## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2017-07-20/FI_Pir_Aka_1_2017-07-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2017-07-20/FI_Pir_Aka_1_2017-07-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2017-07-20/FI_Pir_Aka_1_2017-07-20.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: Thu Jan 19 08:45:17 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	3633274	27127673	0	0	2014335	7289635	238999	0.286647	41850742

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.006319	14208049	0	14336078
2.0	1.532609	3820929	233672	3762898
3.0	1.807852	989797	2366	946833
4.0	1.9518	250159	27	231994
5.0	2.027083	63410	13	57376
6.0	2.066455	17091	8	15137
7.0	2.087046	5097	4	4536
8.0	2.097814	1916	1	1709
9.0	2.103446	882	1	826
10.0	2.106392	505	2	475
11.0	2.107932	348	1	350
12.0	2.108738	236	0	227
13.0	2.109159	200	3	194
14.0	2.109379	175	1	171
15.0	2.109495	126	0	131
16.0	2.109555	106	1	101
17.0	2.109586	109	2	104
18.0	2.109603	70	0	72
19.0	2.109612	69	0	67
20.0	2.109616	55	1	57
21.0	2.109618	56	0	51
22.0	2.10962	46	0	49
23.0	2.10962	50	0	50
24.0	2.109621	41	0	39
25.0	2.109621	39	0	37
26.0	2.109621	29	0	28
27.0	2.109621	28	0	28
28.0	2.109621	25	0	26
29.0	2.109621	20	0	21
30.0	2.109621	19	0	22
31.0	2.109621	30	1	26
32.0	2.109621	32	0	34
33.0	2.109621	19	0	17
34.0	2.109621	14	0	17
35.0	2.109621	21	0	18
36.0	2.109621	10	0	9
37.0	2.109621	16	0	18
38.0	2.109621	17	0	16
39.0	2.109621	19	0	18
40.0	2.109621	11	0	12
41.0	2.109621	7	0	9
42.0	2.109621	21	0	20
43.0	2.109621	7	0	6
44.0	2.109621	8	0	8
45.0	2.109621	7	0	8
46.0	2.109621	10	0	8
47.0	2.109621	12	0	14
48.0	2.109621	7	0	8
49.0	2.109621	11	0	9
50.0	2.109621	7	0	6
51.0	2.109621	13	0	15
52.0	2.109621	10	0	10
53.0	2.109621	7	0	5
54.0	2.109621	6	0	8
55.0	2.109621	13	0	13
56.0	2.109621	9	0	7
57.0	2.109621	5	0	6
58.0	2.109621	8	0	10
59.0	2.109621	11	0	10
60.0	2.109621	9	0	8
61.0	2.109621	3	0	2
62.0	2.109621	2	0	3
63.0	2.109621	7	0	8
64.0	2.109621	4	0	3
65.0	2.109621	2	1	2
66.0	2.109621	11	0	10
67.0	2.109621	6	0	7
68.0	2.109621	6	0	8
69.0	2.109621	7	0	4
70.0	2.109621	5	0	5
71.0	2.109621	6	0	8
72.0	2.109621	7	0	6
73.0	2.109621	6	0	7
74.0	2.109621	6	0	4
75.0	2.109621	4	0	4
76.0	2.109621	6	0	6
77.0	2.109621	0	0	0
78.0	2.109621	5	0	5
79.0	2.109621	8	0	9
80.0	2.109621	3	0	2
81.0	2.109621	2	0	3
82.0	2.109621	4	0	3
83.0	2.109621	4	0	5
84.0	2.109621	2	0	1
85.0	2.109621	3	0	3
86.0	2.109621	2	0	2
87.0	2.109621	4	0	4
88.0	2.109621	3	0	4
89.0	2.109621	3	0	3
90.0	2.109621	5	0	4
91.0	2.109621	2	0	2
92.0	2.109621	1	0	1
93.0	2.109621	2	0	2
94.0	2.109621	5	0	5
95.0	2.109621	0	0	3
96.0	2.109621	7	0	5
97.0	2.109621	3	0	3
98.0	2.109621	1	0	1
99.0	2.109621	4	0	3
100.0	2.109621	1	0	1
102.0	0	6	0	6
103.0	0	2	0	2
104.0	0	3	0	3
105.0	0	1	0	1
106.0	0	3	0	3
107.0	0	1	0	1
108.0	0	1	0	1
109.0	0	2	0	2
110.0	0	1	0	1
111.0	0	2	0	2
112.0	0	3	0	3
113.0	0	2	0	3
114.0	0	5	0	6
115.0	0	6	0	4
116.0	0	4	0	4
117.0	0	1	0	2
118.0	0	4	0	4
119.0	0	5	0	4
121.0	0	1	0	2
122.0	0	2	0	1
123.0	0	2	0	2
124.0	0	4	0	4
125.0	0	1	0	1
126.0	0	1	0	1
127.0	0	2	0	3
128.0	0	1	0	1
129.0	0	2	0	1
130.0	0	2	0	2
131.0	0	1	0	2
132.0	0	2	0	2
133.0	0	2	0	1
134.0	0	2	0	2
135.0	0	1	0	1
137.0	0	4	0	4
138.0	0	1	0	1
139.0	0	1	0	1
140.0	0	1	0	1
141.0	0	1	0	1
142.0	0	1	0	1
143.0	0	2	0	2
145.0	0	5	0	5
146.0	0	1	0	1
147.0	0	0	1	0
148.0	0	2	0	2
149.0	0	3	0	3
150.0	0	1	0	2
151.0	0	2	0	2
152.0	0	3	0	3
154.0	0	3	0	3
155.0	0	2	0	2
156.0	0	3	0	2
157.0	0	1	0	1
158.0	0	1	0	1
159.0	0	2	0	3
161.0	0	1	0	1
162.0	0	3	0	2
164.0	0	2	0	2
168.0	0	1	0	1
169.0	0	1	0	1
170.0	0	1	0	2
171.0	0	4	0	3
172.0	0	2	0	2
173.0	0	0	0	1
174.0	0	1	0	1
175.0	0	1	0	1
176.0	0	3	0	2
177.0	0	2	0	2
178.0	0	0	0	1
180.0	0	0	0	1
181.0	0	3	0	2
182.0	0	1	0	1
183.0	0	0	0	1
184.0	0	1	0	0
185.0	0	0	0	1
186.0	0	1	0	0
188.0	0	3	0	2
190.0	0	1	0	2
191.0	0	1	0	0
193.0	0	1	0	1
194.0	0	1	0	1
195.0	0	2	0	2
196.0	0	3	0	3
197.0	0	1	0	1
198.0	0	1	0	1
199.0	0	1	0	2
200.0	0	1	0	0
201.0	0	1	0	1
202.0	0	2	0	2
203.0	0	1	0	1
205.0	0	2	0	2
206.0	0	2	0	2
208.0	0	2	0	2
209.0	0	1	0	1
210.0	0	1	0	1
211.0	0	1	0	1
212.0	0	1	0	1
215.0	0	1	0	1
216.0	0	1	0	1
217.0	0	1	0	1
218.0	0	3	0	3
219.0	0	1	0	1
221.0	0	2	0	2
222.0	0	0	0	1
223.0	0	1	0	0
224.0	0	1	0	1
225.0	0	1	0	1
226.0	0	0	0	1
227.0	0	1	0	0
228.0	0	0	0	1
229.0	0	1	0	0
230.0	0	2	0	2
231.0	0	1	0	1
232.0	0	1	0	2
233.0	0	1	0	0
234.0	0	1	0	1
235.0	0	3	0	3
236.0	0	3	0	3
237.0	0	1	0	1
240.0	0	2	0	2
244.0	0	2	0	2
247.0	0	1	0	2
248.0	0	2	0	2
249.0	0	1	0	0
250.0	0	1	0	1
251.0	0	1	0	1
252.0	0	1	0	1
253.0	0	3	0	3
254.0	0	1	0	2
255.0	0	1	0	1
256.0	0	2	0	1
259.0	0	2	0	2
264.0	0	1	0	1
265.0	0	1	0	2
266.0	0	1	0	0
268.0	0	0	0	2
272.0	0	1	0	0
274.0	0	1	0	1
275.0	0	1	0	0
276.0	0	0	0	2
277.0	0	1	0	0
278.0	0	1	0	0
279.0	0	2	0	2
283.0	0	0	0	1
285.0	0	1	0	0
286.0	0	1	0	1
287.0	0	1	0	1
288.0	0	1	0	1
290.0	0	0	0	1
292.0	0	2	0	1
293.0	0	2	0	2
295.0	0	2	0	2
302.0	0	2	0	2
306.0	0	1	0	1
311.0	0	1	0	2
312.0	0	2	0	1
318.0	0	1	0	1
320.0	0	1	0	1
323.0	0	2	0	2
324.0	0	1	0	1
325.0	0	1	0	1
326.0	0	1	0	1
327.0	0	1	0	1
339.0	0	1	0	1
342.0	0	1	0	2
344.0	0	1	0	0
357.0	0	3	0	3
361.0	0	1	0	1
362.0	0	0	0	1
363.0	0	1	0	1
365.0	0	2	0	2
367.0	0	2	0	1
369.0	0	1	0	1
375.0	0	0	0	1
377.0	0	1	0	1
379.0	0	1	0	0
380.0	0	1	0	1
381.0	0	1	0	1
383.0	0	1	0	2
386.0	0	2	0	2
387.0	0	2	0	2
388.0	0	2	0	2
389.0	0	1	0	1
391.0	0	2	0	1
396.0	0	1	0	1
400.0	0	1	0	2
401.0	0	3	0	2
402.0	0	1	0	1
403.0	0	1	0	1
406.0	0	1	0	1
417.0	0	2	0	2
422.0	0	0	0	1
424.0	0	2	0	1
427.0	0	1	0	1
437.0	0	1	0	1
438.0	0	1	0	1
441.0	0	1	0	1
442.0	0	1	0	1
448.0	0	2	0	2
453.0	0	1	0	1
454.0	0	0	0	1
457.0	0	1	0	0
474.0	0	0	0	1
475.0	0	1	0	0
487.0	0	0	0	1
489.0	0	1	0	0
498.0	0	1	0	1
501.0	0	1	0	1
504.0	0	1	0	1
510.0	0	1	0	1
525.0	0	1	0	1
531.0	0	1	0	1
535.0	0	0	0	1
536.0	0	1	0	1
539.0	0	1	0	0
540.0	0	0	0	1
546.0	0	1	0	0
547.0	0	1	0	1
551.0	0	1	0	1
560.0	0	2	0	2
569.0	0	0	0	1
573.0	0	1	0	0
575.0	0	0	0	1
576.0	0	1	0	1
578.0	0	1	0	0
583.0	0	0	0	1
587.0	0	1	0	0
597.0	0	0	0	1
599.0	0	1	0	0
601.0	0	1	0	1
607.0	0	1	0	1
609.0	0	1	0	1
621.0	0	1	0	1
638.0	0	1	0	1
643.0	0	1	0	1
644.0	0	1	0	1
661.0	0	1	0	1
662.0	0	1	0	1
696.0	0	1	0	1
706.0	0	1	0	1
756.0	0	1	0	1
760.0	0	0	0	1
761.0	0	1	0	0
785.0	0	1	0	1
786.0	0	1	0	1
790.0	0	0	0	1
798.0	0	1	0	0
802.0	0	0	0	1
803.0	0	2	0	1
806.0	0	0	0	1
808.0	0	1	0	0
810.0	0	0	0	1
815.0	0	2	0	1
818.0	0	1	0	1
824.0	0	0	0	1
825.0	0	1	0	0
834.0	0	1	0	1
837.0	0	0	0	1
839.0	0	1	0	0
847.0	0	1	0	1
862.0	0	0	0	1
864.0	0	0	0	1
866.0	0	2	0	0
886.0	0	1	0	1
888.0	0	0	0	1
890.0	0	1	0	0
893.0	0	1	0	1
896.0	0	0	0	1
898.0	0	1	0	0
902.0	0	0	0	1
906.0	0	1	0	0
913.0	0	0	0	2
914.0	0	2	0	0
918.0	0	1	0	1
962.0	0	1	0	2
964.0	0	1	0	1
965.0	0	1	0	0
986.0	0	0	0	1
990.0	0	1	0	0
995.0	0	1	0	1
1001.0	0	1	0	1
1016.0	0	1	0	1
1024.0	0	0	0	1
1029.0	0	0	0	1
1034.0	0	1	0	0
1035.0	0	0	0	1
1036.0	0	1	0	0
1039.0	0	1	0	0
1069.0	0	0	0	1
1075.0	0	1	0	1
1077.0	0	1	0	0
1091.0	0	1	0	1
1121.0	0	0	0	1
1123.0	0	1	0	0
1125.0	0	0	0	1
1130.0	0	1	0	0
1190.0	0	0	0	1
1193.0	0	1	0	0
1245.0	0	0	0	1
1250.0	0	1	0	0
1338.0	0	0	0	1
1342.0	0	1	0	0
1348.0	0	0	0	1
1350.0	0	1	0	0
1390.0	0	0	0	1
1395.0	0	1	0	0
1455.0	0	1	0	1
1471.0	0	1	0	1
1487.0	0	1	0	1
1509.0	0	0	0	1
1512.0	0	1	0	0
1519.0	0	0	0	1
1524.0	0	0	0	1
1525.0	0	1	0	0
1528.0	0	1	0	0
1589.0	0	0	0	1
1598.0	0	1	0	0
2107.0	0	0	0	1
2123.0	0	1	0	0
2182.0	0	0	0	1
2185.0	0	1	0	0
2240.0	0	0	0	1
2250.0	0	1	0	0
2281.0	0	0	0	1
2294.0	0	1	0	0
2421.0	0	0	0	1
2426.0	0	1	0	0
2575.0	0	0	0	1
2581.0	0	1	0	0
2740.0	0	0	0	1
2752.0	0	1	0	0
2823.0	0	0	0	1
2825.0	0	1	0	0
2853.0	0	1	0	1
2860.0	0	0	0	1
2862.0	0	1	0	0
2960.0	0	0	0	1
2972.0	0	1	0	0
3099.0	0	0	0	1
3101.0	0	1	0	0
3131.0	0	0	0	1
3136.0	0	1	0	0
3313.0	0	0	0	1
3328.0	0	1	0	0
5403.0	0	0	0	1
5409.0	0	1	0	0
5874.0	0	0	0	1
5890.0	0	1	0	0
13707.0	0	0	0	1
13726.0	0	1	0	0
14333.0	0	0	0	1
14363.0	0	1	0	0
21874.0	0	0	0	1
21938.0	0	1	0	0
52019.0	0	0	0	1
52165.0	0	1	0	0