## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-07-25/FI_Pir_Aka_1_2014-07-25.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-07-25/FI_Pir_Aka_1_2014-07-25.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2014-07-25/FI_Pir_Aka_1_2014-07-25.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: Fri Jan 20 08:37:34 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	7147340	15578364	0	0	1430578	584423	0	0.067863	202402306

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	14290364	14290364
2.0	1.92592	272184	272184
3.0	2.783248	5500	5500
4.0	3.577065	1072	1072
5.0	4.312077	634	634
6.0	4.992639	418	418
7.0	5.622784	320	320
8.0	6.206249	272	272
9.0	6.746491	220	220
10.0	7.246712	159	159
11.0	7.709876	145	145
12.0	8.138729	131	131
13.0	8.535813	93	93
14.0	8.903481	115	115
15.0	9.243912	98	98
16.0	9.559124	68	68
17.0	9.850985	70	70
18.0	10.121225	75	75
19.0	10.371446	86	86
20.0	10.60313	59	59
21.0	10.817652	58	58
22.0	11.016281	54	54
23.0	11.200196	48	48
24.0	11.370487	44	44
25.0	11.528162	34	34
26.0	11.674157	45	45
27.0	11.809337	37	37
28.0	11.934503	54	54
29.0	12.050396	44	44
30.0	12.157704	24	24
31.0	12.257063	31	31
32.0	12.349061	34	34
33.0	12.434244	42	42
34.0	12.513116	33	33
35.0	12.586146	20	20
36.0	12.653766	36	36
37.0	12.716376	34	34
38.0	12.774348	34	34
39.0	12.828026	23	23
40.0	12.877727	26	26
41.0	12.923746	29	29
42.0	12.966357	19	19
43.0	13.00581	20	20
44.0	13.042341	17	17
45.0	13.076166	28	28
46.0	13.107485	23	23
47.0	13.136484	14	14
48.0	13.163335	20	20
49.0	13.188196	20	20
50.0	13.211216	23	23
51.0	13.232531	14	14
52.0	13.252266	17	17
53.0	13.27054	12	12
54.0	13.28746	12	12
55.0	13.303126	13	13
56.0	13.317632	16	16
57.0	13.331063	8	8
58.0	13.343499	18	18
59.0	13.355014	12	12
60.0	13.365676	8	8
61.0	13.375549	16	16
62.0	13.384689	10	10
63.0	13.393153	7	7
64.0	13.40099	13	13
65.0	13.408246	11	11
66.0	13.414964	21	21
67.0	13.421185	11	11
68.0	13.426945	10	10
69.0	13.432279	12	12
70.0	13.437217	8	8
71.0	13.441789	9	9
72.0	13.446023	14	14
73.0	13.449943	9	9
74.0	13.453573	14	14
75.0	13.456934	8	8
76.0	13.460045	12	12
77.0	13.462927	13	13
78.0	13.465594	5	5
79.0	13.468065	13	13
80.0	13.470352	7	7
81.0	13.47247	9	9
82.0	13.474431	6	6
83.0	13.476246	14	14
84.0	13.477927	7	7
85.0	13.479484	9	9
86.0	13.480925	8	8
87.0	13.48226	8	8
88.0	13.483495	12	12
89.0	13.48464	7	7
90.0	13.485699	7	7
91.0	13.48668	11	11
92.0	13.487588	8	8
93.0	13.488429	1	1
94.0	13.489208	9	9
95.0	13.489929	7	7
96.0	13.490596	7	7
97.0	13.491214	7	7
98.0	13.491786	7	7
99.0	13.492316	5	5
100.0	13.492807	5	5
101.0	0	11	11
102.0	0	7	7
103.0	0	6	6
104.0	0	6	6
105.0	0	2	2
106.0	0	4	4
107.0	0	5	5
108.0	0	4	4
109.0	0	7	7
110.0	0	4	4
111.0	0	7	7
112.0	0	4	4
113.0	0	5	5
114.0	0	4	4
115.0	0	8	8
116.0	0	2	2
117.0	0	4	4
118.0	0	1	1
119.0	0	4	4
120.0	0	7	7
121.0	0	3	3
122.0	0	5	5
123.0	0	5	5
124.0	0	2	2
125.0	0	5	5
126.0	0	3	3
127.0	0	3	3
128.0	0	5	5
129.0	0	3	3
130.0	0	1	1
131.0	0	7	7
132.0	0	2	2
133.0	0	1	1
134.0	0	4	4
135.0	0	4	4
136.0	0	7	7
137.0	0	7	7
138.0	0	2	2
139.0	0	3	3
140.0	0	6	6
141.0	0	1	1
142.0	0	2	2
143.0	0	3	3
144.0	0	1	1
145.0	0	2	2
146.0	0	6	6
147.0	0	3	3
148.0	0	3	3
149.0	0	1	1
150.0	0	1	1
151.0	0	6	6
152.0	0	2	2
153.0	0	4	4
154.0	0	4	4
155.0	0	4	4
156.0	0	4	4
157.0	0	4	4
158.0	0	6	6
159.0	0	5	5
160.0	0	2	2
161.0	0	3	3
162.0	0	1	1
163.0	0	4	4
164.0	0	2	2
165.0	0	7	7
166.0	0	6	6
167.0	0	2	2
168.0	0	2	2
169.0	0	3	3
170.0	0	2	2
171.0	0	1	1
172.0	0	5	5
173.0	0	2	2
174.0	0	4	4
175.0	0	3	3
176.0	0	1	1
177.0	0	6	6
178.0	0	1	1
179.0	0	3	3
180.0	0	1	1
181.0	0	3	3
182.0	0	2	2
183.0	0	3	3
184.0	0	1	1
185.0	0	6	6
186.0	0	4	4
187.0	0	3	3
189.0	0	4	4
190.0	0	1	1
191.0	0	2	2
192.0	0	2	2
193.0	0	1	1
194.0	0	1	1
195.0	0	1	1
196.0	0	5	5
197.0	0	5	5
199.0	0	1	1
200.0	0	1	1
201.0	0	2	2
202.0	0	1	1
203.0	0	2	2
204.0	0	3	3
205.0	0	1	1
206.0	0	2	2
207.0	0	4	4
208.0	0	3	3
209.0	0	3	3
210.0	0	1	1
211.0	0	2	2
212.0	0	2	2
213.0	0	2	2
214.0	0	2	2
215.0	0	3	3
216.0	0	3	3
217.0	0	1	1
218.0	0	3	3
219.0	0	1	1
221.0	0	1	1
224.0	0	3	3
225.0	0	3	3
226.0	0	4	4
229.0	0	1	1
230.0	0	2	2
231.0	0	2	2
232.0	0	3	3
233.0	0	2	2
235.0	0	3	3
236.0	0	2	2
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
242.0	0	2	2
243.0	0	1	1
245.0	0	2	2
246.0	0	2	2
247.0	0	2	2
248.0	0	1	1
250.0	0	1	1
253.0	0	5	5
255.0	0	1	1
256.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	5	5
267.0	0	3	3
269.0	0	1	1
270.0	0	2	2
271.0	0	1	1
272.0	0	2	2
273.0	0	1	1
276.0	0	1	1
277.0	0	1	1
279.0	0	1	1
280.0	0	2	2
281.0	0	1	1
283.0	0	1	1
284.0	0	1	1
287.0	0	1	1
288.0	0	1	1
290.0	0	3	3
296.0	0	1	1
297.0	0	1	1
298.0	0	2	2
301.0	0	1	1
302.0	0	1	1
304.0	0	1	1
306.0	0	2	2
307.0	0	2	2
313.0	0	2	2
314.0	0	1	1
316.0	0	1	1
317.0	0	1	1
319.0	0	1	1
320.0	0	3	3
322.0	0	2	2
323.0	0	3	3
325.0	0	2	2
326.0	0	1	1
328.0	0	1	1
329.0	0	1	1
330.0	0	3	3
331.0	0	1	1
332.0	0	1	1
337.0	0	1	1
341.0	0	2	2
342.0	0	1	1
345.0	0	3	3
346.0	0	2	2
349.0	0	1	1
350.0	0	1	1
351.0	0	1	1
354.0	0	1	1
355.0	0	1	1
357.0	0	1	1
360.0	0	2	2
363.0	0	2	2
364.0	0	1	1
366.0	0	2	2
368.0	0	1	1
373.0	0	1	1
382.0	0	1	1
383.0	0	2	2
386.0	0	1	1
390.0	0	1	1
392.0	0	1	1
393.0	0	1	1
394.0	0	2	2
398.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	2	2
405.0	0	1	1
407.0	0	2	2
409.0	0	1	1
410.0	0	1	1
414.0	0	4	4
416.0	0	2	2
418.0	0	3	3
419.0	0	1	1
420.0	0	1	1
423.0	0	1	1
425.0	0	1	1
426.0	0	2	2
430.0	0	1	1
431.0	0	1	1
433.0	0	2	2
447.0	0	2	2
450.0	0	3	3
453.0	0	2	2
456.0	0	1	1
458.0	0	1	1
460.0	0	1	1
464.0	0	1	1
472.0	0	1	1
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
480.0	0	1	1
487.0	0	1	1
488.0	0	1	1
498.0	0	1	1
501.0	0	2	2
504.0	0	1	1
506.0	0	1	1
508.0	0	1	1
513.0	0	1	1
516.0	0	1	1
520.0	0	1	1
522.0	0	1	1
523.0	0	1	1
525.0	0	1	1
535.0	0	1	1
539.0	0	1	1
540.0	0	1	1
543.0	0	2	2
548.0	0	1	1
556.0	0	1	1
563.0	0	1	1
573.0	0	1	1
575.0	0	1	1
579.0	0	3	3
584.0	0	1	1
586.0	0	1	1
590.0	0	1	1
591.0	0	1	1
598.0	0	1	1
599.0	0	1	1
605.0	0	1	1
609.0	0	1	1
625.0	0	1	1
632.0	0	1	1
633.0	0	1	1
649.0	0	1	1
650.0	0	1	1
652.0	0	1	1
653.0	0	1	1
658.0	0	1	1
663.0	0	1	1
666.0	0	1	1
673.0	0	1	1
685.0	0	1	1
693.0	0	1	1
694.0	0	2	2
705.0	0	1	1
707.0	0	1	1
709.0	0	1	1
721.0	0	1	1
723.0	0	1	1
730.0	0	1	1
734.0	0	1	1
737.0	0	1	1
741.0	0	1	1
765.0	0	1	1
770.0	0	1	1
799.0	0	1	1
809.0	0	1	1
812.0	0	1	1
815.0	0	1	1
826.0	0	1	1
827.0	0	1	1
848.0	0	1	1
852.0	0	1	1
874.0	0	1	1
885.0	0	1	1
897.0	0	1	1
898.0	0	2	2
911.0	0	2	2
924.0	0	1	1
954.0	0	1	1
987.0	0	1	1
1000.0	0	1	1
1004.0	0	1	1
1006.0	0	1	1
1011.0	0	1	1
1017.0	0	1	1
1055.0	0	1	1
1071.0	0	1	1
1118.0	0	1	1
1139.0	0	1	1
1173.0	0	2	2
1199.0	0	1	1
1208.0	0	1	1
1214.0	0	1	1
1246.0	0	1	1
1247.0	0	1	1
1253.0	0	1	1
1255.0	0	1	1
1388.0	0	1	1
1400.0	0	1	1
1418.0	0	1	1
1485.0	0	1	1
1605.0	0	1	1
1664.0	0	1	1
1671.0	0	1	1
1948.0	0	1	1