## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2014-09-26/PT_Por_Rec_1_2014-09-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2014-09-26/PT_Por_Rec_1_2014-09-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2014-09-26/PT_Por_Rec_1_2014-09-26.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 08:29:28 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	7801222	18648430	0	0	1544884	604217	0	0.061052	281530362

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	17253663	17253663
2.0	1.935907	413833	413833
3.0	2.811828	8715	8715
4.0	3.631609	768	768
5.0	4.398847	440	440
6.0	5.11691	279	279
7.0	5.78895	214	214
8.0	6.417917	197	197
9.0	7.006572	141	141
10.0	7.557497	134	134
11.0	8.073112	118	118
12.0	8.55568	110	110
13.0	9.007318	83	83
14.0	9.430009	96	96
15.0	9.825609	84	84
16.0	10.195853	70	70
17.0	10.542367	58	58
18.0	10.866672	57	57
19.0	11.170191	59	59
20.0	11.454256	49	49
21.0	11.720115	54	54
22.0	11.968934	44	44
23.0	12.201805	47	47
24.0	12.419751	44	44
25.0	12.623728	45	45
26.0	12.814632	43	43
27.0	12.9933	44	44
28.0	13.160516	23	23
29.0	13.317015	36	36
30.0	13.463483	38	38
31.0	13.600564	28	28
32.0	13.728859	21	21
33.0	13.848931	26	26
34.0	13.961307	20	20
35.0	14.066481	31	31
36.0	14.164913	19	19
37.0	14.257037	29	29
38.0	14.343257	19	19
39.0	14.42395	17	17
40.0	14.499471	20	20
41.0	14.570152	19	19
42.0	14.636303	20	20
43.0	14.698214	16	16
44.0	14.756156	17	17
45.0	14.810385	14	14
46.0	14.861139	14	14
47.0	14.908639	17	17
48.0	14.953095	22	22
49.0	14.994702	20	20
50.0	15.033642	18	18
51.0	15.070086	12	12
52.0	15.104194	11	11
53.0	15.136116	15	15
54.0	15.165993	13	13
55.0	15.193954	12	12
56.0	15.220123	10	10
57.0	15.244615	3	3
58.0	15.267537	8	8
59.0	15.28899	15	15
60.0	15.309068	7	7
61.0	15.327859	10	10
62.0	15.345446	12	12
63.0	15.361906	14	14
64.0	15.37731	7	7
65.0	15.391727	7	7
66.0	15.405221	7	7
67.0	15.417849	11	11
68.0	15.429668	6	6
69.0	15.44073	8	8
70.0	15.451082	10	10
71.0	15.460771	9	9
72.0	15.469839	5	5
73.0	15.478326	12	12
74.0	15.486269	10	10
75.0	15.493702	9	9
76.0	15.50066	13	13
77.0	15.507171	4	4
78.0	15.513265	5	5
79.0	15.518969	7	7
80.0	15.524307	7	7
81.0	15.529302	4	4
82.0	15.533978	5	5
83.0	15.538354	4	4
84.0	15.542449	8	8
85.0	15.546282	6	6
86.0	15.54987	6	6
87.0	15.553227	3	3
88.0	15.556369	9	9
89.0	15.55931	7	7
90.0	15.562062	6	6
91.0	15.564638	4	4
92.0	15.567049	2	2
93.0	15.569305	5	5
94.0	15.571417	3	3
95.0	15.573393	5	5
96.0	15.575243	3	3
97.0	15.576974	3	3
98.0	15.578594	2	2
99.0	15.580111	4	4
100.0	15.58153	3	3
101.0	0	7	7
102.0	0	6	6
103.0	0	5	5
104.0	0	4	4
105.0	0	3	3
106.0	0	1	1
107.0	0	6	6
108.0	0	7	7
109.0	0	2	2
110.0	0	2	2
111.0	0	5	5
112.0	0	1	1
113.0	0	5	5
115.0	0	6	6
116.0	0	4	4
117.0	0	5	5
118.0	0	2	2
119.0	0	3	3
120.0	0	5	5
121.0	0	3	3
122.0	0	2	2
123.0	0	2	2
124.0	0	4	4
125.0	0	4	4
127.0	0	6	6
128.0	0	3	3
129.0	0	6	6
130.0	0	4	4
131.0	0	4	4
132.0	0	4	4
133.0	0	4	4
134.0	0	2	2
135.0	0	2	2
137.0	0	3	3
138.0	0	3	3
139.0	0	2	2
140.0	0	4	4
141.0	0	4	4
142.0	0	1	1
143.0	0	2	2
144.0	0	1	1
145.0	0	1	1
146.0	0	4	4
147.0	0	6	6
148.0	0	2	2
149.0	0	4	4
150.0	0	2	2
151.0	0	2	2
152.0	0	2	2
153.0	0	2	2
154.0	0	2	2
156.0	0	4	4
157.0	0	2	2
158.0	0	2	2
159.0	0	2	2
161.0	0	1	1
163.0	0	1	1
164.0	0	3	3
165.0	0	2	2
166.0	0	2	2
167.0	0	4	4
168.0	0	3	3
169.0	0	4	4
170.0	0	1	1
172.0	0	3	3
173.0	0	1	1
175.0	0	3	3
176.0	0	4	4
177.0	0	2	2
178.0	0	2	2
179.0	0	2	2
181.0	0	3	3
182.0	0	4	4
183.0	0	4	4
184.0	0	1	1
185.0	0	1	1
186.0	0	2	2
187.0	0	2	2
188.0	0	2	2
189.0	0	3	3
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	2	2
195.0	0	1	1
196.0	0	2	2
197.0	0	1	1
199.0	0	4	4
201.0	0	2	2
202.0	0	1	1
203.0	0	3	3
205.0	0	2	2
207.0	0	2	2
208.0	0	1	1
209.0	0	1	1
210.0	0	1	1
211.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
219.0	0	1	1
220.0	0	1	1
225.0	0	2	2
226.0	0	1	1
227.0	0	1	1
230.0	0	3	3
233.0	0	2	2
234.0	0	1	1
235.0	0	1	1
237.0	0	2	2
239.0	0	1	1
240.0	0	2	2
243.0	0	1	1
246.0	0	1	1
247.0	0	2	2
249.0	0	3	3
250.0	0	1	1
254.0	0	2	2
255.0	0	2	2
256.0	0	1	1
257.0	0	3	3
258.0	0	1	1
262.0	0	1	1
263.0	0	4	4
265.0	0	1	1
266.0	0	1	1
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
274.0	0	2	2
277.0	0	1	1
278.0	0	1	1
279.0	0	2	2
280.0	0	3	3
284.0	0	1	1
289.0	0	1	1
292.0	0	1	1
295.0	0	2	2
296.0	0	1	1
299.0	0	1	1
300.0	0	2	2
301.0	0	2	2
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
310.0	0	1	1
311.0	0	1	1
316.0	0	3	3
317.0	0	1	1
319.0	0	1	1
321.0	0	1	1
322.0	0	2	2
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
332.0	0	1	1
333.0	0	3	3
334.0	0	1	1
338.0	0	1	1
340.0	0	1	1
341.0	0	3	3
342.0	0	1	1
345.0	0	1	1
347.0	0	1	1
351.0	0	2	2
352.0	0	2	2
353.0	0	1	1
360.0	0	2	2
362.0	0	2	2
365.0	0	1	1
368.0	0	1	1
369.0	0	1	1
370.0	0	1	1
376.0	0	2	2
378.0	0	2	2
380.0	0	1	1
382.0	0	1	1
383.0	0	2	2
385.0	0	1	1
386.0	0	1	1
392.0	0	1	1
400.0	0	3	3
401.0	0	1	1
411.0	0	3	3
431.0	0	3	3
434.0	0	1	1
445.0	0	1	1
449.0	0	1	1
455.0	0	1	1
456.0	0	1	1
457.0	0	1	1
460.0	0	1	1
468.0	0	1	1
488.0	0	1	1
489.0	0	1	1
493.0	0	1	1
494.0	0	1	1
523.0	0	1	1
552.0	0	1	1
565.0	0	3	3
599.0	0	1	1
605.0	0	1	1
607.0	0	1	1
611.0	0	1	1
629.0	0	1	1
642.0	0	1	1
643.0	0	1	1
651.0	0	1	1
740.0	0	1	1
744.0	0	1	1
753.0	0	1	1
780.0	0	1	1
801.0	0	1	1
808.0	0	1	1
928.0	0	1	1
1162.0	0	1	1