## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-11-15/US_Cal_Sto_1_2012-11-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-11-15/US_Cal_Sto_1_2012-11-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Sto_1_2012-11-15/US_Cal_Sto_1_2012-11-15.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 17:45:55 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	3337969	26184703	0	0	911703	2105364	0	0.091952	153980884

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22249564	22249564
2.0	1.843621	1258250	1258250
3.0	2.555318	62512	62512
4.0	3.155721	5505	5505
5.0	3.662233	1884	1884
6.0	4.089538	1180	1180
7.0	4.450021	753	753
8.0	4.754132	580	580
9.0	5.010687	433	433
10.0	5.227122	337	337
11.0	5.409711	277	277
12.0	5.563747	222	222
13.0	5.693695	206	206
14.0	5.803322	189	189
15.0	5.895806	158	158
16.0	5.973827	144	144
17.0	6.039648	115	115
18.0	6.095175	89	89
19.0	6.142019	85	85
20.0	6.181538	85	85
21.0	6.214877	84	84
22.0	6.243002	78	78
23.0	6.266729	81	81
24.0	6.286746	64	64
25.0	6.303632	76	76
26.0	6.317878	53	53
27.0	6.329896	59	59
28.0	6.340035	59	59
29.0	6.348588	58	58
30.0	6.355804	63	63
31.0	6.361891	42	42
32.0	6.367027	47	47
33.0	6.371359	48	48
34.0	6.375014	39	39
35.0	6.378097	41	41
36.0	6.380698	39	39
37.0	6.382892	33	33
38.0	6.384744	39	39
39.0	6.386305	26	26
40.0	6.387623	22	22
41.0	6.388734	36	36
42.0	6.389672	24	24
43.0	6.390463	20	20
44.0	6.39113	27	27
45.0	6.391693	21	21
46.0	6.392168	21	21
47.0	6.392569	29	29
48.0	6.392907	19	19
49.0	6.393192	18	18
50.0	6.393433	17	17
51.0	6.393636	20	20
52.0	6.393807	18	18
53.0	6.393951	16	16
54.0	6.394073	15	15
55.0	6.394176	19	19
56.0	6.394263	13	13
57.0	6.394336	11	11
58.0	6.394398	14	14
59.0	6.39445	17	17
60.0	6.394494	18	18
61.0	6.394531	10	10
62.0	6.394562	12	12
63.0	6.394588	14	14
64.0	6.39461	9	9
65.0	6.394629	14	14
66.0	6.394645	11	11
67.0	6.394658	19	19
68.0	6.39467	6	6
69.0	6.394679	11	11
70.0	6.394687	9	9
71.0	6.394694	7	7
72.0	6.3947	8	8
73.0	6.394705	3	3
74.0	6.394709	6	6
75.0	6.394712	11	11
76.0	6.394715	8	8
77.0	6.394717	5	5
78.0	6.394719	5	5
79.0	6.394721	10	10
80.0	6.394723	11	11
81.0	6.394724	12	12
82.0	6.394725	10	10
83.0	6.394726	9	9
84.0	6.394727	10	10
85.0	6.394727	10	10
86.0	6.394728	5	5
87.0	6.394728	10	10
88.0	6.394728	7	7
89.0	6.394729	8	8
90.0	6.394729	5	5
91.0	6.394729	4	4
92.0	6.394729	7	7
93.0	6.39473	6	6
94.0	6.39473	10	10
95.0	6.39473	7	7
96.0	6.39473	9	9
97.0	6.39473	10	10
98.0	6.39473	5	5
99.0	6.39473	9	9
100.0	6.39473	5	5
101.0	0	7	7
102.0	0	7	7
103.0	0	7	7
104.0	0	5	5
105.0	0	5	5
106.0	0	1	1
107.0	0	6	6
108.0	0	8	8
109.0	0	9	9
110.0	0	5	5
111.0	0	6	6
112.0	0	2	2
113.0	0	4	4
114.0	0	2	2
115.0	0	6	6
116.0	0	5	5
117.0	0	10	10
118.0	0	5	5
119.0	0	4	4
120.0	0	4	4
121.0	0	5	5
122.0	0	7	7
123.0	0	5	5
124.0	0	3	3
125.0	0	6	6
126.0	0	2	2
127.0	0	3	3
128.0	0	6	6
129.0	0	4	4
130.0	0	4	4
131.0	0	4	4
132.0	0	2	2
133.0	0	2	2
134.0	0	1	1
135.0	0	2	2
136.0	0	5	5
137.0	0	4	4
138.0	0	5	5
139.0	0	3	3
140.0	0	2	2
141.0	0	2	2
142.0	0	4	4
143.0	0	2	2
144.0	0	3	3
145.0	0	3	3
146.0	0	6	6
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	4	4
151.0	0	1	1
152.0	0	2	2
153.0	0	1	1
154.0	0	2	2
155.0	0	3	3
156.0	0	4	4
157.0	0	2	2
158.0	0	4	4
159.0	0	3	3
160.0	0	4	4
161.0	0	2	2
162.0	0	7	7
163.0	0	8	8
165.0	0	1	1
166.0	0	3	3
167.0	0	1	1
168.0	0	2	2
169.0	0	3	3
170.0	0	3	3
171.0	0	5	5
172.0	0	3	3
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	3	3
177.0	0	1	1
178.0	0	4	4
179.0	0	1	1
180.0	0	2	2
182.0	0	1	1
184.0	0	4	4
185.0	0	2	2
186.0	0	1	1
187.0	0	3	3
188.0	0	2	2
189.0	0	3	3
191.0	0	4	4
192.0	0	2	2
193.0	0	2	2
194.0	0	5	5
195.0	0	4	4
196.0	0	2	2
197.0	0	1	1
198.0	0	3	3
199.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
205.0	0	1	1
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
212.0	0	3	3
213.0	0	1	1
214.0	0	2	2
215.0	0	2	2
216.0	0	1	1
219.0	0	1	1
220.0	0	3	3
221.0	0	3	3
222.0	0	1	1
223.0	0	2	2
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
229.0	0	3	3
230.0	0	4	4
232.0	0	3	3
233.0	0	1	1
234.0	0	3	3
237.0	0	1	1
238.0	0	2	2
239.0	0	3	3
240.0	0	2	2
241.0	0	1	1
242.0	0	1	1
243.0	0	3	3
244.0	0	3	3
245.0	0	4	4
246.0	0	2	2
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	2	2
252.0	0	2	2
253.0	0	3	3
254.0	0	2	2
256.0	0	2	2
258.0	0	4	4
260.0	0	1	1
261.0	0	3	3
262.0	0	3	3
263.0	0	1	1
264.0	0	1	1
265.0	0	1	1
267.0	0	1	1
268.0	0	2	2
270.0	0	2	2
272.0	0	1	1
273.0	0	1	1
274.0	0	3	3
276.0	0	3	3
277.0	0	1	1
278.0	0	1	1
279.0	0	1	1
280.0	0	1	1
281.0	0	1	1
282.0	0	2	2
284.0	0	2	2
285.0	0	3	3
287.0	0	2	2
289.0	0	1	1
290.0	0	2	2
291.0	0	2	2
292.0	0	2	2
293.0	0	1	1
295.0	0	1	1
298.0	0	1	1
299.0	0	3	3
301.0	0	1	1
303.0	0	1	1
305.0	0	2	2
306.0	0	3	3
307.0	0	1	1
308.0	0	2	2
309.0	0	2	2
310.0	0	2	2
312.0	0	1	1
313.0	0	2	2
314.0	0	2	2
316.0	0	2	2
317.0	0	2	2
318.0	0	1	1
319.0	0	3	3
320.0	0	1	1
321.0	0	2	2
322.0	0	1	1
323.0	0	2	2
324.0	0	2	2
325.0	0	1	1
326.0	0	1	1
329.0	0	1	1
330.0	0	1	1
331.0	0	3	3
333.0	0	2	2
335.0	0	4	4
336.0	0	1	1
338.0	0	3	3
340.0	0	2	2
341.0	0	1	1
342.0	0	2	2
343.0	0	1	1
344.0	0	1	1
346.0	0	1	1
347.0	0	2	2
349.0	0	1	1
350.0	0	1	1
351.0	0	1	1
352.0	0	1	1
354.0	0	1	1
355.0	0	2	2
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
361.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	1	1
365.0	0	3	3
366.0	0	3	3
368.0	0	1	1
369.0	0	2	2
370.0	0	4	4
371.0	0	2	2
372.0	0	1	1
373.0	0	1	1
377.0	0	1	1
379.0	0	2	2
380.0	0	1	1
382.0	0	2	2
383.0	0	1	1
386.0	0	2	2
387.0	0	2	2
388.0	0	1	1
389.0	0	2	2
392.0	0	1	1
394.0	0	1	1
395.0	0	1	1
398.0	0	1	1
400.0	0	1	1
403.0	0	2	2
404.0	0	1	1
405.0	0	1	1
406.0	0	1	1
407.0	0	1	1
408.0	0	1	1
409.0	0	1	1
410.0	0	2	2
414.0	0	1	1
415.0	0	1	1
418.0	0	1	1
422.0	0	1	1
425.0	0	1	1
426.0	0	1	1
427.0	0	1	1
428.0	0	1	1
431.0	0	1	1
434.0	0	1	1
435.0	0	1	1
437.0	0	1	1
441.0	0	1	1
442.0	0	1	1
446.0	0	2	2
448.0	0	2	2
449.0	0	1	1
451.0	0	1	1
452.0	0	1	1
453.0	0	1	1
454.0	0	2	2
455.0	0	1	1
459.0	0	1	1
462.0	0	2	2
463.0	0	1	1
467.0	0	1	1
469.0	0	1	1
470.0	0	1	1
471.0	0	1	1
475.0	0	2	2
477.0	0	2	2
479.0	0	1	1
481.0	0	1	1
482.0	0	1	1
493.0	0	1	1
495.0	0	1	1
496.0	0	1	1
498.0	0	2	2
499.0	0	1	1
505.0	0	2	2
510.0	0	1	1
515.0	0	2	2
516.0	0	1	1
522.0	0	1	1
526.0	0	1	1
530.0	0	2	2
531.0	0	1	1
532.0	0	1	1
533.0	0	1	1
535.0	0	1	1
537.0	0	1	1
538.0	0	1	1
539.0	0	1	1
541.0	0	1	1
545.0	0	1	1
547.0	0	1	1
548.0	0	1	1
549.0	0	1	1
552.0	0	1	1
556.0	0	1	1
557.0	0	3	3
558.0	0	2	2
559.0	0	2	2
560.0	0	2	2
561.0	0	1	1
562.0	0	1	1
565.0	0	1	1
568.0	0	1	1
569.0	0	1	1
572.0	0	1	1
574.0	0	2	2
577.0	0	1	1
579.0	0	1	1
584.0	0	1	1
585.0	0	1	1
592.0	0	1	1
593.0	0	1	1
596.0	0	2	2
599.0	0	1	1
600.0	0	2	2
606.0	0	2	2
608.0	0	1	1
609.0	0	2	2
622.0	0	1	1
624.0	0	1	1
627.0	0	1	1
633.0	0	1	1
634.0	0	1	1
635.0	0	1	1
637.0	0	1	1
640.0	0	1	1
642.0	0	1	1
647.0	0	1	1
649.0	0	1	1
659.0	0	1	1
660.0	0	1	1
668.0	0	1	1
670.0	0	1	1
673.0	0	1	1
685.0	0	2	2
692.0	0	1	1
695.0	0	1	1
699.0	0	1	1
703.0	0	1	1
708.0	0	1	1
713.0	0	1	1
716.0	0	1	1
720.0	0	1	1
727.0	0	1	1
734.0	0	1	1
735.0	0	1	1
736.0	0	1	1
741.0	0	1	1
745.0	0	1	1
760.0	0	1	1
761.0	0	1	1
767.0	0	2	2
770.0	0	1	1
780.0	0	1	1
792.0	0	1	1
793.0	0	1	1
805.0	0	1	1
808.0	0	1	1
810.0	0	1	1
811.0	0	2	2
821.0	0	1	1
823.0	0	1	1
839.0	0	1	1
842.0	0	1	1
844.0	0	1	1
861.0	0	4	4
873.0	0	1	1
874.0	0	1	1
876.0	0	1	1
893.0	0	1	1
898.0	0	1	1
903.0	0	1	1
907.0	0	1	1
932.0	0	1	1
948.0	0	1	1
959.0	0	1	1
968.0	0	1	1
970.0	0	1	1
975.0	0	1	1
976.0	0	1	1
977.0	0	2	2
982.0	0	2	2
990.0	0	1	1
992.0	0	1	1
993.0	0	1	1
997.0	0	1	1
1002.0	0	1	1
1014.0	0	1	1
1017.0	0	1	1
1027.0	0	1	1
1043.0	0	1	1
1051.0	0	1	1
1052.0	0	1	1
1058.0	0	1	1
1075.0	0	1	1
1082.0	0	1	1
1084.0	0	1	1
1086.0	0	2	2
1088.0	0	1	1
1089.0	0	1	1
1101.0	0	1	1
1105.0	0	1	1
1119.0	0	1	1
1121.0	0	1	1
1140.0	0	1	1
1180.0	0	1	1
1184.0	0	1	1
1195.0	0	1	1
1198.0	0	2	2
1199.0	0	1	1
1202.0	0	1	1
1232.0	0	1	1
1240.0	0	1	1
1244.0	0	1	1
1252.0	0	1	1
1263.0	0	1	1
1265.0	0	1	1
1271.0	0	1	1
1278.0	0	1	1
1295.0	0	1	1
1300.0	0	1	1
1301.0	0	1	1
1308.0	0	1	1
1309.0	0	1	1
1313.0	0	1	1
1343.0	0	1	1
1348.0	0	1	1
1358.0	0	1	1
1363.0	0	1	1
1371.0	0	1	1
1379.0	0	1	1
1388.0	0	1	1
1399.0	0	1	1
1411.0	0	1	1
1413.0	0	1	1
1417.0	0	1	1
1421.0	0	1	1
1435.0	0	1	1
1441.0	0	1	1
1455.0	0	1	1
1468.0	0	1	1
1473.0	0	1	1
1475.0	0	1	1
1476.0	0	1	1
1490.0	0	1	1
1516.0	0	1	1
1538.0	0	1	1
1540.0	0	1	1
1551.0	0	1	1
1555.0	0	1	1
1586.0	0	1	1
1600.0	0	1	1
1608.0	0	1	1
1627.0	0	1	1
1633.0	0	1	1
1638.0	0	1	1
1646.0	0	1	1
1655.0	0	1	1
1656.0	0	1	1
1658.0	0	1	1
1666.0	0	1	1
1672.0	0	1	1
1680.0	0	2	2
1681.0	0	1	1
1695.0	0	1	1
1723.0	0	1	1
1740.0	0	1	1
1771.0	0	1	1
1777.0	0	1	1
1787.0	0	1	1
1847.0	0	1	1
1852.0	0	1	1
1857.0	0	1	1
1877.0	0	1	1
1924.0	0	1	1
1934.0	0	1	1
1938.0	0	1	1
1939.0	0	1	1
1942.0	0	1	1
1995.0	0	1	1
2005.0	0	1	1
2026.0	0	1	1
2029.0	0	1	1
2035.0	0	1	1
2054.0	0	1	1
2094.0	0	1	1
2098.0	0	1	1
2108.0	0	1	1
2135.0	0	1	1
2156.0	0	1	1
2161.0	0	1	1
2191.0	0	1	1
2231.0	0	1	1
2238.0	0	1	1
2240.0	0	1	1
2268.0	0	1	1
2305.0	0	1	1
2306.0	0	1	1
2312.0	0	1	1
2317.0	0	1	1
2353.0	0	1	1
2357.0	0	1	1
2389.0	0	1	1
2471.0	0	1	1
2493.0	0	1	1
2514.0	0	1	1
2713.0	0	1	1
2738.0	0	1	1
2901.0	0	1	1
2960.0	0	1	1
2967.0	0	1	1
3033.0	0	1	1
3107.0	0	1	1
3173.0	0	1	1
3515.0	0	1	1
3705.0	0	1	1
3726.0	0	1	1
3974.0	0	1	1
4002.0	0	1	1
4105.0	0	1	1
4144.0	0	1	1
4154.0	0	1	1
4674.0	0	1	1
4725.0	0	1	1
4762.0	0	1	1
4764.0	0	1	1
5482.0	0	1	1
5577.0	0	1	1
5701.0	0	1	1
5726.0	0	1	1
5875.0	0	1	1
6689.0	0	1	1
7185.0	0	1	1
7950.0	0	1	1
7976.0	0	1	1
8205.0	0	1	1
8426.0	0	1	1