## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2014-07-08/FR_Dro_Got_1_2014-07-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2014-07-08/FR_Dro_Got_1_2014-07-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FR_Dro_Got_1_2014-07-08/FR_Dro_Got_1_2014-07-08.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 10:43:33 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	3600100	47052887	0	0	1405372	1778464	0	0.050788	606654832

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	42783983	42783983
2.0	1.92537	1467592	1467592
3.0	2.781681	45781	45781
4.0	3.574085	2190	2190
5.0	4.307352	582	582
6.0	4.985896	387	387
7.0	5.613801	281	281
8.0	6.194845	202	202
9.0	6.732526	207	207
10.0	7.23008	135	135
11.0	7.690502	100	100
12.0	8.116563	99	99
13.0	8.510827	108	108
14.0	8.875667	100	100
15.0	9.213279	91	91
16.0	9.525695	82	82
17.0	9.814796	81	81
18.0	10.082322	50	50
19.0	10.329882	51	51
20.0	10.558967	52	52
21.0	10.770955	48	48
22.0	10.967123	49	49
23.0	11.14865	55	55
24.0	11.316631	42	42
25.0	11.472075	50	50
26.0	11.615918	33	33
27.0	11.749027	40	40
28.0	11.872201	36	36
29.0	11.986183	36	36
30.0	12.091659	23	23
31.0	12.189263	26	26
32.0	12.279583	32	32
33.0	12.363162	29	29
34.0	12.440504	22	22
35.0	12.512074	26	26
36.0	12.578302	16	16
37.0	12.639588	22	22
38.0	12.696301	25	25
39.0	12.74878	23	23
40.0	12.797344	23	23
41.0	12.842283	19	19
42.0	12.883868	17	17
43.0	12.92235	24	24
44.0	12.95796	19	19
45.0	12.990912	19	19
46.0	13.021405	13	13
47.0	13.049622	12	12
48.0	13.075734	9	9
49.0	13.099897	11	11
50.0	13.122257	20	20
51.0	13.142947	14	14
52.0	13.162094	13	13
53.0	13.179812	11	11
54.0	13.196208	15	15
55.0	13.21138	13	13
56.0	13.225419	8	8
57.0	13.238411	19	19
58.0	13.250433	9	9
59.0	13.261559	16	16
60.0	13.271853	14	14
61.0	13.28138	11	11
62.0	13.290196	15	15
63.0	13.298353	12	12
64.0	13.305902	11	11
65.0	13.312888	8	8
66.0	13.319352	12	12
67.0	13.325334	8	8
68.0	13.330869	11	11
69.0	13.335991	5	5
70.0	13.340731	13	13
71.0	13.345117	7	7
72.0	13.349176	14	14
73.0	13.352932	6	6
74.0	13.356408	4	4
75.0	13.359624	12	12
76.0	13.3626	7	7
77.0	13.365355	5	5
78.0	13.367903	7	7
79.0	13.370262	9	9
80.0	13.372444	11	11
81.0	13.374463	9	9
82.0	13.376332	8	8
83.0	13.378062	7	7
84.0	13.379662	7	7
85.0	13.381143	5	5
86.0	13.382513	5	5
87.0	13.383781	9	9
88.0	13.384955	8	8
89.0	13.38604	5	5
90.0	13.387045	7	7
91.0	13.387975	3	3
92.0	13.388835	4	4
93.0	13.389632	8	8
94.0	13.390368	4	4
95.0	13.39105	5	5
96.0	13.391681	1	1
97.0	13.392265	3	3
98.0	13.392805	5	5
99.0	13.393305	5	5
100.0	13.393768	5	5
101.0	0	6	6
102.0	0	5	5
103.0	0	5	5
104.0	0	9	9
105.0	0	1	1
106.0	0	5	5
107.0	0	4	4
108.0	0	6	6
109.0	0	3	3
110.0	0	5	5
111.0	0	5	5
112.0	0	1	1
113.0	0	4	4
114.0	0	3	3
115.0	0	4	4
116.0	0	4	4
117.0	0	3	3
118.0	0	4	4
119.0	0	3	3
120.0	0	6	6
121.0	0	4	4
122.0	0	4	4
123.0	0	4	4
124.0	0	3	3
125.0	0	3	3
126.0	0	4	4
127.0	0	2	2
128.0	0	4	4
129.0	0	4	4
130.0	0	2	2
131.0	0	4	4
132.0	0	6	6
133.0	0	10	10
134.0	0	2	2
135.0	0	5	5
136.0	0	4	4
137.0	0	1	1
138.0	0	2	2
139.0	0	1	1
141.0	0	3	3
142.0	0	6	6
143.0	0	1	1
144.0	0	3	3
145.0	0	3	3
146.0	0	1	1
147.0	0	4	4
148.0	0	3	3
149.0	0	2	2
150.0	0	6	6
151.0	0	5	5
152.0	0	4	4
154.0	0	2	2
155.0	0	1	1
156.0	0	2	2
158.0	0	1	1
159.0	0	5	5
160.0	0	3	3
162.0	0	2	2
163.0	0	4	4
164.0	0	7	7
165.0	0	1	1
166.0	0	5	5
167.0	0	6	6
168.0	0	2	2
169.0	0	3	3
170.0	0	5	5
171.0	0	2	2
172.0	0	2	2
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
177.0	0	1	1
178.0	0	4	4
179.0	0	2	2
181.0	0	4	4
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
185.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
190.0	0	8	8
191.0	0	2	2
192.0	0	1	1
193.0	0	2	2
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	4	4
198.0	0	3	3
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	1	1
206.0	0	2	2
207.0	0	1	1
208.0	0	3	3
209.0	0	2	2
210.0	0	3	3
211.0	0	2	2
212.0	0	2	2
213.0	0	3	3
215.0	0	2	2
217.0	0	1	1
218.0	0	2	2
221.0	0	1	1
222.0	0	1	1
224.0	0	2	2
226.0	0	2	2
227.0	0	1	1
228.0	0	2	2
229.0	0	3	3
231.0	0	3	3
232.0	0	4	4
234.0	0	2	2
235.0	0	1	1
236.0	0	1	1
237.0	0	2	2
238.0	0	1	1
239.0	0	1	1
240.0	0	2	2
244.0	0	2	2
247.0	0	2	2
248.0	0	2	2
249.0	0	1	1
250.0	0	1	1
251.0	0	2	2
252.0	0	2	2
253.0	0	1	1
254.0	0	3	3
257.0	0	1	1
258.0	0	1	1
259.0	0	4	4
260.0	0	1	1
262.0	0	1	1
263.0	0	2	2
264.0	0	4	4
267.0	0	1	1
273.0	0	1	1
275.0	0	1	1
276.0	0	1	1
277.0	0	1	1
279.0	0	1	1
280.0	0	1	1
281.0	0	2	2
282.0	0	1	1
285.0	0	3	3
287.0	0	1	1
288.0	0	1	1
289.0	0	1	1
291.0	0	1	1
299.0	0	1	1
300.0	0	1	1
301.0	0	1	1
302.0	0	2	2
304.0	0	1	1
305.0	0	1	1
306.0	0	1	1
307.0	0	2	2
308.0	0	2	2
313.0	0	1	1
314.0	0	1	1
316.0	0	2	2
317.0	0	1	1
318.0	0	1	1
321.0	0	1	1
322.0	0	1	1
326.0	0	1	1
327.0	0	1	1
328.0	0	1	1
331.0	0	1	1
333.0	0	1	1
334.0	0	1	1
338.0	0	1	1
340.0	0	3	3
341.0	0	2	2
344.0	0	1	1
345.0	0	1	1
346.0	0	1	1
347.0	0	2	2
349.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	3	3
355.0	0	1	1
363.0	0	1	1
365.0	0	1	1
369.0	0	1	1
370.0	0	1	1
373.0	0	1	1
376.0	0	1	1
379.0	0	1	1
380.0	0	1	1
390.0	0	1	1
393.0	0	1	1
394.0	0	2	2
402.0	0	3	3
407.0	0	1	1
413.0	0	1	1
420.0	0	1	1
422.0	0	1	1
423.0	0	2	2
424.0	0	1	1
425.0	0	1	1
427.0	0	1	1
430.0	0	1	1
436.0	0	1	1
439.0	0	1	1
445.0	0	3	3
446.0	0	1	1
447.0	0	1	1
448.0	0	2	2
449.0	0	1	1
453.0	0	1	1
460.0	0	1	1
462.0	0	1	1
468.0	0	1	1
475.0	0	1	1
476.0	0	1	1
480.0	0	1	1
487.0	0	1	1
489.0	0	1	1
492.0	0	1	1
494.0	0	1	1
495.0	0	1	1
503.0	0	1	1
521.0	0	1	1
522.0	0	1	1
530.0	0	1	1
532.0	0	1	1
536.0	0	1	1
544.0	0	1	1
546.0	0	1	1
548.0	0	1	1
566.0	0	1	1
578.0	0	1	1
581.0	0	1	1
588.0	0	1	1
600.0	0	1	1
603.0	0	1	1
606.0	0	1	1
617.0	0	2	2
630.0	0	1	1
641.0	0	1	1
657.0	0	1	1
660.0	0	1	1
662.0	0	1	1
666.0	0	2	2
675.0	0	1	1
680.0	0	1	1
707.0	0	1	1
708.0	0	1	1
714.0	0	1	1
736.0	0	1	1
737.0	0	1	1
770.0	0	2	2
782.0	0	1	1
814.0	0	1	1
842.0	0	2	2
873.0	0	1	1
874.0	0	1	1
886.0	0	1	1
987.0	0	1	1
994.0	0	1	1
1030.0	0	1	1
1082.0	0	1	1
1347.0	0	1	1
1365.0	0	1	1