## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2016-08-06/GB_Fif_Dai_1_2016-08-06.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2016-08-06/GB_Fif_Dai_1_2016-08-06.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/GB_Fif_Dai_1_2016-08-06/GB_Fif_Dai_1_2016-08-06.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 09:09:43 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	31196629	13387999	0	0	7998690	1142948	0	0.177404	73881387

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	11060452	11060452
2.0	1.834261	771370	771370
3.0	2.530252	60612	60612
4.0	3.110889	7168	7168
5.0	3.595293	2154	2154
6.0	3.999411	1306	1306
7.0	4.336552	893	893
8.0	4.617814	649	649
9.0	4.852461	505	505
10.0	5.048217	392	392
11.0	5.211529	308	308
12.0	5.347774	274	274
13.0	5.461438	238	238
14.0	5.556263	173	173
15.0	5.635371	169	169
16.0	5.701369	156	156
17.0	5.756428	127	127
18.0	5.802361	131	131
19.0	5.840682	115	115
20.0	5.872651	101	101
21.0	5.899322	109	109
22.0	5.921572	97	97
23.0	5.940135	77	77
24.0	5.955621	86	86
25.0	5.96854	104	104
26.0	5.979319	90	90
27.0	5.98831	84	84
28.0	5.995812	61	61
29.0	6.00207	80	80
30.0	6.007291	72	72
31.0	6.011647	69	69
32.0	6.01528	56	56
33.0	6.018312	58	58
34.0	6.020841	53	53
35.0	6.022951	63	63
36.0	6.024711	50	50
37.0	6.02618	45	45
38.0	6.027405	49	49
39.0	6.028427	48	48
40.0	6.029279	36	36
41.0	6.029991	41	41
42.0	6.030584	41	41
43.0	6.031079	33	33
44.0	6.031492	22	22
45.0	6.031837	28	28
46.0	6.032124	34	34
47.0	6.032364	21	21
48.0	6.032564	27	27
49.0	6.032731	26	26
50.0	6.03287	18	18
51.0	6.032986	16	16
52.0	6.033083	24	24
53.0	6.033164	20	20
54.0	6.033232	16	16
55.0	6.033288	14	14
56.0	6.033335	18	18
57.0	6.033374	15	15
58.0	6.033407	18	18
59.0	6.033434	20	20
60.0	6.033457	14	14
61.0	6.033476	14	14
62.0	6.033492	22	22
63.0	6.033505	9	9
64.0	6.033516	23	23
65.0	6.033525	13	13
66.0	6.033533	10	10
67.0	6.033539	8	8
68.0	6.033544	7	7
69.0	6.033549	19	19
70.0	6.033553	11	11
71.0	6.033556	12	12
72.0	6.033558	12	12
73.0	6.03356	18	18
74.0	6.033562	16	16
75.0	6.033564	14	14
76.0	6.033565	9	9
77.0	6.033566	15	15
78.0	6.033567	7	7
79.0	6.033568	3	3
80.0	6.033568	9	9
81.0	6.033569	10	10
82.0	6.033569	20	20
83.0	6.033569	11	11
84.0	6.03357	13	13
85.0	6.03357	8	8
86.0	6.03357	7	7
87.0	6.03357	9	9
88.0	6.03357	8	8
89.0	6.033571	7	7
90.0	6.033571	7	7
91.0	6.033571	7	7
92.0	6.033571	19	19
93.0	6.033571	7	7
94.0	6.033571	11	11
95.0	6.033571	7	7
96.0	6.033571	6	6
97.0	6.033571	10	10
98.0	6.033571	6	6
99.0	6.033571	5	5
100.0	6.033571	7	7
101.0	0	8	8
102.0	0	3	3
103.0	0	6	6
104.0	0	9	9
105.0	0	10	10
106.0	0	8	8
107.0	0	5	5
108.0	0	5	5
109.0	0	4	4
110.0	0	6	6
111.0	0	4	4
112.0	0	10	10
113.0	0	6	6
114.0	0	10	10
115.0	0	8	8
116.0	0	7	7
117.0	0	5	5
118.0	0	2	2
119.0	0	8	8
120.0	0	5	5
121.0	0	5	5
122.0	0	9	9
123.0	0	6	6
124.0	0	3	3
125.0	0	6	6
126.0	0	2	2
127.0	0	3	3
128.0	0	7	7
129.0	0	5	5
130.0	0	3	3
131.0	0	2	2
132.0	0	1	1
133.0	0	5	5
134.0	0	2	2
135.0	0	5	5
136.0	0	5	5
137.0	0	3	3
138.0	0	4	4
139.0	0	4	4
140.0	0	4	4
142.0	0	5	5
143.0	0	5	5
144.0	0	2	2
145.0	0	2	2
146.0	0	4	4
147.0	0	1	1
148.0	0	2	2
149.0	0	3	3
153.0	0	1	1
155.0	0	2	2
156.0	0	5	5
157.0	0	6	6
158.0	0	2	2
159.0	0	5	5
161.0	0	3	3
163.0	0	2	2
164.0	0	3	3
165.0	0	2	2
166.0	0	2	2
167.0	0	1	1
168.0	0	2	2
169.0	0	3	3
172.0	0	2	2
173.0	0	2	2
174.0	0	3	3
176.0	0	1	1
177.0	0	2	2
178.0	0	3	3
179.0	0	1	1
180.0	0	2	2
182.0	0	1	1
183.0	0	2	2
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
191.0	0	1	1
192.0	0	2	2
193.0	0	1	1
194.0	0	1	1
196.0	0	3	3
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	2	2
203.0	0	2	2
205.0	0	2	2
206.0	0	3	3
207.0	0	1	1
208.0	0	3	3
209.0	0	1	1
210.0	0	1	1
212.0	0	1	1
213.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
224.0	0	2	2
228.0	0	1	1
229.0	0	1	1
231.0	0	2	2
232.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
250.0	0	1	1
251.0	0	1	1
257.0	0	2	2
263.0	0	1	1
264.0	0	1	1
270.0	0	1	1
272.0	0	2	2
274.0	0	1	1
277.0	0	1	1
278.0	0	1	1
279.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	3	3
287.0	0	1	1
288.0	0	1	1
296.0	0	1	1
299.0	0	1	1
303.0	0	2	2
310.0	0	1	1
319.0	0	1	1
321.0	0	1	1
325.0	0	1	1
334.0	0	1	1
336.0	0	1	1
338.0	0	1	1
339.0	0	1	1
340.0	0	1	1
341.0	0	1	1
346.0	0	1	1
352.0	0	1	1
355.0	0	1	1
356.0	0	1	1
357.0	0	1	1
364.0	0	2	2
365.0	0	1	1
369.0	0	1	1
370.0	0	1	1
372.0	0	1	1
380.0	0	1	1
394.0	0	1	1
396.0	0	2	2
400.0	0	1	1
401.0	0	1	1
409.0	0	1	1
416.0	0	1	1
423.0	0	1	1
426.0	0	1	1
439.0	0	2	2
440.0	0	1	1
447.0	0	1	1
450.0	0	3	3
480.0	0	1	1
496.0	0	1	1
498.0	0	1	1
528.0	0	1	1
612.0	0	1	1
690.0	0	1	1
725.0	0	1	1
767.0	0	1	1
1219.0	0	1	1
2225.0	0	1	1