## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2014-08-24/UA_Lvi_Dro_1_2014-08-24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2014-08-24/UA_Lvi_Dro_1_2014-08-24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2014-08-24/UA_Lvi_Dro_1_2014-08-24.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 16:55:15 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	15914010	15855999	0	0	3123843	542754	0	0.088383	226292289

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	14673289	14673289
2.0	1.93233	330136	330136
3.0	2.801569	6807	6807
4.0	3.611986	713	713
5.0	4.367562	453	453
6.0	5.072008	276	276
7.0	5.728784	205	205
8.0	6.341116	168	168
9.0	6.912012	151	151
10.0	7.444275	133	133
11.0	7.940519	129	129
12.0	8.403182	101	101
13.0	8.834537	78	78
14.0	9.236702	78	78
15.0	9.611653	87	87
16.0	9.96123	59	59
17.0	10.287152	73	73
18.0	10.591018	71	71
19.0	10.874322	42	42
20.0	11.138454	59	59
21.0	11.384713	41	41
22.0	11.614307	51	51
23.0	11.828365	41	41
24.0	12.027937	33	33
25.0	12.214004	29	29
26.0	12.38748	32	32
27.0	12.549216	42	42
28.0	12.700008	35	35
29.0	12.840596	27	27
30.0	12.971671	22	22
31.0	13.093875	22	22
32.0	13.20781	20	20
33.0	13.314035	29	29
34.0	13.413071	16	16
35.0	13.505406	20	20
36.0	13.591492	32	32
37.0	13.671753	21	21
38.0	13.746583	19	19
39.0	13.816349	14	14
40.0	13.881394	11	11
41.0	13.942037	17	17
42.0	13.998577	24	24
43.0	14.05129	18	18
44.0	14.100437	16	16
45.0	14.146257	12	12
46.0	14.188977	20	20
47.0	14.228806	14	14
48.0	14.26594	15	15
49.0	14.300561	13	13
50.0	14.332839	10	10
51.0	14.362933	11	11
52.0	14.39099	8	8
53.0	14.417149	15	15
54.0	14.441538	8	8
55.0	14.464276	9	9
56.0	14.485475	12	12
57.0	14.50524	10	10
58.0	14.523668	10	10
59.0	14.540848	5	5
60.0	14.556866	7	7
61.0	14.5718	8	8
62.0	14.585723	10	10
63.0	14.598705	7	7
64.0	14.610807	11	11
65.0	14.622091	1	1
66.0	14.632611	7	7
67.0	14.642419	12	12
68.0	14.651564	8	8
69.0	14.66009	6	6
70.0	14.668038	5	5
71.0	14.675449	9	9
72.0	14.682359	10	10
73.0	14.6888	3	3
74.0	14.694806	13	13
75.0	14.700406	6	6
76.0	14.705626	5	5
77.0	14.710494	8	8
78.0	14.715032	7	7
79.0	14.719262	6	6
80.0	14.723207	6	6
81.0	14.726885	3	3
82.0	14.730313	8	8
83.0	14.73351	8	8
84.0	14.73649	9	9
85.0	14.739269	5	5
86.0	14.74186	3	3
87.0	14.744275	5	5
88.0	14.746527	8	8
89.0	14.748627	9	9
90.0	14.750584	13	13
91.0	14.752409	5	5
92.0	14.754111	4	4
93.0	14.755697	8	8
94.0	14.757176	7	7
95.0	14.758555	8	8
96.0	14.75984	4	4
97.0	14.761039	5	5
98.0	14.762157	6	6
99.0	14.763198	6	6
100.0	14.76417	5	5
101.0	0	4	4
102.0	0	5	5
103.0	0	4	4
104.0	0	5	5
105.0	0	3	3
106.0	0	5	5
107.0	0	1	1
108.0	0	4	4
109.0	0	6	6
110.0	0	3	3
111.0	0	3	3
112.0	0	1	1
113.0	0	1	1
114.0	0	5	5
115.0	0	5	5
116.0	0	3	3
118.0	0	4	4
119.0	0	4	4
121.0	0	4	4
122.0	0	2	2
123.0	0	4	4
124.0	0	2	2
125.0	0	4	4
126.0	0	2	2
127.0	0	3	3
128.0	0	2	2
129.0	0	1	1
130.0	0	3	3
131.0	0	3	3
132.0	0	4	4
133.0	0	2	2
134.0	0	2	2
135.0	0	1	1
136.0	0	1	1
137.0	0	2	2
139.0	0	2	2
140.0	0	1	1
141.0	0	1	1
142.0	0	4	4
143.0	0	2	2
144.0	0	2	2
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
149.0	0	4	4
150.0	0	1	1
152.0	0	3	3
153.0	0	1	1
154.0	0	1	1
155.0	0	1	1
156.0	0	4	4
157.0	0	1	1
159.0	0	2	2
161.0	0	3	3
162.0	0	2	2
163.0	0	2	2
164.0	0	1	1
166.0	0	1	1
167.0	0	4	4
168.0	0	2	2
169.0	0	3	3
170.0	0	4	4
172.0	0	3	3
173.0	0	4	4
174.0	0	2	2
175.0	0	2	2
176.0	0	3	3
177.0	0	2	2
179.0	0	2	2
180.0	0	2	2
181.0	0	4	4
182.0	0	1	1
183.0	0	4	4
184.0	0	2	2
185.0	0	2	2
186.0	0	3	3
188.0	0	2	2
189.0	0	3	3
190.0	0	3	3
191.0	0	1	1
192.0	0	1	1
193.0	0	3	3
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	1	1
201.0	0	2	2
202.0	0	4	4
203.0	0	4	4
204.0	0	1	1
205.0	0	3	3
206.0	0	1	1
207.0	0	1	1
211.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
220.0	0	2	2
222.0	0	3	3
224.0	0	3	3
225.0	0	2	2
226.0	0	1	1
227.0	0	2	2
228.0	0	3	3
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	2	2
235.0	0	3	3
236.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	1	1
242.0	0	2	2
243.0	0	1	1
244.0	0	1	1
245.0	0	4	4
246.0	0	1	1
247.0	0	1	1
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	1	1
257.0	0	2	2
259.0	0	3	3
261.0	0	2	2
263.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	1	1
269.0	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	1	1
276.0	0	1	1
278.0	0	1	1
279.0	0	1	1
282.0	0	1	1
285.0	0	3	3
286.0	0	3	3
287.0	0	2	2
289.0	0	1	1
290.0	0	2	2
291.0	0	3	3
293.0	0	1	1
294.0	0	1	1
295.0	0	2	2
298.0	0	1	1
300.0	0	2	2
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
308.0	0	1	1
310.0	0	1	1
312.0	0	2	2
313.0	0	2	2
316.0	0	3	3
317.0	0	1	1
318.0	0	1	1
321.0	0	3	3
324.0	0	1	1
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
329.0	0	2	2
332.0	0	2	2
333.0	0	2	2
334.0	0	3	3
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
342.0	0	3	3
344.0	0	2	2
345.0	0	1	1
346.0	0	1	1
348.0	0	1	1
350.0	0	1	1
351.0	0	2	2
352.0	0	1	1
354.0	0	1	1
357.0	0	1	1
358.0	0	1	1
362.0	0	1	1
364.0	0	2	2
368.0	0	1	1
369.0	0	2	2
371.0	0	2	2
380.0	0	1	1
383.0	0	1	1
387.0	0	1	1
389.0	0	1	1
390.0	0	2	2
391.0	0	2	2
392.0	0	1	1
393.0	0	2	2
396.0	0	1	1
398.0	0	1	1
399.0	0	1	1
400.0	0	1	1
404.0	0	1	1
406.0	0	1	1
407.0	0	1	1
412.0	0	1	1
415.0	0	1	1
421.0	0	1	1
424.0	0	1	1
429.0	0	1	1
433.0	0	2	2
437.0	0	2	2
443.0	0	1	1
445.0	0	1	1
446.0	0	1	1
448.0	0	1	1
449.0	0	1	1
453.0	0	2	2
456.0	0	1	1
458.0	0	1	1
462.0	0	1	1
463.0	0	1	1
467.0	0	1	1
474.0	0	2	2
482.0	0	1	1
483.0	0	1	1
486.0	0	1	1
490.0	0	1	1
494.0	0	1	1
495.0	0	1	1
498.0	0	1	1
501.0	0	1	1
503.0	0	1	1
505.0	0	1	1
509.0	0	1	1
511.0	0	1	1
518.0	0	1	1
523.0	0	1	1
527.0	0	2	2
529.0	0	1	1
534.0	0	1	1
545.0	0	1	1
552.0	0	1	1
554.0	0	1	1
556.0	0	1	1
557.0	0	1	1
564.0	0	2	2
566.0	0	1	1
578.0	0	1	1
581.0	0	1	1
582.0	0	1	1
583.0	0	1	1
589.0	0	1	1
594.0	0	1	1
597.0	0	1	1
598.0	0	1	1
602.0	0	1	1
606.0	0	1	1
627.0	0	1	1
650.0	0	1	1
662.0	0	1	1
665.0	0	1	1
671.0	0	1	1
688.0	0	1	1
689.0	0	1	1
722.0	0	1	1
727.0	0	1	1
732.0	0	1	1
751.0	0	1	1
805.0	0	1	1
872.0	0	1	1
875.0	0	1	1
887.0	0	1	1
888.0	0	1	1
900.0	0	1	1
911.0	0	1	1