## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-11-20/US_Cal_Esp_1_2012-11-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-11-20/US_Cal_Esp_1_2012-11-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Esp_1_2012-11-20/US_Cal_Esp_1_2012-11-20.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 17:13:22 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	965443	26760155	0	0	265707	1652173	0	0.065523	207701385

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23646641	23646641
2.0	1.879115	945836	945836
3.0	2.651958	35271	35271
4.0	3.331376	3490	3490
5.0	3.928663	1502	1502
6.0	4.453746	1035	1035
7.0	4.915355	690	690
8.0	5.321163	505	505
9.0	5.677914	391	391
10.0	5.991539	300	300
11.0	6.267252	280	280
12.0	6.509635	191	191
13.0	6.722718	179	179
14.0	6.910042	151	151
15.0	7.074722	148	148
16.0	7.219494	126	126
17.0	7.346765	120	120
18.0	7.458652	112	112
19.0	7.557013	98	98
20.0	7.643483	88	88
21.0	7.719501	59	59
22.0	7.786329	69	69
23.0	7.845078	73	73
24.0	7.896726	63	63
25.0	7.94213	57	57
26.0	7.982046	73	73
27.0	8.017136	55	55
28.0	8.047985	46	46
29.0	8.075104	51	51
30.0	8.098945	57	57
31.0	8.119904	61	61
32.0	8.13833	40	40
33.0	8.154528	29	29
34.0	8.168768	51	51
35.0	8.181286	32	32
36.0	8.192291	37	37
37.0	8.201966	33	33
38.0	8.210471	35	35
39.0	8.217949	32	32
40.0	8.224522	25	25
41.0	8.230301	17	17
42.0	8.235381	22	22
43.0	8.239847	34	34
44.0	8.243773	18	18
45.0	8.247224	25	25
46.0	8.250259	20	20
47.0	8.252926	29	29
48.0	8.255271	23	23
49.0	8.257333	21	21
50.0	8.259145	20	20
51.0	8.260738	24	24
52.0	8.262139	22	22
53.0	8.26337	13	13
54.0	8.264453	12	12
55.0	8.265404	19	19
56.0	8.266241	16	16
57.0	8.266976	18	18
58.0	8.267623	13	13
59.0	8.268191	14	14
60.0	8.268691	18	18
61.0	8.26913	14	14
62.0	8.269517	14	14
63.0	8.269856	8	8
64.0	8.270154	12	12
65.0	8.270417	23	23
66.0	8.270647	11	11
67.0	8.27085	7	7
68.0	8.271029	17	17
69.0	8.271185	12	12
70.0	8.271323	12	12
71.0	8.271444	12	12
72.0	8.271551	8	8
73.0	8.271644	14	14
74.0	8.271726	7	7
75.0	8.271799	7	7
76.0	8.271862	9	9
77.0	8.271918	6	6
78.0	8.271967	9	9
79.0	8.272011	10	10
80.0	8.272049	10	10
81.0	8.272082	11	11
82.0	8.272111	10	10
83.0	8.272137	15	15
84.0	8.27216	14	14
85.0	8.27218	8	8
86.0	8.272197	10	10
87.0	8.272213	5	5
88.0	8.272226	10	10
89.0	8.272238	9	9
90.0	8.272249	2	2
91.0	8.272258	7	7
92.0	8.272266	16	16
93.0	8.272273	3	3
94.0	8.272279	6	6
95.0	8.272285	5	5
96.0	8.27229	4	4
97.0	8.272294	10	10
98.0	8.272298	5	5
99.0	8.272301	4	4
100.0	8.272304	6	6
101.0	0	5	5
102.0	0	3	3
103.0	0	5	5
104.0	0	10	10
105.0	0	5	5
106.0	0	6	6
107.0	0	7	7
108.0	0	6	6
109.0	0	2	2
110.0	0	5	5
111.0	0	4	4
112.0	0	5	5
113.0	0	7	7
114.0	0	12	12
115.0	0	5	5
116.0	0	3	3
117.0	0	7	7
118.0	0	3	3
119.0	0	5	5
120.0	0	3	3
121.0	0	4	4
122.0	0	2	2
123.0	0	7	7
124.0	0	5	5
125.0	0	6	6
126.0	0	3	3
127.0	0	6	6
128.0	0	6	6
129.0	0	9	9
130.0	0	5	5
131.0	0	5	5
132.0	0	6	6
133.0	0	7	7
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
137.0	0	3	3
138.0	0	4	4
139.0	0	5	5
140.0	0	4	4
141.0	0	3	3
142.0	0	3	3
143.0	0	5	5
144.0	0	5	5
145.0	0	7	7
146.0	0	6	6
147.0	0	5	5
148.0	0	2	2
149.0	0	3	3
150.0	0	4	4
151.0	0	6	6
152.0	0	2	2
153.0	0	3	3
154.0	0	3	3
155.0	0	3	3
156.0	0	2	2
157.0	0	5	5
158.0	0	3	3
159.0	0	2	2
160.0	0	5	5
161.0	0	1	1
162.0	0	1	1
163.0	0	2	2
164.0	0	3	3
165.0	0	2	2
166.0	0	6	6
167.0	0	4	4
168.0	0	2	2
169.0	0	3	3
170.0	0	3	3
171.0	0	3	3
172.0	0	2	2
173.0	0	1	1
174.0	0	4	4
175.0	0	4	4
176.0	0	2	2
178.0	0	3	3
179.0	0	5	5
180.0	0	1	1
181.0	0	3	3
182.0	0	2	2
183.0	0	3	3
184.0	0	4	4
186.0	0	7	7
187.0	0	4	4
188.0	0	4	4
189.0	0	2	2
190.0	0	1	1
191.0	0	3	3
192.0	0	5	5
193.0	0	3	3
194.0	0	3	3
195.0	0	5	5
196.0	0	3	3
197.0	0	4	4
198.0	0	5	5
199.0	0	3	3
200.0	0	5	5
201.0	0	3	3
202.0	0	4	4
203.0	0	2	2
204.0	0	4	4
205.0	0	4	4
206.0	0	1	1
207.0	0	4	4
208.0	0	5	5
209.0	0	1	1
210.0	0	3	3
211.0	0	2	2
212.0	0	3	3
213.0	0	2	2
214.0	0	1	1
215.0	0	1	1
216.0	0	3	3
217.0	0	3	3
218.0	0	2	2
219.0	0	3	3
220.0	0	4	4
221.0	0	1	1
222.0	0	4	4
223.0	0	1	1
224.0	0	4	4
225.0	0	2	2
226.0	0	5	5
227.0	0	2	2
228.0	0	2	2
229.0	0	1	1
230.0	0	1	1
231.0	0	3	3
232.0	0	2	2
233.0	0	3	3
234.0	0	4	4
236.0	0	2	2
237.0	0	4	4
238.0	0	4	4
239.0	0	4	4
240.0	0	4	4
241.0	0	3	3
242.0	0	2	2
243.0	0	1	1
245.0	0	1	1
246.0	0	2	2
247.0	0	3	3
248.0	0	1	1
249.0	0	2	2
250.0	0	3	3
251.0	0	2	2
252.0	0	2	2
253.0	0	2	2
254.0	0	1	1
255.0	0	2	2
256.0	0	2	2
257.0	0	2	2
258.0	0	4	4
259.0	0	4	4
260.0	0	2	2
261.0	0	5	5
262.0	0	5	5
263.0	0	1	1
264.0	0	2	2
265.0	0	3	3
266.0	0	4	4
267.0	0	3	3
268.0	0	2	2
269.0	0	2	2
270.0	0	4	4
271.0	0	1	1
272.0	0	1	1
273.0	0	1	1
274.0	0	1	1
275.0	0	3	3
276.0	0	2	2
280.0	0	1	1
281.0	0	3	3
282.0	0	1	1
284.0	0	2	2
285.0	0	1	1
286.0	0	1	1
287.0	0	2	2
288.0	0	1	1
289.0	0	5	5
290.0	0	1	1
291.0	0	1	1
292.0	0	4	4
294.0	0	2	2
295.0	0	1	1
296.0	0	5	5
297.0	0	3	3
298.0	0	2	2
300.0	0	1	1
301.0	0	1	1
302.0	0	3	3
303.0	0	2	2
307.0	0	3	3
308.0	0	3	3
309.0	0	3	3
310.0	0	1	1
311.0	0	3	3
312.0	0	2	2
314.0	0	3	3
316.0	0	3	3
317.0	0	2	2
318.0	0	2	2
319.0	0	1	1
320.0	0	1	1
322.0	0	2	2
323.0	0	3	3
324.0	0	3	3
326.0	0	4	4
327.0	0	1	1
328.0	0	1	1
329.0	0	1	1
332.0	0	3	3
333.0	0	1	1
334.0	0	2	2
335.0	0	3	3
336.0	0	1	1
338.0	0	1	1
339.0	0	2	2
341.0	0	1	1
343.0	0	3	3
344.0	0	3	3
346.0	0	1	1
347.0	0	1	1
350.0	0	5	5
351.0	0	1	1
353.0	0	2	2
355.0	0	1	1
357.0	0	1	1
358.0	0	4	4
359.0	0	1	1
360.0	0	2	2
362.0	0	1	1
363.0	0	1	1
364.0	0	1	1
365.0	0	1	1
366.0	0	1	1
367.0	0	5	5
368.0	0	2	2
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
373.0	0	4	4
374.0	0	1	1
375.0	0	3	3
376.0	0	1	1
377.0	0	2	2
379.0	0	1	1
380.0	0	1	1
381.0	0	2	2
382.0	0	2	2
384.0	0	1	1
385.0	0	1	1
386.0	0	3	3
388.0	0	1	1
389.0	0	1	1
390.0	0	1	1
391.0	0	1	1
392.0	0	2	2
393.0	0	1	1
394.0	0	1	1
397.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
404.0	0	1	1
405.0	0	4	4
406.0	0	1	1
408.0	0	3	3
411.0	0	2	2
413.0	0	2	2
415.0	0	1	1
416.0	0	3	3
418.0	0	2	2
421.0	0	1	1
425.0	0	1	1
426.0	0	2	2
429.0	0	1	1
431.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	3	3
436.0	0	2	2
437.0	0	1	1
438.0	0	3	3
440.0	0	2	2
442.0	0	1	1
448.0	0	1	1
450.0	0	2	2
452.0	0	2	2
453.0	0	2	2
454.0	0	2	2
457.0	0	2	2
458.0	0	1	1
461.0	0	2	2
466.0	0	1	1
468.0	0	2	2
470.0	0	1	1
471.0	0	2	2
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
476.0	0	2	2
479.0	0	3	3
480.0	0	1	1
481.0	0	1	1
482.0	0	1	1
483.0	0	1	1
487.0	0	1	1
489.0	0	1	1
491.0	0	1	1
492.0	0	1	1
493.0	0	1	1
498.0	0	1	1
502.0	0	1	1
504.0	0	1	1
508.0	0	1	1
513.0	0	1	1
514.0	0	2	2
517.0	0	1	1
520.0	0	2	2
526.0	0	3	3
527.0	0	1	1
529.0	0	1	1
530.0	0	2	2
531.0	0	1	1
532.0	0	1	1
534.0	0	1	1
536.0	0	2	2
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
542.0	0	1	1
545.0	0	2	2
546.0	0	1	1
548.0	0	1	1
549.0	0	2	2
551.0	0	2	2
555.0	0	1	1
557.0	0	1	1
559.0	0	1	1
566.0	0	2	2
568.0	0	1	1
570.0	0	1	1
574.0	0	1	1
575.0	0	2	2
588.0	0	1	1
591.0	0	2	2
592.0	0	1	1
593.0	0	1	1
595.0	0	1	1
598.0	0	1	1
600.0	0	1	1
601.0	0	2	2
602.0	0	1	1
604.0	0	1	1
606.0	0	2	2
611.0	0	1	1
615.0	0	1	1
619.0	0	1	1
620.0	0	1	1
621.0	0	1	1
633.0	0	1	1
636.0	0	1	1
637.0	0	3	3
638.0	0	2	2
640.0	0	1	1
644.0	0	1	1
648.0	0	1	1
652.0	0	4	4
654.0	0	2	2
659.0	0	1	1
664.0	0	1	1
669.0	0	1	1
677.0	0	1	1
681.0	0	1	1
682.0	0	1	1
685.0	0	1	1
686.0	0	1	1
687.0	0	1	1
694.0	0	3	3
698.0	0	3	3
700.0	0	1	1
701.0	0	1	1
702.0	0	1	1
703.0	0	2	2
706.0	0	1	1
707.0	0	1	1
708.0	0	1	1
709.0	0	1	1
711.0	0	1	1
712.0	0	1	1
715.0	0	2	2
717.0	0	1	1
718.0	0	1	1
719.0	0	1	1
720.0	0	1	1
722.0	0	1	1
723.0	0	1	1
724.0	0	1	1
727.0	0	1	1
729.0	0	1	1
731.0	0	1	1
732.0	0	1	1
736.0	0	1	1
741.0	0	1	1
743.0	0	1	1
744.0	0	2	2
748.0	0	1	1
753.0	0	1	1
757.0	0	1	1
763.0	0	1	1
767.0	0	2	2
768.0	0	1	1
771.0	0	1	1
775.0	0	2	2
777.0	0	1	1
778.0	0	1	1
779.0	0	1	1
780.0	0	1	1
784.0	0	1	1
785.0	0	1	1
789.0	0	1	1
792.0	0	1	1
794.0	0	1	1
800.0	0	1	1
805.0	0	1	1
813.0	0	1	1
821.0	0	1	1
822.0	0	1	1
824.0	0	1	1
827.0	0	1	1
828.0	0	1	1
829.0	0	2	2
831.0	0	2	2
834.0	0	2	2
836.0	0	1	1
840.0	0	1	1
841.0	0	1	1
843.0	0	2	2
852.0	0	1	1
856.0	0	1	1
857.0	0	1	1
858.0	0	1	1
862.0	0	1	1
864.0	0	1	1
870.0	0	1	1
873.0	0	1	1
879.0	0	1	1
882.0	0	1	1
891.0	0	1	1
919.0	0	1	1
924.0	0	1	1
927.0	0	3	3
930.0	0	1	1
932.0	0	1	1
935.0	0	1	1
945.0	0	1	1
946.0	0	1	1
947.0	0	2	2
952.0	0	1	1
960.0	0	1	1
969.0	0	1	1
974.0	0	1	1
975.0	0	1	1
1000.0	0	1	1
1004.0	0	1	1
1035.0	0	1	1
1037.0	0	1	1
1041.0	0	1	1
1044.0	0	1	1
1046.0	0	1	1
1053.0	0	1	1
1056.0	0	1	1
1061.0	0	1	1
1067.0	0	1	1
1068.0	0	1	1
1071.0	0	1	1
1075.0	0	1	1
1078.0	0	1	1
1086.0	0	1	1
1088.0	0	1	1
1093.0	0	1	1
1094.0	0	1	1
1096.0	0	1	1
1115.0	0	1	1
1129.0	0	1	1
1133.0	0	1	1
1134.0	0	1	1
1138.0	0	1	1
1141.0	0	1	1
1149.0	0	1	1
1156.0	0	1	1
1159.0	0	1	1
1177.0	0	1	1
1186.0	0	1	1
1197.0	0	1	1
1200.0	0	1	1
1203.0	0	1	1
1212.0	0	1	1
1216.0	0	1	1
1218.0	0	1	1
1239.0	0	1	1
1265.0	0	1	1
1289.0	0	1	1
1301.0	0	1	1
1308.0	0	1	1
1311.0	0	1	1
1323.0	0	1	1
1328.0	0	2	2
1353.0	0	1	1
1359.0	0	1	1
1366.0	0	1	1
1413.0	0	1	1
1417.0	0	1	1
1429.0	0	1	1
1433.0	0	1	1
1438.0	0	1	1
1445.0	0	1	1
1452.0	0	1	1
1459.0	0	1	1
1471.0	0	1	1
1477.0	0	1	1
1512.0	0	1	1
1520.0	0	1	1
1529.0	0	1	1
1554.0	0	1	1
1573.0	0	1	1
1576.0	0	1	1
1600.0	0	1	1
1604.0	0	1	1
1621.0	0	1	1
1641.0	0	1	1
1659.0	0	1	1
1691.0	0	2	2
1694.0	0	1	1
1706.0	0	1	1
1736.0	0	1	1
1759.0	0	1	1
1766.0	0	1	1
1904.0	0	1	1
1920.0	0	1	1
2020.0	0	2	2
2024.0	0	1	1
2147.0	0	1	1
2159.0	0	1	1
2211.0	0	1	1
2213.0	0	1	1
2265.0	0	1	1
2398.0	0	1	1
2500.0	0	1	1
2506.0	0	1	1
2570.0	0	1	1
2686.0	0	1	1
2707.0	0	1	1
3060.0	0	1	1
3093.0	0	1	1
3262.0	0	1	1
3429.0	0	1	1
3472.0	0	1	1
4117.0	0	1	1
4429.0	0	1	1
4812.0	0	1	1
5610.0	0	1	1
6155.0	0	1	1