## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-08-27/FI_Pir_Aka_1_2014-08-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-08-27/FI_Pir_Aka_1_2014-08-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-08-27/FI_Pir_Aka_1_2014-08-27.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 08:18:05 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	7701103	15021110	0	0	1408925	561205	0	0.067067	195987284

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	13780525	13780525
2.0	1.92622	334175	334175
3.0	2.784104	7622	7622
4.0	3.578693	840	840
5.0	4.314658	486	486
6.0	4.996323	356	356
7.0	5.627696	261	261
8.0	6.212485	201	201
9.0	6.754129	191	191
10.0	7.255811	151	151
11.0	7.720479	133	133
12.0	8.150863	95	95
13.0	8.549494	87	87
14.0	8.918714	85	85
15.0	9.260693	96	96
16.0	9.577441	60	60
17.0	9.870819	81	81
18.0	10.142552	59	59
19.0	10.394236	66	66
20.0	10.627351	51	51
21.0	10.843267	59	59
22.0	11.043253	64	64
23.0	11.228484	36	36
24.0	11.400049	61	61
25.0	11.558955	34	34
26.0	11.706138	39	39
27.0	11.842461	32	32
28.0	11.968726	42	42
29.0	12.085676	22	22
30.0	12.193997	29	29
31.0	12.294326	36	36
32.0	12.387253	32	32
33.0	12.473324	25	25
34.0	12.553044	25	25
35.0	12.626883	33	33
36.0	12.695274	19	19
37.0	12.758619	19	19
38.0	12.817291	18	18
39.0	12.871633	22	22
40.0	12.921967	27	27
41.0	12.968586	24	24
42.0	13.011767	22	22
43.0	13.051761	28	28
44.0	13.088804	22	22
45.0	13.123115	14	14
46.0	13.154894	19	19
47.0	13.184328	18	18
48.0	13.211591	14	14
49.0	13.236842	20	20
50.0	13.260231	16	16
51.0	13.281893	18	18
52.0	13.301958	15	15
53.0	13.320542	8	8
54.0	13.337755	11	11
55.0	13.353698	15	15
56.0	13.368464	8	8
57.0	13.382142	16	16
58.0	13.39481	7	7
59.0	13.406543	15	15
60.0	13.417411	11	11
61.0	13.427477	14	14
62.0	13.4368	14	14
63.0	13.445436	17	17
64.0	13.453434	12	12
65.0	13.460842	9	9
66.0	13.467704	7	7
67.0	13.474059	11	11
68.0	13.479945	16	16
69.0	13.485398	7	7
70.0	13.490447	10	10
71.0	13.495125	12	12
72.0	13.499457	5	5
73.0	13.50347	6	6
74.0	13.507186	10	10
75.0	13.510629	9	9
76.0	13.513817	8	8
77.0	13.51677	6	6
78.0	13.519505	10	10
79.0	13.522039	10	10
80.0	13.524385	6	6
81.0	13.526559	4	4
82.0	13.528572	6	6
83.0	13.530436	9	9
84.0	13.532163	6	6
85.0	13.533763	9	9
86.0	13.535244	12	12
87.0	13.536616	8	8
88.0	13.537887	5	5
89.0	13.539065	5	5
90.0	13.540155	8	8
91.0	13.541165	3	3
92.0	13.5421	9	9
93.0	13.542967	2	2
94.0	13.543769	9	9
95.0	13.544512	5	5
96.0	13.545201	4	4
97.0	13.545838	9	9
98.0	13.546429	3	3
99.0	13.546976	4	4
100.0	13.547483	4	4
101.0	0	5	5
102.0	0	4	4
103.0	0	6	6
104.0	0	4	4
105.0	0	5	5
106.0	0	4	4
107.0	0	3	3
108.0	0	4	4
109.0	0	5	5
110.0	0	2	2
111.0	0	2	2
112.0	0	4	4
113.0	0	8	8
114.0	0	7	7
115.0	0	2	2
116.0	0	4	4
117.0	0	6	6
118.0	0	9	9
119.0	0	5	5
120.0	0	2	2
121.0	0	2	2
122.0	0	3	3
123.0	0	4	4
124.0	0	6	6
125.0	0	1	1
126.0	0	2	2
127.0	0	2	2
128.0	0	5	5
129.0	0	1	1
130.0	0	6	6
131.0	0	6	6
132.0	0	5	5
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	3	3
139.0	0	2	2
140.0	0	5	5
141.0	0	2	2
142.0	0	4	4
143.0	0	4	4
144.0	0	2	2
145.0	0	1	1
146.0	0	3	3
147.0	0	3	3
148.0	0	4	4
149.0	0	1	1
150.0	0	2	2
151.0	0	2	2
152.0	0	5	5
153.0	0	1	1
154.0	0	1	1
155.0	0	2	2
156.0	0	4	4
157.0	0	8	8
158.0	0	2	2
159.0	0	2	2
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
163.0	0	1	1
164.0	0	1	1
165.0	0	2	2
166.0	0	3	3
167.0	0	2	2
168.0	0	2	2
169.0	0	3	3
170.0	0	1	1
171.0	0	1	1
172.0	0	3	3
173.0	0	1	1
174.0	0	2	2
176.0	0	3	3
178.0	0	1	1
179.0	0	3	3
180.0	0	3	3
181.0	0	3	3
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	5	5
186.0	0	2	2
188.0	0	3	3
189.0	0	1	1
191.0	0	2	2
192.0	0	1	1
194.0	0	3	3
195.0	0	2	2
196.0	0	1	1
197.0	0	1	1
198.0	0	4	4
200.0	0	2	2
202.0	0	1	1
203.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
207.0	0	3	3
209.0	0	1	1
210.0	0	1	1
211.0	0	2	2
212.0	0	2	2
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	3	3
218.0	0	2	2
219.0	0	2	2
220.0	0	1	1
221.0	0	1	1
222.0	0	1	1
223.0	0	2	2
224.0	0	1	1
225.0	0	2	2
226.0	0	2	2
229.0	0	1	1
230.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	2	2
237.0	0	1	1
238.0	0	3	3
239.0	0	3	3
240.0	0	2	2
241.0	0	3	3
243.0	0	1	1
244.0	0	4	4
245.0	0	1	1
247.0	0	1	1
248.0	0	2	2
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
257.0	0	1	1
258.0	0	2	2
259.0	0	1	1
260.0	0	2	2
261.0	0	1	1
262.0	0	1	1
263.0	0	2	2
265.0	0	1	1
266.0	0	1	1
270.0	0	2	2
271.0	0	1	1
273.0	0	2	2
274.0	0	1	1
276.0	0	1	1
277.0	0	1	1
279.0	0	1	1
280.0	0	1	1
283.0	0	1	1
284.0	0	2	2
286.0	0	3	3
287.0	0	2	2
288.0	0	1	1
291.0	0	1	1
292.0	0	1	1
295.0	0	1	1
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
304.0	0	2	2
309.0	0	2	2
311.0	0	2	2
312.0	0	1	1
315.0	0	1	1
319.0	0	1	1
320.0	0	2	2
323.0	0	1	1
324.0	0	1	1
325.0	0	1	1
327.0	0	1	1
329.0	0	1	1
330.0	0	1	1
333.0	0	1	1
336.0	0	1	1
339.0	0	2	2
340.0	0	1	1
341.0	0	1	1
342.0	0	2	2
348.0	0	2	2
353.0	0	1	1
355.0	0	1	1
357.0	0	3	3
360.0	0	3	3
363.0	0	1	1
364.0	0	1	1
367.0	0	1	1
368.0	0	2	2
370.0	0	2	2
371.0	0	2	2
374.0	0	2	2
375.0	0	1	1
380.0	0	1	1
382.0	0	3	3
386.0	0	1	1
387.0	0	1	1
390.0	0	1	1
392.0	0	1	1
397.0	0	3	3
398.0	0	2	2
399.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	1	1
405.0	0	2	2
410.0	0	1	1
412.0	0	1	1
414.0	0	1	1
431.0	0	1	1
432.0	0	1	1
436.0	0	1	1
441.0	0	1	1
444.0	0	1	1
447.0	0	1	1
454.0	0	1	1
459.0	0	2	2
462.0	0	2	2
472.0	0	1	1
473.0	0	1	1
481.0	0	1	1
485.0	0	1	1
486.0	0	1	1
487.0	0	1	1
506.0	0	1	1
508.0	0	1	1
510.0	0	1	1
514.0	0	1	1
521.0	0	1	1
525.0	0	1	1
530.0	0	1	1
539.0	0	2	2
550.0	0	1	1
556.0	0	1	1
558.0	0	2	2
560.0	0	1	1
566.0	0	1	1
567.0	0	2	2
579.0	0	1	1
604.0	0	1	1
609.0	0	1	1
610.0	0	1	1
613.0	0	1	1
615.0	0	2	2
616.0	0	1	1
618.0	0	1	1
640.0	0	1	1
674.0	0	1	1
682.0	0	1	1
686.0	0	1	1
707.0	0	1	1
719.0	0	1	1
739.0	0	1	1
797.0	0	1	1
798.0	0	1	1
804.0	0	1	1
813.0	0	1	1
820.0	0	1	1
824.0	0	1	1
829.0	0	1	1
840.0	0	1	1
919.0	0	1	1
936.0	0	1	1
943.0	0	1	1
1095.0	0	1	1
1142.0	0	1	1
1144.0	0	1	1
1175.0	0	1	1