2
183.0	0	1	0	1
184.0	0	2	0	1
185.0	0	0	0	1
186.0	0	2	0	2
187.0	0	2	0	1
188.0	0	1	0	2
190.0	0	1	0	2
191.0	0	3	0	2
192.0	0	1	0	0
193.0	0	0	0	1
194.0	0	2	0	3
195.0	0	3	0	1
196.0	0	1	0	1
197.0	0	1	0	1
198.0	0	2	0	2
199.0	0	2	0	2
200.0	0	3	0	3
201.0	0	2	0	3
202.0	0	1	0	0
203.0	0	2	0	2
204.0	0	1	1	2
205.0	0	1	0	1
206.0	0	1	0	2
207.0	0	1	0	0
208.0	0	1	0	2
209.0	0	2	0	1
210.0	0	2	0	1
211.0	0	0	0	1
212.0	0	2	0	2
213.0	0	5	0	4
214.0	0	4	0	4
215.0	0	1	0	1
217.0	0	0	0	1
218.0	0	2	0	3
219.0	0	1	0	0
220.0	0	2	0	1
221.0	0	1	0	2
223.0	0	1	0	0
224.0	0	1	0	2
225.0	0	1	0	1
226.0	0	3	0	2
228.0	0	2	0	2
229.0	0	1	0	1
230.0	0	1	0	1
231.0	0	1	0	2
232.0	0	2	0	1
233.0	0	1	0	1
239.0	0	1	0	1
240.0	0	1	0	1
241.0	0	2	0	2
242.0	0	0	0	1
243.0	0	3	0	2
245.0	0	1	0	2
246.0	0	2	0	1
247.0	0	3	0	3
248.0	0	1	0	1
249.0	0	2	0	3
250.0	0	1	0	0
251.0	0	1	0	1
253.0	0	1	0	1
254.0	0	2	0	2
255.0	0	1	0	1
257.0	0	0	0	1
259.0	0	1	0	0
262.0	0	0	0	1
263.0	0	1	0	1
264.0	0	2	0	2
265.0	0	3	0	2
272.0	0	1	0	1
273.0	0	1	0	2
274.0	0	2	0	2
275.0	0	2	0	1
276.0	0	0	0	2
277.0	0	2	0	1
279.0	0	1	0	0
281.0	0	1	0	1
282.0	0	3	0	4
283.0	0	1	0	0
286.0	0	1	0	1
288.0	0	1	0	2
289.0	0	1	0	0
291.0	0	1	0	2
293.0	0	1	0	0
295.0	0	0	0	1
300.0	0	1	0	1
301.0	0	1	0	0
304.0	0	1	0	1
305.0	0	1	0	1
306.0	0	1	0	2
307.0	0	0	0	1
308.0	0	1	0	0
311.0	0	3	0	2
312.0	0	1	0	1
313.0	0	2	0	2
314.0	0	2	0	2
317.0	0	1	0	1
322.0	0	1	0	1
324.0	0	0	0	1
325.0	0	2	0	1
327.0	0	4	0	4
330.0	0	1	0	1
331.0	0	1	0	1
333.0	0	1	0	1
334.0	0	1	0	1
335.0	0	1	0	1
337.0	0	2	0	2
338.0	0	1	0	1
339.0	0	0	0	1
340.0	0	0	0	1
342.0	0	1	0	0
344.0	0	2	0	1
345.0	0	0	0	1
349.0	0	1	0	1
350.0	0	2	0	1
353.0	0	0	0	1
354.0	0	3	0	2
355.0	0	1	0	1
356.0	0	1	0	1
361.0	0	2	0	2
365.0	0	1	0	1
367.0	0	1	0	2
369.0	0	1	0	0
376.0	0	0	0	1
380.0	0	1	0	0
381.0	0	2	0	2
382.0	0	2	0	2
383.0	0	1	0	1
386.0	0	0	0	1
387.0	0	2	0	1
388.0	0	0	0	1
389.0	0	2	0	2
391.0	0	2	0	2
392.0	0	1	0	0
394.0	0	1	0	1
399.0	0	2	0	3
400.0	0	1	0	1
402.0	0	1	0	1
403.0	0	1	0	0
404.0	0	1	0	1
406.0	0	0	0	1
407.0	0	2	0	2
408.0	0	1	0	0
409.0	0	1	0	1
414.0	0	0	0	1
415.0	0	1	0	0
417.0	0	1	0	1
418.0	0	1	0	1
421.0	0	1	0	1
423.0	0	0	0	1
424.0	0	2	0	1
426.0	0	0	0	1
429.0	0	1	0	1
430.0	0	1	0	0
434.0	0	1	0	1
435.0	0	1	0	1
436.0	0	0	0	1
437.0	0	1	0	0
450.0	0	0	0	1
454.0	0	1	0	0
455.0	0	1	0	1
456.0	0	1	0	1
460.0	0	2	0	2
462.0	0	1	0	1
463.0	0	1	0	1
464.0	0	1	0	1
468.0	0	1	0	1
470.0	0	1	0	1
473.0	0	0	0	1
476.0	0	1	0	0
477.0	0	0	0	1
478.0	0	1	0	0
481.0	0	0	0	1
483.0	0	1	0	0
487.0	0	0	0	1
490.0	0	0	0	1
491.0	0	1	0	0
493.0	0	1	0	0
509.0	0	1	0	1
512.0	0	0	0	1
514.0	0	1	0	0
519.0	0	0	0	1
527.0	0	1	0	0
530.0	0	1	0	1
533.0	0	0	0	1
534.0	0	1	0	0
550.0	0	1	0	1
553.0	0	1	0	2
557.0	0	1	0	0
560.0	0	1	0	1
563.0	0	1	0	1
564.0	0	1	0	1
568.0	0	0	0	1
576.0	0	1	0	0
577.0	0	0	0	1
579.0	0	1	0	0
588.0	0	0	0	1
589.0	0	1	0	0
595.0	0	1	0	1
602.0	0	0	0	1
603.0	0	1	0	0
606.0	0	1	0	2
609.0	0	1	0	0
612.0	0	1	0	1
617.0	0	1	0	1
621.0	0	1	0	1
627.0	0	1	0	1
628.0	0	1	0	1
630.0	0	1	0	1
634.0	0	0	0	1
636.0	0	0	0	1
639.0	0	2	0	0
641.0	0	1	0	1
651.0	0	1	0	1
652.0	0	0	0	1
655.0	0	1	0	0
684.0	0	1	0	1
687.0	0	1	0	1
702.0	0	1	0	1
707.0	0	0	0	1
709.0	0	1	0	0
710.0	0	1	0	1
713.0	0	0	0	1
715.0	0	1	0	0
754.0	0	0	0	2
755.0	0	2	0	0
759.0	0	1	0	1
762.0	0	0	0	1
765.0	0	1	0	0
768.0	0	0	0	1
773.0	0	1	0	2
775.0	0	1	0	0
779.0	0	1	0	0
790.0	0	1	0	1
791.0	0	0	0	1
794.0	0	1	0	0
795.0	0	1	0	1
796.0	0	1	0	1
811.0	0	1	0	1
817.0	0	1	0	1
848.0	0	1	0	2
849.0	0	1	0	0
851.0	0	0	0	1
852.0	0	1	0	0
858.0	0	0	0	1
859.0	0	1	0	0
881.0	0	0	0	1
884.0	0	1	0	0
889.0	0	1	0	1
909.0	0	1	0	1
917.0	0	1	0	1
919.0	0	1	0	1
920.0	0	1	0	1
922.0	0	1	0	1
927.0	0	1	0	1
932.0	0	1	0	1
944.0	0	1	0	1
961.0	0	1	0	1
966.0	0	1	0	1
988.0	0	0	0	1
994.0	0	1	0	1
998.0	0	1	0	0
1022.0	0	1	0	1
1024.0	0	0	0	1
1025.0	0	1	0	0
1036.0	0	0	0	1
1037.0	0	0	0	1
1039.0	0	1	0	0
1040.0	0	0	0	1
1042.0	0	1	0	0
1043.0	0	1	0	0
1052.0	0	0	0	1
1053.0	0	1	0	0
1058.0	0	1	0	1
1068.0	0	0	0	1
1077.0	0	1	0	1
1085.0	0	1	0	1
1087.0	0	1	0	0
1089.0	0	0	0	1
1091.0	0	1	0	0
1112.0	0	0	0	1
1118.0	0	1	0	2
1123.0	0	1	0	0
1125.0	0	1	0	0
1139.0	0	1	0	1
1163.0	0	1	0	1
1164.0	0	1	0	1
1194.0	0	1	0	1
1222.0	0	0	0	1
1230.0	0	2	0	1
1241.0	0	1	0	1
1274.0	0	0	0	1
1277.0	0	1	0	1
1282.0	0	1	0	0
1345.0	0	1	0	1
1352.0	0	0	0	1
1357.0	0	1	0	1
1362.0	0	2	0	1
1377.0	0	0	0	1
1385.0	0	1	0	0
1430.0	0	0	0	1
1431.0	0	1	0	0
1433.0	0	1	0	1
1460.0	0	0	0	1
1462.0	0	1	0	0
1508.0	0	0	0	1
1514.0	0	1	0	1
1521.0	0	1	0	0
1528.0	0	0	0	1
1540.0	0	1	0	0
1580.0	0	0	0	1
1586.0	0	1	0	0
1607.0	0	0	0	1
1614.0	0	1	0	0
1619.0	0	1	0	1
1630.0	0	1	0	1
1651.0	0	0	0	1
1654.0	0	1	0	0
1658.0	0	0	0	1
1668.0	0	0	0	1
1669.0	0	1	0	0
1683.0	0	1	0	0
1702.0	0	0	0	1
1713.0	0	1	0	0
1747.0	0	1	0	1
1794.0	0	0	0	1
1801.0	0	1	0	0
1806.0	0	0	0	1
1807.0	0	1	0	0
1815.0	0	1	0	1
1881.0	0	0	0	1
1898.0	0	1	0	0
1959.0	0	1	0	1
2041.0	0	0	0	1
2049.0	0	1	0	0
2174.0	0	0	0	1
2175.0	0	1	0	0
2204.0	0	0	0	1
2217.0	0	1	0	0
2291.0	0	1	0	1
2635.0	0	0	0	1
2654.0	0	1	0	0
2813.0	0	1	0	1
2851.0	0	0	0	1
2871.0	0	1	0	0
2901.0	0	0	0	1
2906.0	0	1	0	0
3089.0	0	0	0	1
3093.0	0	1	0	0
3257.0	0	0	0	1
3264.0	0	1	0	0
3273.0	0	0	0	1
3287.0	0	1	0	0
3398.0	0	1	0	1
3439.0	0	0	0	1
3454.0	0	1	0	0
3608.0	0	0	0	1
3630.0	0	1	0	0
3640.0	0	0	0	1
3648.0	0	1	0	0
3885.0	0	0	0	1
3892.0	0	1	0	0
4163.0	0	0	0	1
4178.0	0	1	0	0
4389.0	0	0	0	1
4405.0	0	1	0	0
4478.0	0	0	0	1
4483.0	0	1	0	0
4623.0	0	0	0	1
4630.0	0	1	0	0
5115.0	0	1	0	1
6070.0	0	0	0	1
6079.0	0	1	0	0
6123.0	0	0	0	1
6136.0	0	1	0	0
15133.0	0	0	0	1
15168.0	0	1	0	0
19145.0	0	0	0	1
19175.0	0	1	0	0
23859.0	0	0	0	1
23944.0	0	1	0	0
59172.0	0	0	0	1
59375.0	0	1	0	0