## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-08-27/RU_Cri_Yal_1_2014-08-27.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-08-27/RU_Cri_Yal_1_2014-08-27.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/RU_Cri_Yal_1_2014-08-27/RU_Cri_Yal_1_2014-08-27.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 08:26:04 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	5833032	24853161	0	0	1403993	739835	0	0.051921	409118013

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23146109	23146109
2.0	1.94106	567068	567068
3.0	2.826655	10809	10809
4.0	3.660052	767	767
5.0	4.444329	378	378
6.0	5.182382	304	304
7.0	5.876933	206	206
8.0	6.530548	191	191
9.0	7.145639	165	165
10.0	7.724477	155	155
11.0	8.269198	135	135
12.0	8.781813	124	124
13.0	9.264215	110	110
14.0	9.718184	109	109
15.0	10.145396	104	104
16.0	10.547429	92	92
17.0	10.925766	98	98
18.0	11.281804	79	79
19.0	11.616857	71	71
20.0	11.932162	69	69
21.0	12.228883	68	68
22.0	12.508115	54	54
23.0	12.770889	45	45
24.0	13.018176	51	51
25.0	13.250888	54	54
26.0	13.469883	45	45
27.0	13.675971	41	41
28.0	13.869912	53	53
29.0	14.052423	37	37
30.0	14.224176	22	22
31.0	14.385806	38	38
32.0	14.53791	25	25
33.0	14.681049	21	21
34.0	14.815751	26	26
35.0	14.942514	27	27
36.0	15.061805	21	21
37.0	15.174066	27	27
38.0	15.27971	23	23
39.0	15.379127	16	16
40.0	15.472685	26	26
41.0	15.560728	23	23
42.0	15.643582	17	17
43.0	15.721553	17	17
44.0	15.794928	22	22
45.0	15.863978	17	17
46.0	15.928959	16	16
47.0	15.99011	13	13
48.0	16.047656	16	16
49.0	16.101811	12	12
50.0	16.152774	19	19
51.0	16.200733	16	16
52.0	16.245865	13	13
53.0	16.288337	16	16
54.0	16.328306	12	12
55.0	16.365919	8	8
56.0	16.401316	12	12
57.0	16.434626	11	11
58.0	16.465973	16	16
59.0	16.495472	12	12
60.0	16.523232	7	7
61.0	16.549357	9	9
62.0	16.573941	11	11
63.0	16.597077	12	12
64.0	16.618849	7	7
65.0	16.639337	14	14
66.0	16.658618	6	6
67.0	16.676763	9	9
68.0	16.693838	8	8
69.0	16.709907	10	10
70.0	16.725029	14	14
71.0	16.739259	3	3
72.0	16.752651	12	12
73.0	16.765253	7	7
74.0	16.777113	4	4
75.0	16.788274	5	5
76.0	16.798777	5	5
77.0	16.80866	7	7
78.0	16.817962	7	7
79.0	16.826715	3	3
80.0	16.834952	4	4
81.0	16.842703	5	5
82.0	16.849998	7	7
83.0	16.856863	11	11
84.0	16.863323	2	2
85.0	16.869403	9	9
86.0	16.875124	2	2
87.0	16.880508	4	4
88.0	16.885574	6	6
89.0	16.890342	4	4
90.0	16.894829	3	3
91.0	16.899052	4	4
92.0	16.903025	9	9
93.0	16.906765	5	5
94.0	16.910284	9	9
95.0	16.913595	1	1
96.0	16.916712	3	3
97.0	16.919644	9	9
98.0	16.922404	2	2
99.0	16.925001	4	4
100.0	16.927446	2	2
101.0	0	3	3
102.0	0	7	7
103.0	0	1	1
104.0	0	3	3
105.0	0	5	5
106.0	0	1	1
107.0	0	5	5
108.0	0	5	5
109.0	0	6	6
110.0	0	4	4
111.0	0	4	4
112.0	0	4	4
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
116.0	0	5	5
117.0	0	3	3
118.0	0	1	1
119.0	0	5	5
120.0	0	2	2
122.0	0	2	2
123.0	0	3	3
124.0	0	2	2
125.0	0	3	3
126.0	0	5	5
127.0	0	3	3
128.0	0	2	2
129.0	0	1	1
131.0	0	2	2
133.0	0	5	5
134.0	0	2	2
136.0	0	2	2
137.0	0	3	3
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
141.0	0	1	1
142.0	0	3	3
143.0	0	2	2
144.0	0	1	1
145.0	0	3	3
146.0	0	1	1
147.0	0	1	1
151.0	0	2	2
152.0	0	2	2
153.0	0	2	2
154.0	0	3	3
156.0	0	1	1
157.0	0	2	2
158.0	0	4	4
160.0	0	2	2
161.0	0	3	3
163.0	0	4	4
164.0	0	4	4
165.0	0	2	2
166.0	0	2	2
167.0	0	2	2
168.0	0	4	4
172.0	0	1	1
175.0	0	4	4
176.0	0	1	1
177.0	0	1	1
178.0	0	3	3
179.0	0	1	1
180.0	0	1	1
181.0	0	2	2
184.0	0	4	4
186.0	0	2	2
188.0	0	3	3
189.0	0	2	2
192.0	0	1	1
194.0	0	2	2
195.0	0	3	3
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	2	2
207.0	0	1	1
208.0	0	2	2
209.0	0	2	2
210.0	0	1	1
212.0	0	1	1
214.0	0	1	1
215.0	0	1	1
217.0	0	4	4
218.0	0	1	1
220.0	0	3	3
221.0	0	2	2
224.0	0	2	2
226.0	0	2	2
227.0	0	2	2
228.0	0	2	2
233.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
240.0	0	1	1
242.0	0	2	2
243.0	0	1	1
245.0	0	2	2
249.0	0	2	2
250.0	0	1	1
251.0	0	3	3
253.0	0	3	3
258.0	0	1	1
260.0	0	1	1
263.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	2	2
269.0	0	1	1
270.0	0	2	2
271.0	0	1	1
274.0	0	2	2
275.0	0	1	1
277.0	0	1	1
280.0	0	1	1
281.0	0	2	2
283.0	0	2	2
285.0	0	1	1
289.0	0	1	1
291.0	0	2	2
292.0	0	1	1
297.0	0	2	2
298.0	0	1	1
302.0	0	1	1
305.0	0	2	2
307.0	0	1	1
309.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
321.0	0	1	1
333.0	0	2	2
334.0	0	1	1
335.0	0	1	1
339.0	0	1	1
340.0	0	1	1
343.0	0	1	1
345.0	0	3	3
346.0	0	1	1
351.0	0	1	1
356.0	0	3	3
368.0	0	1	1
378.0	0	1	1
380.0	0	1	1
387.0	0	1	1
389.0	0	1	1
390.0	0	1	1
391.0	0	1	1
404.0	0	2	2
405.0	0	1	1
406.0	0	2	2
413.0	0	1	1
428.0	0	1	1
434.0	0	1	1
448.0	0	2	2
453.0	0	1	1
454.0	0	2	2
455.0	0	1	1
464.0	0	1	1
466.0	0	1	1
468.0	0	1	1
472.0	0	1	1
495.0	0	1	1
499.0	0	2	2
515.0	0	1	1
516.0	0	1	1
526.0	0	1	1
549.0	0	1	1
573.0	0	1	1
614.0	0	1	1
697.0	0	1	1
737.0	0	1	1
812.0	0	1	1