## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//PA_li_10_fall/PA_li_10_fall.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_10_fall/PA_li_10_fall.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/PA_li_10_fall/PA_li_10_fall.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: Sun Jun 07 19:15:39 UTC 2020

## 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	3097759	46616004	0	0	1294854	294898	0	0.019565	3668857518

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	45783790	45783790
2.0	1.987375	81128	81128
3.0	2.962283	3339	3339
4.0	3.924883	884	884
5.0	4.875329	426	426
6.0	5.813776	274	274
7.0	6.740374	164	164
8.0	7.655274	124	124
9.0	8.558622	93	93
10.0	9.450565	76	76
11.0	10.331247	58	58
12.0	11.20081	49	49
13.0	12.059395	37	37
14.0	12.907139	34	34
15.0	13.74418	30	30
16.0	14.570653	28	28
17.0	15.386691	22	22
18.0	16.192427	27	27
19.0	16.98799	25	25
20.0	17.773508	24	24
21.0	18.549109	27	27
22.0	19.314918	17	17
23.0	20.071057	13	13
24.0	20.81765	13	13
25.0	21.554818	9	9
26.0	22.282678	17	17
27.0	23.001348	17	17
28.0	23.710945	15	15
29.0	24.411583	11	11
30.0	25.103374	12	12
31.0	25.786432	22	22
32.0	26.460866	5	5
33.0	27.126785	11	11
34.0	27.784296	13	13
35.0	28.433506	8	8
36.0	29.074519	13	13
37.0	29.707439	11	11
38.0	30.332368	15	15
39.0	30.949407	8	8
40.0	31.558656	5	5
41.0	32.160213	7	7
42.0	32.754174	6	6
43.0	33.340637	6	6
44.0	33.919695	6	6
45.0	34.491443	10	10
46.0	35.055971	2	2
47.0	35.613373	9	9
48.0	36.163737	10	10
49.0	36.707152	9	9
50.0	37.243706	3	3
51.0	37.773487	9	9
52.0	38.296578	3	3
53.0	38.813065	8	8
54.0	39.323031	6	6
55.0	39.826559	6	6
56.0	40.323729	3	3
57.0	40.814623	9	9
58.0	41.299318	11	11
59.0	41.777894	3	3
60.0	42.250428	6	6
61.0	42.716996	5	5
62.0	43.177673	4	4
63.0	43.632534	6	6
64.0	44.081652	5	5
65.0	44.5251	6	6
66.0	44.962949	4	4
67.0	45.39527	9	9
68.0	45.822133	6	6
69.0	46.243606	7	7
70.0	46.659758	7	7
71.0	47.070656	5	5
72.0	47.476366	1	1
73.0	47.876954	3	3
74.0	48.272484	1	1
75.0	48.663021	3	3
76.0	49.048626	2	2
77.0	49.429364	3	3
78.0	49.805294	6	6
79.0	50.176478	3	3
80.0	50.542976	7	7
81.0	50.904846	4	4
82.0	51.262148	9	9
83.0	51.614938	2	2
84.0	51.963275	7	7
85.0	52.307213	6	6
86.0	52.646809	5	5
87.0	52.982118	6	6
88.0	53.313193	3	3
89.0	53.640088	5	5
90.0	53.962856	5	5
91.0	54.281548	4	4
92.0	54.596217	2	2
93.0	54.906914	4	4
94.0	55.213687	3	3
95.0	55.516588	4	4
96.0	55.815664	3	3
97.0	56.110964	7	7
98.0	56.402536	1	1
99.0	56.690427	4	4
100.0	56.974682	1	1
101.0	0	1	1
102.0	0	3	3
103.0	0	1	1
104.0	0	2	2
105.0	0	3	3
106.0	0	2	2
107.0	0	2	2
108.0	0	3	3
109.0	0	3	3
110.0	0	1	1
111.0	0	4	4
112.0	0	3	3
113.0	0	2	2
114.0	0	3	3
115.0	0	6	6
116.0	0	4	4
117.0	0	2	2
118.0	0	3	3
119.0	0	4	4
120.0	0	4	4
121.0	0	3	3
122.0	0	5	5
123.0	0	2	2
124.0	0	2	2
125.0	0	2	2
126.0	0	1	1
128.0	0	3	3
129.0	0	3	3
130.0	0	4	4
131.0	0	1	1
132.0	0	2	2
133.0	0	3	3
134.0	0	5	5
135.0	0	1	1
136.0	0	2	2
137.0	0	1	1
138.0	0	1	1
139.0	0	2	2
140.0	0	1	1
142.0	0	3	3
143.0	0	1	1
145.0	0	2	2
146.0	0	3	3
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	3	3
151.0	0	3	3
152.0	0	3	3
154.0	0	5	5
155.0	0	4	4
159.0	0	2	2
160.0	0	2	2
162.0	0	4	4
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
168.0	0	2	2
169.0	0	1	1
170.0	0	3	3
172.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	2	2
176.0	0	2	2
177.0	0	2	2
178.0	0	2	2
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
183.0	0	5	5
185.0	0	1	1
187.0	0	1	1
189.0	0	1	1
190.0	0	3	3
191.0	0	3	3
192.0	0	1	1
193.0	0	2	2
194.0	0	2	2
195.0	0	2	2
197.0	0	1	1
198.0	0	1	1
199.0	0	2	2
200.0	0	1	1
203.0	0	2	2
205.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	2	2
210.0	0	3	3
211.0	0	3	3
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	2	2
218.0	0	2	2
219.0	0	1	1
223.0	0	3	3
224.0	0	2	2
225.0	0	1	1
229.0	0	1	1
230.0	0	2	2
231.0	0	1	1
232.0	0	1	1
233.0	0	3	3
236.0	0	2	2
237.0	0	1	1
239.0	0	3	3
242.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
248.0	0	1	1
249.0	0	1	1
251.0	0	1	1
253.0	0	1	1
257.0	0	2	2
258.0	0	1	1
262.0	0	1	1
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	2	2
268.0	0	1	1
270.0	0	2	2
271.0	0	1	1
275.0	0	1	1
277.0	0	2	2
278.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	4	4
286.0	0	1	1
290.0	0	2	2
291.0	0	1	1
292.0	0	2	2
294.0	0	1	1
295.0	0	1	1
300.0	0	1	1
303.0	0	2	2
314.0	0	1	1
316.0	0	1	1
318.0	0	1	1
321.0	0	1	1
325.0	0	1	1
326.0	0	1	1
330.0	0	1	1
337.0	0	1	1
339.0	0	1	1
341.0	0	1	1
342.0	0	1	1
345.0	0	1	1
348.0	0	1	1
351.0	0	1	1
353.0	0	2	2
360.0	0	1	1
364.0	0	1	1
366.0	0	2	2
379.0	0	2	2
382.0	0	2	2
388.0	0	1	1
392.0	0	1	1
402.0	0	1	1
403.0	0	1	1
412.0	0	1	1
413.0	0	2	2
416.0	0	1	1
417.0	0	1	1
418.0	0	2	2
420.0	0	1	1
423.0	0	1	1
427.0	0	1	1
431.0	0	1	1
436.0	0	1	1
439.0	0	1	1
440.0	0	1	1
443.0	0	2	2
450.0	0	2	2
460.0	0	2	2
466.0	0	1	1
467.0	0	1	1
473.0	0	1	1
478.0	0	1	1
481.0	0	1	1
493.0	0	1	1
501.0	0	1	1
518.0	0	1	1
521.0	0	1	1
523.0	0	2	2
524.0	0	1	1
527.0	0	1	1
530.0	0	2	2
540.0	0	1	1
544.0	0	1	1
548.0	0	1	1
551.0	0	1	1
559.0	0	1	1
563.0	0	1	1
570.0	0	1	1
571.0	0	1	1
579.0	0	1	1
584.0	0	1	1
585.0	0	1	1
599.0	0	1	1
601.0	0	1	1
602.0	0	1	1
603.0	0	1	1
607.0	0	1	1
614.0	0	1	1
639.0	0	1	1
655.0	0	1	1
661.0	0	2	2
663.0	0	1	1
674.0	0	1	1
692.0	0	1	1
697.0	0	1	1
773.0	0	1	1
789.0	0	1	1
805.0	0	1	1
811.0	0	1	1
812.0	0	1	1
821.0	0	1	1
841.0	0	1	1
868.0	0	1	1
871.0	0	1	1
913.0	0	1	1
917.0	0	1	1
969.0	0	1	1
975.0	0	1	1
1032.0	0	1	1
1080.0	0	1	1
1083.0	0	1	1
1086.0	0	1	1
1248.0	0	1	1
1421.0	0	1	1
1482.0	0	1	1
1508.0	0	1	1
1563.0	0	1	1
1594.0	0	1	1
1655.0	0	1	1
1758.0	0	1	1
1809.0	0	1	1
1892.0	0	1	1
2201.0	0	1	1
2338.0	0	1	1
2401.0	0	1	1
2423.0	0	1	1
2514.0	0	1	1
2610.0	0	1	1
2623.0	0	1	1
2859.0	0	1	1
3000.0	0	1	1
3286.0	0	1	1
3715.0	0	1	1
3869.0	0	1	1
5300.0	0	1	1
5853.0	0	1	1