## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Hah_1_2008-07-16/US_Geo_Hah_1_2008-07-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Hah_1_2008-07-16/US_Geo_Hah_1_2008-07-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Hah_1_2008-07-16/US_Geo_Hah_1_2008-07-16.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 18:18:35 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	8671395	57988445	0	0	4056477	433569	0	0.0395	3858529386

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	56933865	56933865
2.0	1.985084	64354	64354
3.0	2.955474	3805	3805
4.0	3.911389	1176	1176
5.0	4.853046	638	638
6.0	5.780656	360	360
7.0	6.69443	264	264
8.0	7.594575	199	199
9.0	8.481292	129	129
10.0	9.354783	103	103
11.0	10.215244	85	85
12.0	11.062871	69	69
13.0	11.897854	57	57
14.0	12.720382	46	46
15.0	13.530642	33	33
16.0	14.328815	43	43
17.0	15.115082	34	34
18.0	15.889622	30	30
19.0	16.652608	26	26
20.0	17.404213	23	23
21.0	18.144607	24	24
22.0	18.873957	18	18
23.0	19.592428	20	20
24.0	20.300182	14	14
25.0	20.997379	18	18
26.0	21.684176	17	17
27.0	22.360729	21	21
28.0	23.02719	14	14
29.0	23.683711	12	12
30.0	24.330438	10	10
31.0	24.967518	12	12
32.0	25.595096	17	17
33.0	26.213313	12	12
34.0	26.822308	6	6
35.0	27.422219	16	16
36.0	28.013182	13	13
37.0	28.595329	7	7
38.0	29.168794	9	9
39.0	29.733704	11	11
40.0	30.290188	10	10
41.0	30.838371	12	12
42.0	31.378378	7	7
43.0	31.910329	15	15
44.0	32.434346	7	7
45.0	32.950547	16	16
46.0	33.459047	7	7
47.0	33.959963	7	7
48.0	34.453407	5	5
49.0	34.93949	11	11
50.0	35.418324	7	7
51.0	35.890014	5	5
52.0	36.354669	4	4
53.0	36.812393	10	10
54.0	37.263289	9	9
55.0	37.70746	11	11
56.0	38.145005	1	1
57.0	38.576024	5	5
58.0	39.000613	8	8
59.0	39.418869	8	8
60.0	39.830887	6	6
61.0	40.236758	3	3
62.0	40.636576	4	4
63.0	41.03043	5	5
64.0	41.418409	3	3
65.0	41.8006	6	6
66.0	42.177091	10	10
67.0	42.547966	5	5
68.0	42.913309	3	3
69.0	43.273203	7	7
70.0	43.627728	5	5
71.0	43.976965	7	7
72.0	44.320992	3	3
73.0	44.659888	4	4
74.0	44.993729	5	5
75.0	45.32259	3	3
76.0	45.646546	4	4
77.0	45.96567	4	4
78.0	46.280034	4	4
79.0	46.589708	4	4
80.0	46.894763	2	2
81.0	47.195268	3	3
82.0	47.491291	2	2
83.0	47.782898	5	5
84.0	48.070155	1	1
85.0	48.353127	1	1
86.0	48.631879	7	7
87.0	48.906473	1	1
88.0	49.17697	4	4
89.0	49.443433	6	6
90.0	49.705921	7	7
91.0	49.964494	0	0
92.0	50.21921	11	11
93.0	50.470127	5	5
94.0	50.717301	4	4
95.0	50.960788	1	1
96.0	51.200643	4	4
97.0	51.43692	5	5
98.0	51.669673	4	4
99.0	51.898954	5	5
100.0	52.124815	2	2
101.0	0	3	3
102.0	0	2	2
103.0	0	4	4
104.0	0	3	3
105.0	0	3	3
106.0	0	3	3
107.0	0	2	2
108.0	0	2	2
109.0	0	4	4
110.0	0	2	2
111.0	0	1	1
112.0	0	2	2
113.0	0	3	3
116.0	0	3	3
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
120.0	0	3	3
121.0	0	2	2
122.0	0	3	3
123.0	0	5	5
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	4	4
129.0	0	3	3
130.0	0	1	1
131.0	0	2	2
132.0	0	3	3
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
137.0	0	4	4
138.0	0	1	1
139.0	0	2	2
140.0	0	3	3
141.0	0	1	1
143.0	0	2	2
145.0	0	3	3
146.0	0	1	1
147.0	0	3	3
148.0	0	2	2
149.0	0	1	1
150.0	0	2	2
151.0	0	2	2
153.0	0	4	4
154.0	0	3	3
155.0	0	2	2
156.0	0	1	1
157.0	0	3	3
158.0	0	1	1
159.0	0	2	2
160.0	0	2	2
163.0	0	3	3
164.0	0	2	2
165.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	5	5
170.0	0	3	3
171.0	0	1	1
172.0	0	1	1
173.0	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
181.0	0	1	1
183.0	0	3	3
184.0	0	1	1
186.0	0	1	1
188.0	0	3	3
189.0	0	1	1
190.0	0	2	2
191.0	0	2	2
192.0	0	1	1
193.0	0	2	2
196.0	0	1	1
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	3	3
203.0	0	3	3
204.0	0	2	2
205.0	0	3	3
207.0	0	2	2
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	3	3
213.0	0	2	2
214.0	0	2	2
217.0	0	1	1
218.0	0	3	3
219.0	0	1	1
220.0	0	1	1
222.0	0	3	3
223.0	0	2	2
224.0	0	1	1
226.0	0	4	4
227.0	0	1	1
230.0	0	2	2
232.0	0	3	3
233.0	0	2	2
235.0	0	1	1
236.0	0	2	2
239.0	0	3	3
240.0	0	3	3
243.0	0	1	1
245.0	0	2	2
246.0	0	3	3
247.0	0	2	2
248.0	0	2	2
251.0	0	2	2
252.0	0	1	1
253.0	0	2	2
254.0	0	1	1
256.0	0	1	1
258.0	0	1	1
261.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	2	2
268.0	0	3	3
269.0	0	1	1
271.0	0	2	2
272.0	0	1	1
273.0	0	2	2
274.0	0	2	2
276.0	0	3	3
277.0	0	1	1
279.0	0	2	2
282.0	0	2	2
287.0	0	2	2
288.0	0	1	1
290.0	0	2	2
296.0	0	1	1
297.0	0	3	3
299.0	0	3	3
300.0	0	2	2
301.0	0	1	1
303.0	0	1	1
308.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	1	1
315.0	0	1	1
319.0	0	2	2
320.0	0	2	2
326.0	0	1	1
328.0	0	2	2
330.0	0	1	1
338.0	0	2	2
339.0	0	3	3
344.0	0	1	1
347.0	0	1	1
350.0	0	1	1
352.0	0	2	2
353.0	0	1	1
355.0	0	1	1
358.0	0	2	2
360.0	0	2	2
361.0	0	2	2
365.0	0	1	1
366.0	0	1	1
368.0	0	1	1
371.0	0	1	1
372.0	0	2	2
373.0	0	1	1
376.0	0	1	1
377.0	0	1	1
379.0	0	1	1
380.0	0	1	1
381.0	0	1	1
387.0	0	1	1
388.0	0	3	3
389.0	0	1	1
390.0	0	1	1
391.0	0	1	1
393.0	0	2	2
394.0	0	1	1
395.0	0	1	1
397.0	0	2	2
398.0	0	1	1
399.0	0	2	2
403.0	0	1	1
405.0	0	1	1
406.0	0	1	1
410.0	0	1	1
411.0	0	1	1
413.0	0	1	1
420.0	0	1	1
423.0	0	1	1
427.0	0	1	1
429.0	0	1	1
432.0	0	1	1
434.0	0	1	1
448.0	0	1	1
451.0	0	1	1
453.0	0	1	1
454.0	0	1	1
456.0	0	1	1
458.0	0	2	2
459.0	0	1	1
463.0	0	1	1
468.0	0	1	1
469.0	0	1	1
470.0	0	1	1
474.0	0	1	1
478.0	0	1	1
481.0	0	2	2
482.0	0	1	1
487.0	0	1	1
488.0	0	1	1
489.0	0	2	2
491.0	0	2	2
493.0	0	1	1
497.0	0	1	1
499.0	0	1	1
500.0	0	1	1
501.0	0	1	1
509.0	0	1	1
512.0	0	1	1
515.0	0	1	1
519.0	0	1	1
523.0	0	1	1
529.0	0	1	1
530.0	0	1	1
531.0	0	2	2
532.0	0	1	1
534.0	0	1	1
537.0	0	1	1
539.0	0	1	1
543.0	0	1	1
550.0	0	1	1
552.0	0	1	1
557.0	0	1	1
558.0	0	1	1
561.0	0	2	2
565.0	0	1	1
569.0	0	2	2
570.0	0	1	1
571.0	0	2	2
572.0	0	1	1
574.0	0	1	1
578.0	0	1	1
579.0	0	1	1
580.0	0	1	1
588.0	0	1	1
590.0	0	2	2
596.0	0	1	1
597.0	0	1	1
598.0	0	1	1
599.0	0	1	1
611.0	0	1	1
612.0	0	1	1
615.0	0	1	1
619.0	0	1	1
626.0	0	1	1
633.0	0	1	1
645.0	0	1	1
650.0	0	1	1
658.0	0	1	1
660.0	0	1	1
677.0	0	1	1
680.0	0	2	2
686.0	0	2	2
699.0	0	1	1
702.0	0	1	1
705.0	0	1	1
709.0	0	1	1
722.0	0	1	1
735.0	0	1	1
741.0	0	1	1
746.0	0	2	2
752.0	0	1	1
755.0	0	1	1
756.0	0	1	1
758.0	0	1	1
761.0	0	1	1
780.0	0	1	1
798.0	0	1	1
808.0	0	1	1
829.0	0	1	1
834.0	0	1	1
839.0	0	1	1
840.0	0	1	1
845.0	0	1	1
849.0	0	1	1
853.0	0	1	1
855.0	0	1	1
865.0	0	1	1
878.0	0	1	1
881.0	0	1	1
910.0	0	1	1
911.0	0	1	1
935.0	0	1	1
961.0	0	1	1
962.0	0	1	1
964.0	0	1	1
977.0	0	1	1
992.0	0	1	1
1002.0	0	1	1
1026.0	0	1	1
1081.0	0	1	1
1089.0	0	1	1
1135.0	0	1	1
1178.0	0	1	1
1256.0	0	1	1
1280.0	0	1	1
1309.0	0	1	1
1373.0	0	1	1
1383.0	0	1	1
1422.0	0	1	1
1695.0	0	1	1
1762.0	0	1	1
2019.0	0	1	1
2394.0	0	1	1
2697.0	0	1	1
3004.0	0	1	1
3079.0	0	1	1
3113.0	0	1	1
3400.0	0	1	1
3430.0	0	1	1
4172.0	0	1	1
4561.0	0	1	1
4776.0	0	1	1
4879.0	0	1	1
5538.0	0	1	1
5838.0	0	1	1
5878.0	0	1	1
5977.0	0	1	1
6108.0	0	1	1
6551.0	0	1	1
6592.0	0	1	1
6759.0	0	1	1
7358.0	0	1	1
8423.0	0	1	1
8476.0	0	1	1
13364.0	0	1	1
13450.0	0	1	1