## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2019-08-25/FI_Pir_Aka_1_2019-08-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2019-08-25/FI_Pir_Aka_1_2019-08-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/FI_Pir_Aka_1_2019-08-25/FI_Pir_Aka_1_2019-08-25.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 Jan 18 04:07:30 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	2514700	23694038	0	0	1317008	7569757	204167	0.329772	29129908

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.005633	10600640	0	10694035
2.0	1.451483	3429379	199207	3398505
3.0	1.649151	1060621	2181	1027010
4.0	1.736787	318119	48	300631
5.0	1.775641	93759	12	86499
6.0	1.792867	28719	2	26083
7.0	1.800504	9645	4	8723
8.0	1.80389	3610	1	3256
9.0	1.805391	1797	0	1689
10.0	1.806056	1060	1	983
11.0	1.806351	715	3	727
12.0	1.806482	571	2	538
13.0	1.80654	463	0	469
14.0	1.806566	393	2	375
15.0	1.806577	286	0	279
16.0	1.806582	274	0	273
17.0	1.806585	214	1	222
18.0	1.806586	178	1	166
19.0	1.806586	162	1	154
20.0	1.806586	130	0	134
21.0	1.806586	133	0	130
22.0	1.806586	113	0	111
23.0	1.806586	82	0	80
24.0	1.806586	64	0	64
25.0	1.806586	72	0	74
26.0	1.806586	81	0	82
27.0	1.806586	58	0	51
28.0	1.806586	62	0	61
29.0	1.806586	47	1	50
30.0	1.806586	37	0	35
31.0	1.806586	42	0	45
32.0	1.806586	31	0	23
33.0	1.806586	23	0	27
34.0	1.806586	31	0	32
35.0	1.806586	23	0	22
36.0	1.806586	24	0	24
37.0	1.806586	25	0	25
38.0	1.806586	23	0	22
39.0	1.806586	19	0	21
40.0	1.806586	19	0	17
41.0	1.806586	22	0	22
42.0	1.806586	18	0	19
43.0	1.806586	26	0	23
44.0	1.806586	17	0	16
45.0	1.806586	13	0	14
46.0	1.806586	11	0	11
47.0	1.806586	14	0	18
48.0	1.806586	17	0	18
49.0	1.806586	23	0	19
50.0	1.806586	14	0	13
51.0	1.806586	10	0	9
52.0	1.806586	8	0	12
53.0	1.806586	9	0	10
54.0	1.806586	18	0	13
55.0	1.806586	3	1	5
56.0	1.806586	13	0	11
57.0	1.806586	8	0	10
58.0	1.806586	11	0	9
59.0	1.806586	3	0	9
60.0	1.806586	14	0	8
61.0	1.806586	11	0	11
62.0	1.806586	13	0	15
63.0	1.806586	8	0	7
64.0	1.806586	8	0	8
65.0	1.806586	7	0	9
66.0	1.806586	10	0	9
67.0	1.806586	7	0	5
68.0	1.806586	10	0	11
69.0	1.806586	5	0	5
70.0	1.806586	8	0	8
71.0	1.806586	8	0	7
72.0	1.806586	8	0	9
73.0	1.806586	7	0	7
74.0	1.806586	3	0	3
75.0	1.806586	4	0	5
76.0	1.806586	8	0	9
77.0	1.806586	4	0	4
78.0	1.806586	4	0	3
79.0	1.806586	6	0	6
80.0	1.806586	12	0	10
81.0	1.806586	4	0	5
82.0	1.806586	6	0	6
83.0	1.806586	1	0	0
84.0	1.806586	6	0	8
85.0	1.806586	1	0	1
86.0	1.806586	9	0	8
87.0	1.806586	4	0	5
88.0	1.806586	5	0	6
89.0	1.806586	7	0	4
90.0	1.806586	4	0	5
91.0	1.806586	3	0	2
92.0	1.806586	1	0	2
93.0	1.806586	2	0	1
94.0	1.806586	2	0	3
95.0	1.806586	4	0	4
96.0	1.806586	8	0	7
97.0	1.806586	5	0	7
98.0	1.806586	3	0	3
99.0	1.806586	4	0	3
100.0	1.806586	8	0	9
101.0	0	6	0	4
102.0	0	1	0	1
103.0	0	5	0	6
104.0	0	6	0	6
105.0	0	4	0	4
106.0	0	3	0	2
107.0	0	3	0	3
108.0	0	1	0	1
109.0	0	4	0	4
110.0	0	3	0	4
111.0	0	5	0	5
112.0	0	4	0	3
113.0	0	1	0	1
114.0	0	2	0	3
115.0	0	4	0	5
116.0	0	4	0	4
117.0	0	9	0	9
118.0	0	5	0	4
119.0	0	4	0	3
120.0	0	0	0	1
121.0	0	4	0	3
122.0	0	4	0	4
123.0	0	1	0	1
124.0	0	2	0	2
125.0	0	3	0	3
126.0	0	2	0	3
127.0	0	3	0	2
128.0	0	2	0	3
129.0	0	4	0	4
130.0	0	1	0	1
131.0	0	1	0	0
132.0	0	4	0	4
133.0	0	2	0	2
134.0	0	2	0	4
135.0	0	5	0	4
136.0	0	5	0	4
137.0	0	2	0	2
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	4	0	5
143.0	0	5	0	4
144.0	0	1	0	3
145.0	0	1	0	0
146.0	0	3	1	2
147.0	0	1	0	3
148.0	0	4	0	2
149.0	0	1	0	1
150.0	0	2	0	2
151.0	0	3	0	3
152.0	0	2	0	2
153.0	0	2	0	2
155.0	0	1	0	1
156.0	0	2	0	3
157.0	0	1	0	0
158.0	0	1	0	1
159.0	0	1	0	1
160.0	0	0	0	1
161.0	0	3	0	2
162.0	0	1	0	1
163.0	0	1	0	1
164.0	0	2	0	2
165.0	0	2	0	2
166.0	0	1	0	2
167.0	0	1	0	0
168.0	0	1	0	2
169.0	0	3	0	4
170.0	0	2	0	1
171.0	0	2	0	2
172.0	0	1	0	2
173.0	0	1	0	0
174.0	0	2	0	1
175.0	0	0	0	2
176.0	0	2	0	0
177.0	0	2	0	2
178.0	0	1	0	1
180.0	0	1	0	1
181.0	0	2	0	3
182.0	0	1	0	1
183.0	0	3	0	2
184.0	0	1	0	1
185.0	0	3	0	3
187.0	0	2	0	2
188.0	0	1	0	1
189.0	0	2	0	2
190.0	0	2	0	2
193.0	0	0	0	1
194.0	0	2	0	2
195.0	0	2	0	1
198.0	0	1	0	1
199.0	0	1	0	2
200.0	0	1	0	2
201.0	0	2	0	0
202.0	0	3	0	3
205.0	0	4	0	4
206.0	0	1	0	1
207.0	0	1	0	1
208.0	0	1	0	1
209.0	0	2	0	2
212.0	0	2	0	2
213.0	0	1	0	1
217.0	0	2	0	2
218.0	0	1	0	1
219.0	0	1	0	1
220.0	0	1	0	1
221.0	0	3	0	5
222.0	0	2	0	1
223.0	0	3	0	2
224.0	0	1	0	2
225.0	0	1	0	0
228.0	0	2	0	2
229.0	0	2	0	2
230.0	0	1	0	1
231.0	0	0	0	1
232.0	0	2	0	1
233.0	0	1	0	1
234.0	0	1	0	1
237.0	0	1	0	1
238.0	0	1	0	1
242.0	0	1	0	1
243.0	0	1	0	1
244.0	0	2	0	2
245.0	0	1	0	1
248.0	0	1	0	2
249.0	0	1	0	1
250.0	0	4	0	3
251.0	0	2	0	2
252.0	0	1	0	1
253.0	0	1	0	1
254.0	0	2	0	2
255.0	0	1	0	1
258.0	0	2	0	2
259.0	0	1	0	1
261.0	0	1	0	1
263.0	0	0	0	1
265.0	0	1	0	0
267.0	0	1	0	1
270.0	0	1	0	1
271.0	0	1	0	1
272.0	0	0	0	1
273.0	0	3	0	3
275.0	0	1	0	1
276.0	0	1	0	0
279.0	0	1	0	1
280.0	0	1	0	1
281.0	0	3	0	3
283.0	0	1	0	1
284.0	0	0	0	1
285.0	0	1	0	0
286.0	0	1	0	1
288.0	0	2	0	2
292.0	0	1	0	1
293.0	0	1	0	1
298.0	0	1	0	1
299.0	0	0	0	1
300.0	0	1	0	1
301.0	0	2	0	2
302.0	0	1	0	0
305.0	0	1	0	1
306.0	0	1	0	1
312.0	0	1	0	1
314.0	0	1	0	1
315.0	0	0	0	1
316.0	0	1	0	1
317.0	0	1	0	0
318.0	0	2	0	2
319.0	0	1	0	1
321.0	0	0	0	1
322.0	0	1	0	0
323.0	0	2	0	2
324.0	0	0	0	1
325.0	0	2	0	2
326.0	0	1	0	0
327.0	0	0	0	1
328.0	0	2	0	1
329.0	0	1	0	1
332.0	0	0	0	1
333.0	0	2	0	2
334.0	0	2	0	2
335.0	0	2	0	1
336.0	0	0	0	1
337.0	0	2	0	1
338.0	0	1	0	1
340.0	0	1	0	1
346.0	0	1	0	1
348.0	0	1	0	1
350.0	0	1	0	1
351.0	0	0	0	1
353.0	0	1	0	1
355.0	0	3	0	3
356.0	0	2	0	1
357.0	0	1	0	1
361.0	0	1	0	1
362.0	0	1	0	1
363.0	0	1	0	1
364.0	0	1	0	1
369.0	0	0	0	1
370.0	0	1	0	0
372.0	0	0	0	1
373.0	0	1	0	1
375.0	0	1	0	0
377.0	0	1	0	1
378.0	0	1	0	1
381.0	0	0	0	1
382.0	0	1	0	0
386.0	0	1	0	1
387.0	0	0	0	1
388.0	0	1	0	1
389.0	0	0	0	1
390.0	0	2	0	0
391.0	0	1	0	1
392.0	0	1	0	1
394.0	0	0	0	1
396.0	0	0	0	1
397.0	0	4	0	2
398.0	0	0	0	1
399.0	0	1	0	1
401.0	0	1	0	0
404.0	0	0	0	1
405.0	0	1	0	1
407.0	0	2	0	1
412.0	0	1	0	1
414.0	0	1	0	1
418.0	0	1	0	1
419.0	0	1	0	1
421.0	0	2	0	3
422.0	0	1	0	2
423.0	0	1	0	0
425.0	0	1	0	0
430.0	0	1	0	1
436.0	0	0	0	1
438.0	0	2	0	1
445.0	0	1	0	1
452.0	0	1	0	1
453.0	0	1	0	1
468.0	0	0	0	1
470.0	0	1	0	0
475.0	0	2	0	2
476.0	0	0	0	1
477.0	0	2	0	1
480.0	0	1	0	1
481.0	0	1	0	1
495.0	0	1	0	1
501.0	0	1	0	1
503.0	0	1	0	1
504.0	0	0	0	1
508.0	0	1	0	0
514.0	0	0	0	1
515.0	0	1	0	0
518.0	0	1	0	1
526.0	0	2	0	2
531.0	0	1	0	1
537.0	0	1	0	1
546.0	0	1	0	1
550.0	0	1	0	1
554.0	0	0	0	1
556.0	0	1	0	0
563.0	0	0	0	1
564.0	0	1	0	0
565.0	0	1	0	1
575.0	0	0	0	1
576.0	0	1	0	0
580.0	0	1	0	1
592.0	0	0	0	1
594.0	0	1	0	0
596.0	0	0	0	1
599.0	0	1	0	0
602.0	0	1	0	1
603.0	0	0	0	1
605.0	0	0	0	1
607.0	0	1	0	0
609.0	0	1	0	1
611.0	0	1	0	0
616.0	0	1	0	1
619.0	0	0	0	2
620.0	0	1	0	0
622.0	0	1	0	0
626.0	0	0	0	1
631.0	0	1	0	0
663.0	0	1	0	1
669.0	0	0	0	1
670.0	0	1	0	0
680.0	0	1	0	1
683.0	0	1	0	1
700.0	0	0	0	1
702.0	0	1	0	1
704.0	0	0	0	1
706.0	0	2	0	0
713.0	0	1	0	1
714.0	0	1	0	1
722.0	0	0	0	1
723.0	0	1	0	1
727.0	0	1	0	0
739.0	0	1	0	1
746.0	0	1	0	1
747.0	0	0	0	1
748.0	0	1	0	1
749.0	0	1	0	0
767.0	0	1	0	1
773.0	0	1	0	1
814.0	0	0	0	1
817.0	0	1	0	0
822.0	0	1	0	1
826.0	0	1	0	2
827.0	0	0	0	1
828.0	0	1	0	0
829.0	0	1	0	0
838.0	0	0	0	1
840.0	0	1	0	0
841.0	0	1	0	1
844.0	0	0	0	1
845.0	0	1	0	0
865.0	0	1	0	1
869.0	0	0	0	1
871.0	0	1	0	0
883.0	0	1	0	1
889.0	0	0	0	1
890.0	0	1	0	0
903.0	0	1	0	1
906.0	0	1	0	2
907.0	0	2	0	1
950.0	0	1	0	1
978.0	0	1	0	1
996.0	0	0	0	1
998.0	0	1	0	0
1006.0	0	1	0	2
1007.0	0	2	0	1
1022.0	0	1	0	1
1023.0	0	0	0	1
1027.0	0	1	0	0
1029.0	0	1	0	1
1046.0	0	1	0	1
1056.0	0	1	0	1
1079.0	0	1	0	1
1083.0	0	1	0	1
1086.0	0	0	0	1
1087.0	0	1	0	0
1095.0	0	1	0	1
1123.0	0	1	0	1
1125.0	0	1	0	1
1155.0	0	0	0	1
1162.0	0	1	0	0
1165.0	0	0	0	1
1169.0	0	1	0	0
1191.0	0	0	0	1
1194.0	0	0	0	1
1200.0	0	1	0	0
1201.0	0	1	0	0
1211.0	0	1	0	1
1231.0	0	0	0	1
1235.0	0	1	0	0
1245.0	0	1	0	1
1261.0	0	0	0	1
1262.0	0	1	0	1
1264.0	0	1	0	0
1267.0	0	0	0	1
1270.0	0	1	0	0
1320.0	0	0	0	1
1323.0	0	1	0	0
1416.0	0	0	0	1
1420.0	0	1	0	0
1463.0	0	1	0	1
1486.0	0	0	0	1
1487.0	0	1	0	0
1494.0	0	1	0	1
1570.0	0	1	0	1
1587.0	0	0	0	1
1590.0	0	1	0	0
1591.0	0	0	0	1
1604.0	0	1	0	0
1649.0	0	0	0	1
1650.0	0	1	0	0
1662.0	0	1	0	1
1745.0	0	0	0	1
1747.0	0	1	0	0
1794.0	0	1	0	1
1865.0	0	0	0	1
1869.0	0	1	0	0
1943.0	0	0	0	1
1946.0	0	1	0	0
2034.0	0	1	0	1
2118.0	0	0	0	1
2135.0	0	1	0	0
2178.0	0	0	0	1
2189.0	0	1	0	0
2425.0	0	0	0	1
2441.0	0	1	0	0
2460.0	0	1	0	1
2534.0	0	0	0	1
2535.0	0	1	0	0
2691.0	0	0	0	1
2695.0	0	1	0	0
2699.0	0	0	0	1
2702.0	0	1	0	0
2782.0	0	0	0	1
2784.0	0	1	0	0
2910.0	0	0	0	1
2920.0	0	1	0	0
3069.0	0	0	0	1
3075.0	0	1	0	0
3276.0	0	0	0	1
3280.0	0	1	0	0
3382.0	0	0	0	1
3393.0	0	1	0	0
3731.0	0	0	0	1
3732.0	0	1	0	0
3733.0	0	0	0	1
3743.0	0	1	0	0
3804.0	0	0	0	1
3806.0	0	1	0	0
4080.0	0	0	0	1
4093.0	0	1	0	0
4659.0	0	0	0	1
4663.0	0	1	0	0
5341.0	0	0	0	1
5350.0	0	1	0	0
13128.0	0	0	0	1
13156.0	0	1	0	0
16095.0	0	0	0	1
16113.0	0	1	0	0
20617.0	0	0	0	1
20671.0	0	1	0	0
50310.0	0	0	0	1
50455.0	0	1	0	0