## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-08-30/US_Cal_Pla_1_2013-08-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-08-30/US_Cal_Pla_1_2013-08-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Pla_1_2013-08-30/US_Cal_Pla_1_2013-08-30.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 18:12:33 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	3361447	41225535	0	0	1168979	1408329	0	0.046446	589568975

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	37842196	37842196
2.0	1.932464	919824	919824
3.0	2.801953	35210	35210
4.0	3.61272	6814	6814
5.0	4.368731	3210	3210
6.0	5.073683	1720	1720
7.0	5.731027	1088	1088
8.0	6.343975	776	776
9.0	6.915528	510	510
10.0	7.44848	400	400
11.0	7.945438	331	331
12.0	8.408834	291	291
13.0	8.840934	213	213
14.0	9.243852	197	197
15.0	9.619558	189	189
16.0	9.96989	143	143
17.0	10.296562	119	119
18.0	10.601172	126	126
19.0	10.88521	125	125
20.0	11.150065	92	92
21.0	11.397033	82	82
22.0	11.627321	60	60
23.0	11.842057	68	68
24.0	12.04229	58	58
25.0	12.229001	55	55
26.0	12.403101	61	61
27.0	12.565444	62	62
28.0	12.716823	44	44
29.0	12.857978	44	44
30.0	12.9896	53	53
31.0	13.112332	40	40
32.0	13.226776	38	38
33.0	13.333491	39	39
34.0	13.432999	33	33
35.0	13.525786	40	40
36.0	13.612307	34	34
37.0	13.692984	38	38
38.0	13.768213	25	25
39.0	13.838361	29	29
40.0	13.903772	27	27
41.0	13.964765	22	22
42.0	14.021639	24	24
43.0	14.074672	28	28
44.0	14.124123	26	26
45.0	14.170234	31	31
46.0	14.213231	22	22
47.0	14.253325	29	29
48.0	14.29071	23	23
49.0	14.325571	18	18
50.0	14.358078	20	20
51.0	14.388389	16	16
52.0	14.416653	16	16
53.0	14.443008	20	20
54.0	14.467583	21	21
55.0	14.490498	16	16
56.0	14.511866	13	13
57.0	14.531791	18	18
58.0	14.55037	14	14
59.0	14.567694	18	18
60.0	14.583849	11	11
61.0	14.598912	13	13
62.0	14.612958	13	13
63.0	14.626055	12	12
64.0	14.638268	18	18
65.0	14.649656	12	12
66.0	14.660275	18	18
67.0	14.670177	10	10
68.0	14.67941	16	16
69.0	14.688019	8	8
70.0	14.696048	12	12
71.0	14.703533	15	15
72.0	14.710514	13	13
73.0	14.717023	9	9
74.0	14.723092	11	11
75.0	14.728751	15	15
76.0	14.734028	10	10
77.0	14.738949	8	8
78.0	14.743538	13	13
79.0	14.747816	16	16
80.0	14.751806	12	12
81.0	14.755526	9	9
82.0	14.758995	15	15
83.0	14.762229	3	3
84.0	14.765246	11	11
85.0	14.768058	4	4
86.0	14.770681	10	10
87.0	14.773126	8	8
88.0	14.775406	8	8
89.0	14.777533	17	17
90.0	14.779515	5	5
91.0	14.781364	6	6
92.0	14.783088	4	4
93.0	14.784695	12	12
94.0	14.786194	7	7
95.0	14.787592	4	4
96.0	14.788895	4	4
97.0	14.790111	8	8
98.0	14.791244	3	3
99.0	14.7923	7	7
100.0	14.793286	2	2
101.0	0	1	1
102.0	0	5	5
103.0	0	6	6
104.0	0	9	9
105.0	0	4	4
106.0	0	6	6
107.0	0	5	5
108.0	0	3	3
109.0	0	5	5
110.0	0	4	4
111.0	0	6	6
112.0	0	7	7
113.0	0	5	5
114.0	0	6	6
115.0	0	4	4
116.0	0	3	3
117.0	0	3	3
118.0	0	5	5
119.0	0	1	1
120.0	0	5	5
121.0	0	2	2
122.0	0	5	5
123.0	0	5	5
124.0	0	4	4
125.0	0	5	5
126.0	0	2	2
127.0	0	2	2
128.0	0	7	7
129.0	0	4	4
130.0	0	5	5
131.0	0	6	6
132.0	0	3	3
133.0	0	6	6
134.0	0	2	2
135.0	0	6	6
136.0	0	6	6
137.0	0	1	1
138.0	0	3	3
139.0	0	8	8
140.0	0	7	7
141.0	0	3	3
142.0	0	6	6
143.0	0	2	2
144.0	0	5	5
145.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	3	3
149.0	0	8	8
150.0	0	5	5
151.0	0	5	5
152.0	0	4	4
153.0	0	3	3
154.0	0	4	4
155.0	0	2	2
156.0	0	2	2
157.0	0	1	1
158.0	0	5	5
159.0	0	3	3
160.0	0	1	1
161.0	0	2	2
162.0	0	2	2
163.0	0	4	4
165.0	0	3	3
166.0	0	1	1
167.0	0	3	3
168.0	0	4	4
169.0	0	1	1
170.0	0	6	6
171.0	0	3	3
172.0	0	3	3
173.0	0	3	3
174.0	0	2	2
175.0	0	2	2
176.0	0	2	2
177.0	0	1	1
178.0	0	1	1
179.0	0	4	4
180.0	0	4	4
181.0	0	2	2
182.0	0	3	3
183.0	0	4	4
185.0	0	2	2
186.0	0	2	2
187.0	0	2	2
188.0	0	1	1
189.0	0	2	2
191.0	0	2	2
192.0	0	1	1
194.0	0	3	3
195.0	0	1	1
197.0	0	3	3
198.0	0	2	2
199.0	0	1	1
200.0	0	4	4
201.0	0	2	2
202.0	0	1	1
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	5	5
207.0	0	3	3
208.0	0	1	1
209.0	0	3	3
210.0	0	1	1
211.0	0	1	1
213.0	0	3	3
214.0	0	1	1
215.0	0	2	2
216.0	0	2	2
217.0	0	2	2
218.0	0	2	2
219.0	0	4	4
220.0	0	2	2
221.0	0	3	3
224.0	0	6	6
225.0	0	2	2
226.0	0	2	2
227.0	0	1	1
228.0	0	3	3
229.0	0	2	2
230.0	0	2	2
231.0	0	4	4
233.0	0	3	3
234.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	3	3
242.0	0	5	5
243.0	0	2	2
245.0	0	1	1
247.0	0	6	6
248.0	0	2	2
249.0	0	1	1
252.0	0	1	1
255.0	0	1	1
256.0	0	1	1
257.0	0	2	2
258.0	0	2	2
259.0	0	3	3
262.0	0	1	1
263.0	0	2	2
264.0	0	2	2
266.0	0	1	1
267.0	0	2	2
268.0	0	2	2
269.0	0	2	2
270.0	0	3	3
271.0	0	4	4
272.0	0	2	2
273.0	0	3	3
274.0	0	3	3
275.0	0	1	1
276.0	0	5	5
277.0	0	2	2
278.0	0	1	1
279.0	0	4	4
280.0	0	2	2
281.0	0	2	2
282.0	0	3	3
284.0	0	2	2
285.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	4	4
291.0	0	1	1
292.0	0	2	2
293.0	0	2	2
294.0	0	1	1
295.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	3	3
306.0	0	1	1
307.0	0	2	2
309.0	0	1	1
311.0	0	5	5
312.0	0	2	2
313.0	0	1	1
314.0	0	2	2
317.0	0	1	1
318.0	0	1	1
319.0	0	2	2
320.0	0	1	1
321.0	0	1	1
322.0	0	1	1
323.0	0	2	2
325.0	0	2	2
327.0	0	1	1
328.0	0	1	1
329.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	1	1
337.0	0	3	3
338.0	0	2	2
339.0	0	3	3
340.0	0	2	2
342.0	0	1	1
346.0	0	1	1
350.0	0	3	3
351.0	0	1	1
352.0	0	1	1
354.0	0	1	1
356.0	0	1	1
357.0	0	1	1
358.0	0	2	2
359.0	0	1	1
361.0	0	1	1
362.0	0	1	1
363.0	0	2	2
364.0	0	3	3
366.0	0	1	1
367.0	0	1	1
368.0	0	2	2
369.0	0	2	2
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
374.0	0	2	2
376.0	0	1	1
379.0	0	2	2
380.0	0	1	1
381.0	0	4	4
382.0	0	1	1
383.0	0	3	3
384.0	0	3	3
385.0	0	2	2
387.0	0	1	1
389.0	0	1	1
390.0	0	1	1
391.0	0	1	1
393.0	0	3	3
395.0	0	1	1
396.0	0	2	2
399.0	0	2	2
400.0	0	2	2
401.0	0	2	2
402.0	0	2	2
407.0	0	1	1
408.0	0	1	1
409.0	0	2	2
411.0	0	2	2
414.0	0	1	1
416.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	2	2
422.0	0	2	2
424.0	0	1	1
425.0	0	1	1
426.0	0	3	3
432.0	0	1	1
434.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
439.0	0	2	2
443.0	0	2	2
445.0	0	1	1
446.0	0	1	1
448.0	0	1	1
450.0	0	2	2
452.0	0	1	1
455.0	0	1	1
457.0	0	3	3
458.0	0	3	3
463.0	0	1	1
464.0	0	1	1
469.0	0	2	2
472.0	0	1	1
481.0	0	2	2
483.0	0	1	1
484.0	0	1	1
486.0	0	1	1
489.0	0	1	1
490.0	0	1	1
491.0	0	2	2
492.0	0	1	1
497.0	0	1	1
499.0	0	1	1
500.0	0	1	1
501.0	0	1	1
502.0	0	1	1
505.0	0	1	1
507.0	0	1	1
509.0	0	1	1
510.0	0	1	1
511.0	0	1	1
512.0	0	1	1
524.0	0	1	1
527.0	0	1	1
528.0	0	1	1
531.0	0	1	1
532.0	0	1	1
533.0	0	1	1
535.0	0	1	1
540.0	0	1	1
548.0	0	1	1
550.0	0	1	1
553.0	0	1	1
559.0	0	1	1
566.0	0	1	1
575.0	0	1	1
577.0	0	1	1
581.0	0	1	1
591.0	0	1	1
596.0	0	1	1
597.0	0	1	1
599.0	0	1	1
600.0	0	1	1
604.0	0	1	1
612.0	0	1	1
613.0	0	1	1
624.0	0	1	1
636.0	0	1	1
638.0	0	1	1
639.0	0	2	2
641.0	0	1	1
648.0	0	1	1
654.0	0	1	1
660.0	0	1	1
663.0	0	1	1
667.0	0	1	1
668.0	0	1	1
673.0	0	2	2
680.0	0	1	1
687.0	0	1	1
699.0	0	1	1
703.0	0	1	1
704.0	0	1	1
710.0	0	1	1
714.0	0	1	1
715.0	0	1	1
725.0	0	1	1
733.0	0	2	2
759.0	0	1	1
764.0	0	2	2
765.0	0	1	1
769.0	0	2	2
776.0	0	1	1
785.0	0	1	1
789.0	0	1	1
815.0	0	2	2
824.0	0	1	1
829.0	0	1	1
842.0	0	1	1
860.0	0	1	1
865.0	0	1	1
889.0	0	1	1
909.0	0	1	1
912.0	0	1	1
922.0	0	1	1
988.0	0	1	1
995.0	0	1	1
1015.0	0	1	1
1063.0	0	1	1
1137.0	0	1	1
1160.0	0	1	1
1163.0	0	1	1
1182.0	0	1	1
1187.0	0	1	1
1192.0	0	1	1
1258.0	0	1	1
1276.0	0	1	1
1315.0	0	1	1
1320.0	0	1	1
1346.0	0	1	1
1349.0	0	1	1
1435.0	0	1	1
1490.0	0	1	1
1513.0	0	1	1
1535.0	0	1	1
1537.0	0	1	1
1601.0	0	1	1
1692.0	0	2	2
1809.0	0	1	1
1822.0	0	1	1
1872.0	0	1	1
1937.0	0	1	1
1951.0	0	1	1
2047.0	0	1	1
2276.0	0	1	1
2289.0	0	1	1
2464.0	0	1	1