## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2014-07-26/FI_Cen_Ves_1_2014-07-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2014-07-26/FI_Cen_Ves_1_2014-07-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Cen_Ves_1_2014-07-26/FI_Cen_Ves_1_2014-07-26.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 08:54:11 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	12885415	20435452	0	0	2963409	738055	0	0.082586	276057331

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18789519	18789519
2.0	1.928647	468984	468984
3.0	2.791034	10679	10679
4.0	3.591886	1060	1060
5.0	4.335596	540	540
6.0	5.02624	397	397
7.0	5.667605	297	297
8.0	6.263207	216	216
9.0	6.816311	175	175
10.0	7.32995	142	142
11.0	7.806939	143	143
12.0	8.249894	131	131
13.0	8.661243	99	99
14.0	9.043241	95	95
15.0	9.397983	93	93
16.0	9.727413	82	82
17.0	10.033337	86	86
18.0	10.317433	71	71
19.0	10.581257	64	64
20.0	10.826258	70	70
21.0	11.053776	62	62
22.0	11.265061	40	40
23.0	11.46127	53	53
24.0	11.643479	36	36
25.0	11.812687	40	40
26.0	11.969822	47	47
27.0	12.115744	28	28
28.0	12.251255	34	34
29.0	12.377097	37	37
30.0	12.493959	43	43
31.0	12.602483	40	40
32.0	12.703264	31	31
33.0	12.796853	32	32
34.0	12.883765	38	38
35.0	12.964475	27	27
36.0	13.039427	33	33
37.0	13.10903	24	24
38.0	13.173668	22	22
39.0	13.233693	23	23
40.0	13.289435	24	24
41.0	13.3412	23	23
42.0	13.389271	15	15
43.0	13.433912	15	15
44.0	13.475368	25	25
45.0	13.513866	19	19
46.0	13.549617	16	16
47.0	13.582817	20	20
48.0	13.613649	28	28
49.0	13.64228	17	17
50.0	13.668868	17	17
51.0	13.69356	15	15
52.0	13.716489	12	12
53.0	13.737783	14	14
54.0	13.757557	7	7
55.0	13.77592	14	14
56.0	13.792973	21	21
57.0	13.808809	14	14
58.0	13.823515	12	12
59.0	13.837172	16	16
60.0	13.849854	23	23
61.0	13.861632	18	18
62.0	13.872569	12	12
63.0	13.882725	9	9
64.0	13.892157	15	15
65.0	13.900916	11	11
66.0	13.90905	16	16
67.0	13.916604	11	11
68.0	13.923619	12	12
69.0	13.930133	7	7
70.0	13.936182	12	12
71.0	13.9418	9	9
72.0	13.947017	7	7
73.0	13.951862	9	9
74.0	13.956361	7	7
75.0	13.960539	8	8
76.0	13.964418	5	5
77.0	13.968021	10	10
78.0	13.971367	6	6
79.0	13.974475	14	14
80.0	13.97736	4	4
81.0	13.98004	7	7
82.0	13.982528	6	6
83.0	13.984839	10	10
84.0	13.986985	7	7
85.0	13.988978	11	11
86.0	13.990828	4	4
87.0	13.992547	5	5
88.0	13.994143	6	6
89.0	13.995625	8	8
90.0	13.997001	6	6
91.0	13.998279	5	5
92.0	13.999466	12	12
93.0	14.000569	5	5
94.0	14.001592	7	7
95.0	14.002543	4	4
96.0	14.003426	1	1
97.0	14.004245	9	9
98.0	14.005007	1	1
99.0	14.005713	7	7
100.0	14.00637	4	4
101.0	0	6	6
102.0	0	8	8
103.0	0	7	7
104.0	0	10	10
106.0	0	7	7
107.0	0	4	4
108.0	0	3	3
109.0	0	9	9
110.0	0	6	6
111.0	0	4	4
112.0	0	4	4
113.0	0	6	6
114.0	0	6	6
115.0	0	8	8
116.0	0	2	2
117.0	0	3	3
118.0	0	2	2
119.0	0	3	3
120.0	0	5	5
121.0	0	3	3
122.0	0	3	3
123.0	0	9	9
124.0	0	1	1
126.0	0	4	4
127.0	0	4	4
128.0	0	5	5
129.0	0	5	5
130.0	0	1	1
131.0	0	4	4
133.0	0	4	4
134.0	0	3	3
135.0	0	3	3
136.0	0	7	7
137.0	0	6	6
138.0	0	1	1
140.0	0	3	3
141.0	0	6	6
142.0	0	4	4
143.0	0	4	4
144.0	0	6	6
146.0	0	3	3
147.0	0	4	4
148.0	0	4	4
149.0	0	3	3
150.0	0	3	3
151.0	0	1	1
152.0	0	8	8
153.0	0	2	2
154.0	0	5	5
156.0	0	3	3
158.0	0	4	4
159.0	0	6	6
160.0	0	3	3
161.0	0	6	6
162.0	0	3	3
164.0	0	1	1
165.0	0	3	3
166.0	0	2	2
167.0	0	2	2
168.0	0	4	4
169.0	0	3	3
170.0	0	1	1
172.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	2	2
177.0	0	3	3
178.0	0	1	1
179.0	0	4	4
180.0	0	3	3
181.0	0	3	3
182.0	0	3	3
183.0	0	2	2
184.0	0	2	2
185.0	0	3	3
186.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	1	1
191.0	0	5	5
192.0	0	1	1
193.0	0	8	8
194.0	0	2	2
195.0	0	2	2
196.0	0	2	2
198.0	0	3	3
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	4	4
204.0	0	3	3
205.0	0	4	4
206.0	0	4	4
207.0	0	1	1
208.0	0	1	1
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
217.0	0	2	2
218.0	0	1	1
219.0	0	2	2
220.0	0	3	3
221.0	0	1	1
223.0	0	2	2
224.0	0	2	2
226.0	0	1	1
227.0	0	2	2
228.0	0	1	1
229.0	0	1	1
230.0	0	2	2
231.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	3	3
236.0	0	2	2
237.0	0	4	4
238.0	0	2	2
239.0	0	1	1
240.0	0	2	2
241.0	0	1	1
242.0	0	1	1
243.0	0	2	2
245.0	0	4	4
246.0	0	3	3
247.0	0	3	3
249.0	0	2	2
250.0	0	1	1
251.0	0	3	3
252.0	0	3	3
253.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
261.0	0	1	1
264.0	0	3	3
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
273.0	0	1	1
274.0	0	2	2
277.0	0	1	1
280.0	0	2	2
281.0	0	4	4
283.0	0	1	1
285.0	0	2	2
286.0	0	2	2
289.0	0	1	1
292.0	0	2	2
293.0	0	3	3
294.0	0	1	1
295.0	0	2	2
296.0	0	2	2
299.0	0	2	2
302.0	0	1	1
305.0	0	1	1
308.0	0	1	1
311.0	0	2	2
312.0	0	2	2
313.0	0	1	1
314.0	0	2	2
315.0	0	1	1
316.0	0	1	1
318.0	0	1	1
320.0	0	1	1
321.0	0	1	1
322.0	0	2	2
324.0	0	1	1
325.0	0	1	1
327.0	0	1	1
331.0	0	1	1
333.0	0	2	2
334.0	0	1	1
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
340.0	0	2	2
343.0	0	1	1
344.0	0	2	2
347.0	0	1	1
349.0	0	1	1
351.0	0	1	1
352.0	0	2	2
355.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
364.0	0	1	1
366.0	0	1	1
368.0	0	1	1
372.0	0	1	1
373.0	0	1	1
374.0	0	1	1
376.0	0	1	1
379.0	0	3	3
382.0	0	2	2
385.0	0	2	2
386.0	0	5	5
389.0	0	1	1
393.0	0	2	2
398.0	0	1	1
399.0	0	1	1
400.0	0	2	2
402.0	0	1	1
415.0	0	1	1
418.0	0	2	2
419.0	0	4	4
420.0	0	1	1
421.0	0	1	1
422.0	0	1	1
425.0	0	1	1
426.0	0	1	1
427.0	0	1	1
434.0	0	2	2
436.0	0	1	1
437.0	0	1	1
439.0	0	1	1
446.0	0	1	1
451.0	0	1	1
454.0	0	2	2
455.0	0	1	1
456.0	0	1	1
460.0	0	2	2
461.0	0	2	2
473.0	0	1	1
478.0	0	2	2
480.0	0	1	1
487.0	0	1	1
499.0	0	2	2
500.0	0	1	1
502.0	0	1	1
504.0	0	1	1
513.0	0	1	1
516.0	0	1	1
517.0	0	2	2
518.0	0	1	1
531.0	0	2	2
532.0	0	1	1
534.0	0	2	2
544.0	0	1	1
545.0	0	1	1
559.0	0	1	1
561.0	0	1	1
568.0	0	1	1
569.0	0	1	1
574.0	0	1	1
577.0	0	1	1
579.0	0	1	1
581.0	0	1	1
596.0	0	1	1
597.0	0	1	1
603.0	0	1	1
612.0	0	1	1
622.0	0	1	1
635.0	0	1	1
644.0	0	1	1
648.0	0	1	1
653.0	0	1	1
664.0	0	1	1
673.0	0	1	1
678.0	0	1	1
684.0	0	1	1
686.0	0	1	1
687.0	0	1	1
690.0	0	1	1
699.0	0	1	1
721.0	0	2	2
722.0	0	1	1
766.0	0	1	1
773.0	0	1	1
781.0	0	1	1
821.0	0	1	1
843.0	0	1	1
874.0	0	1	1
882.0	0	1	1
904.0	0	1	1
906.0	0	1	1
919.0	0	1	1
933.0	0	1	1
942.0	0	1	1
959.0	0	1	1
1021.0	0	1	1
1161.0	0	1	1
1191.0	0	1	1
1224.0	0	1	1
1229.0	0	1	1
1238.0	0	1	1