## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-09-01/US_Cal_Esp_1_2013-09-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-09-01/US_Cal_Esp_1_2013-09-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2013-09-01/US_Cal_Esp_1_2013-09-01.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 18:25:03 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	3512590	42520163	0	0	1259805	2235608	0	0.064719	390055080

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	37363751	37363751
2.0	1.896721	1440272	1440272
3.0	2.700829	77386	77386
4.0	3.42189	14620	14620
5.0	4.06848	6141	6141
6.0	4.648291	3398	3398
7.0	5.168219	2051	2051
8.0	5.63445	1299	1299
9.0	6.052529	932	932
10.0	6.427429	691	691
11.0	6.76361	552	552
12.0	7.06507	428	428
13.0	7.335395	353	353
14.0	7.577802	314	314
15.0	7.795173	243	243
16.0	7.990094	225	225
17.0	8.164884	185	185
18.0	8.321622	165	165
19.0	8.462172	177	177
20.0	8.588206	140	140
21.0	8.701223	116	116
22.0	8.802569	130	130
23.0	8.893447	105	105
24.0	8.974939	113	113
25.0	9.048015	104	104
26.0	9.113544	78	78
27.0	9.172305	81	81
28.0	9.224997	73	73
29.0	9.272247	61	61
30.0	9.314618	73	73
31.0	9.352612	60	60
32.0	9.386682	66	66
33.0	9.417234	57	57
34.0	9.44463	45	45
35.0	9.469196	56	56
36.0	9.491226	51	51
37.0	9.51098	52	52
38.0	9.528694	37	37
39.0	9.544579	46	46
40.0	9.558823	43	43
41.0	9.571596	30	30
42.0	9.58305	42	42
43.0	9.593321	30	30
44.0	9.602531	34	34
45.0	9.610789	30	30
46.0	9.618195	19	19
47.0	9.624836	23	23
48.0	9.630791	30	30
49.0	9.636132	28	28
50.0	9.64092	24	24
51.0	9.645214	24	24
52.0	9.649065	20	20
53.0	9.652518	22	22
54.0	9.655614	14	14
55.0	9.65839	30	30
56.0	9.66088	17	17
57.0	9.663113	28	28
58.0	9.665115	29	29
59.0	9.66691	20	20
60.0	9.66852	20	20
61.0	9.669963	18	18
62.0	9.671258	13	13
63.0	9.672418	19	19
64.0	9.673459	18	18
65.0	9.674393	26	26
66.0	9.67523	18	18
67.0	9.67598	16	16
68.0	9.676653	16	16
69.0	9.677257	9	9
70.0	9.677798	12	12
71.0	9.678283	16	16
72.0	9.678719	9	9
73.0	9.679109	7	7
74.0	9.679459	9	9
75.0	9.679772	13	13
76.0	9.680054	14	14
77.0	9.680306	10	10
78.0	9.680532	12	12
79.0	9.680735	6	6
80.0	9.680917	6	6
81.0	9.68108	10	10
82.0	9.681227	14	14
83.0	9.681358	12	12
84.0	9.681476	11	11
85.0	9.681581	16	16
86.0	9.681676	13	13
87.0	9.68176	12	12
88.0	9.681836	9	9
89.0	9.681905	10	10
90.0	9.681966	13	13
91.0	9.682021	8	8
92.0	9.68207	7	7
93.0	9.682114	6	6
94.0	9.682154	11	11
95.0	9.682189	9	9
96.0	9.682221	6	6
97.0	9.682249	5	5
98.0	9.682275	4	4
99.0	9.682298	9	9
100.0	9.682318	9	9
101.0	0	3	3
102.0	0	9	9
103.0	0	8	8
104.0	0	3	3
105.0	0	5	5
106.0	0	2	2
107.0	0	5	5
108.0	0	6	6
109.0	0	6	6
110.0	0	6	6
111.0	0	12	12
112.0	0	7	7
113.0	0	9	9
114.0	0	8	8
115.0	0	3	3
116.0	0	10	10
117.0	0	5	5
118.0	0	5	5
119.0	0	4	4
120.0	0	6	6
121.0	0	9	9
122.0	0	6	6
123.0	0	4	4
124.0	0	6	6
125.0	0	9	9
126.0	0	4	4
127.0	0	2	2
128.0	0	4	4
129.0	0	6	6
130.0	0	10	10
131.0	0	3	3
132.0	0	9	9
133.0	0	8	8
134.0	0	6	6
135.0	0	3	3
136.0	0	5	5
137.0	0	2	2
138.0	0	9	9
139.0	0	3	3
140.0	0	5	5
141.0	0	5	5
142.0	0	3	3
143.0	0	7	7
144.0	0	3	3
145.0	0	4	4
147.0	0	3	3
148.0	0	2	2
149.0	0	2	2
150.0	0	7	7
151.0	0	6	6
152.0	0	4	4
153.0	0	4	4
154.0	0	1	1
155.0	0	3	3
156.0	0	3	3
157.0	0	4	4
158.0	0	3	3
159.0	0	4	4
160.0	0	6	6
161.0	0	2	2
162.0	0	6	6
163.0	0	7	7
164.0	0	3	3
165.0	0	3	3
166.0	0	2	2
167.0	0	4	4
168.0	0	3	3
169.0	0	3	3
170.0	0	3	3
171.0	0	3	3
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	2	2
177.0	0	1	1
178.0	0	2	2
179.0	0	3	3
180.0	0	2	2
181.0	0	4	4
182.0	0	2	2
183.0	0	1	1
184.0	0	5	5
185.0	0	1	1
186.0	0	4	4
187.0	0	3	3
188.0	0	4	4
189.0	0	4	4
190.0	0	2	2
191.0	0	3	3
192.0	0	3	3
194.0	0	7	7
195.0	0	1	1
196.0	0	5	5
197.0	0	4	4
199.0	0	1	1
200.0	0	3	3
201.0	0	2	2
202.0	0	3	3
203.0	0	2	2
204.0	0	4	4
205.0	0	7	7
206.0	0	3	3
207.0	0	2	2
208.0	0	1	1
209.0	0	3	3
210.0	0	2	2
211.0	0	3	3
212.0	0	1	1
213.0	0	2	2
214.0	0	2	2
216.0	0	2	2
217.0	0	3	3
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	2	2
222.0	0	2	2
223.0	0	4	4
225.0	0	1	1
226.0	0	1	1
227.0	0	3	3
228.0	0	4	4
229.0	0	2	2
230.0	0	3	3
231.0	0	1	1
232.0	0	1	1
233.0	0	2	2
234.0	0	2	2
235.0	0	4	4
236.0	0	3	3
237.0	0	3	3
238.0	0	3	3
239.0	0	3	3
240.0	0	2	2
241.0	0	3	3
242.0	0	2	2
243.0	0	3	3
244.0	0	3	3
245.0	0	3	3
246.0	0	2	2
247.0	0	1	1
248.0	0	2	2
249.0	0	1	1
251.0	0	2	2
252.0	0	1	1
253.0	0	1	1
254.0	0	2	2
255.0	0	1	1
256.0	0	1	1
257.0	0	1	1
258.0	0	5	5
259.0	0	1	1
260.0	0	1	1
262.0	0	1	1
263.0	0	4	4
265.0	0	4	4
267.0	0	2	2
268.0	0	1	1
270.0	0	1	1
271.0	0	2	2
272.0	0	2	2
274.0	0	2	2
275.0	0	3	3
276.0	0	2	2
277.0	0	1	1
280.0	0	2	2
281.0	0	1	1
283.0	0	2	2
286.0	0	3	3
287.0	0	2	2
288.0	0	1	1
290.0	0	1	1
291.0	0	4	4
292.0	0	2	2
293.0	0	1	1
295.0	0	1	1
296.0	0	2	2
297.0	0	1	1
298.0	0	4	4
299.0	0	1	1
300.0	0	1	1
303.0	0	2	2
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
307.0	0	2	2
308.0	0	3	3
309.0	0	2	2
311.0	0	2	2
312.0	0	2	2
313.0	0	3	3
315.0	0	2	2
316.0	0	1	1
317.0	0	3	3
318.0	0	4	4
319.0	0	3	3
320.0	0	2	2
322.0	0	1	1
324.0	0	1	1
327.0	0	2	2
332.0	0	1	1
333.0	0	2	2
334.0	0	2	2
335.0	0	2	2
336.0	0	1	1
337.0	0	2	2
338.0	0	1	1
339.0	0	4	4
340.0	0	1	1
342.0	0	3	3
343.0	0	1	1
345.0	0	1	1
346.0	0	2	2
347.0	0	2	2
348.0	0	1	1
349.0	0	1	1
352.0	0	2	2
353.0	0	1	1
354.0	0	2	2
355.0	0	1	1
357.0	0	1	1
359.0	0	2	2
361.0	0	2	2
362.0	0	1	1
365.0	0	2	2
366.0	0	2	2
367.0	0	2	2
370.0	0	3	3
372.0	0	1	1
373.0	0	2	2
374.0	0	1	1
375.0	0	1	1
377.0	0	2	2
379.0	0	1	1
380.0	0	1	1
381.0	0	1	1
384.0	0	1	1
387.0	0	1	1
388.0	0	3	3
391.0	0	2	2
392.0	0	1	1
393.0	0	2	2
394.0	0	1	1
395.0	0	1	1
396.0	0	1	1
397.0	0	1	1
399.0	0	1	1
400.0	0	4	4
401.0	0	2	2
403.0	0	1	1
404.0	0	1	1
405.0	0	3	3
406.0	0	2	2
408.0	0	1	1
410.0	0	1	1
411.0	0	2	2
417.0	0	2	2
418.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	2	2
430.0	0	1	1
431.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	3	3
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
439.0	0	2	2
440.0	0	1	1
441.0	0	1	1
443.0	0	1	1
445.0	0	1	1
446.0	0	2	2
448.0	0	1	1
451.0	0	1	1
456.0	0	3	3
457.0	0	1	1
459.0	0	1	1
460.0	0	1	1
461.0	0	1	1
464.0	0	2	2
465.0	0	2	2
467.0	0	1	1
468.0	0	1	1
469.0	0	1	1
470.0	0	1	1
472.0	0	1	1
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
479.0	0	2	2
481.0	0	1	1
482.0	0	1	1
483.0	0	2	2
485.0	0	1	1
486.0	0	1	1
487.0	0	1	1
490.0	0	1	1
492.0	0	2	2
494.0	0	1	1
495.0	0	1	1
498.0	0	1	1
499.0	0	1	1
500.0	0	1	1
501.0	0	1	1
502.0	0	1	1
503.0	0	1	1
505.0	0	1	1
509.0	0	2	2
512.0	0	1	1
513.0	0	1	1
515.0	0	2	2
517.0	0	1	1
518.0	0	1	1
519.0	0	1	1
520.0	0	1	1
523.0	0	1	1
524.0	0	3	3
527.0	0	1	1
530.0	0	1	1
533.0	0	1	1
534.0	0	1	1
536.0	0	2	2
540.0	0	1	1
541.0	0	1	1
542.0	0	1	1
543.0	0	2	2
545.0	0	1	1
549.0	0	2	2
551.0	0	1	1
552.0	0	1	1
554.0	0	3	3
556.0	0	1	1
557.0	0	1	1
559.0	0	1	1
563.0	0	1	1
566.0	0	1	1
568.0	0	1	1
569.0	0	3	3
572.0	0	1	1
575.0	0	1	1
577.0	0	2	2
578.0	0	1	1
580.0	0	1	1
583.0	0	1	1
585.0	0	1	1
586.0	0	3	3
587.0	0	1	1
588.0	0	1	1
590.0	0	1	1
594.0	0	2	2
597.0	0	2	2
598.0	0	1	1
601.0	0	2	2
606.0	0	1	1
616.0	0	1	1
617.0	0	1	1
618.0	0	1	1
620.0	0	2	2
624.0	0	1	1
626.0	0	1	1
627.0	0	1	1
628.0	0	1	1
630.0	0	2	2
633.0	0	2	2
634.0	0	2	2
636.0	0	1	1
639.0	0	2	2
641.0	0	1	1
646.0	0	1	1
658.0	0	1	1
659.0	0	1	1
662.0	0	1	1
663.0	0	1	1
665.0	0	1	1
673.0	0	2	2
675.0	0	1	1
677.0	0	1	1
680.0	0	1	1
681.0	0	1	1
682.0	0	1	1
683.0	0	1	1
689.0	0	1	1
690.0	0	1	1
692.0	0	1	1
694.0	0	1	1
695.0	0	1	1
697.0	0	1	1
700.0	0	1	1
701.0	0	2	2
708.0	0	1	1
713.0	0	1	1
714.0	0	2	2
716.0	0	1	1
717.0	0	1	1
721.0	0	1	1
728.0	0	1	1
731.0	0	1	1
747.0	0	1	1
757.0	0	1	1
758.0	0	1	1
760.0	0	1	1
764.0	0	1	1
775.0	0	2	2
781.0	0	1	1
786.0	0	1	1
788.0	0	1	1
790.0	0	1	1
792.0	0	1	1
795.0	0	1	1
796.0	0	1	1
801.0	0	1	1
814.0	0	1	1
827.0	0	1	1
828.0	0	2	2
831.0	0	1	1
834.0	0	1	1
840.0	0	1	1
841.0	0	1	1
846.0	0	1	1
848.0	0	1	1
852.0	0	2	2
872.0	0	1	1
875.0	0	1	1
878.0	0	1	1
881.0	0	1	1
893.0	0	1	1
895.0	0	1	1
897.0	0	1	1
905.0	0	1	1
906.0	0	1	1
909.0	0	1	1
915.0	0	1	1
926.0	0	1	1
943.0	0	1	1
944.0	0	1	1
963.0	0	1	1
967.0	0	1	1
968.0	0	1	1
969.0	0	2	2
981.0	0	1	1
987.0	0	2	2
1001.0	0	1	1
1005.0	0	1	1
1015.0	0	1	1
1022.0	0	1	1
1031.0	0	1	1
1037.0	0	1	1
1048.0	0	1	1
1049.0	0	1	1
1058.0	0	1	1
1112.0	0	1	1
1124.0	0	1	1
1138.0	0	1	1
1151.0	0	1	1
1155.0	0	1	1
1165.0	0	1	1
1167.0	0	1	1
1184.0	0	1	1
1232.0	0	1	1
1241.0	0	1	1
1249.0	0	2	2
1255.0	0	1	1
1270.0	0	1	1
1288.0	0	1	1
1338.0	0	1	1
1339.0	0	1	1
1349.0	0	1	1
1354.0	0	1	1
1369.0	0	1	1
1398.0	0	1	1
1410.0	0	1	1
1421.0	0	1	1
1422.0	0	1	1
1463.0	0	1	1
1469.0	0	1	1
1496.0	0	1	1
1513.0	0	1	1
1517.0	0	1	1
1578.0	0	1	1
1629.0	0	1	1
1744.0	0	1	1
1749.0	0	1	1
1756.0	0	1	1
1780.0	0	1	1
1825.0	0	1	1
1840.0	0	1	1
1856.0	0	1	1
1885.0	0	1	1
1934.0	0	1	1
1963.0	0	1	1
2048.0	0	1	1
2122.0	0	1	1
2278.0	0	1	1
2384.0	0	1	1
2506.0	0	1	1
2629.0	0	1	1
2663.0	0	1	1
3267.0	0	1	1
3366.0	0	1	1