## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-06-17/US_Geo_Ath_1_2014-06-17.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-06-17/US_Geo_Ath_1_2014-06-17.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Geo_Ath_1_2014-06-17/US_Geo_Ath_1_2014-06-17.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 20:21:32 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	1874412	44214580	0	0	805400	4001139	0	0.097534	229324671

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	35037382	35037382
2.0	1.824644	3016926	3016926
3.0	2.504682	264025	264025
4.0	3.065471	34053	34053
5.0	3.527923	9848	9848
6.0	3.90928	4727	4727
7.0	4.223765	2819	2819
8.0	4.483103	1837	1837
9.0	4.696964	1252	1252
10.0	4.873324	919	919
11.0	5.018757	713	713
12.0	5.138688	574	574
13.0	5.237589	469	469
14.0	5.319147	366	366
15.0	5.386403	278	278
16.0	5.441865	284	284
17.0	5.487602	219	219
18.0	5.525318	219	219
19.0	5.556421	153	153
20.0	5.58207	170	170
21.0	5.603221	145	145
22.0	5.620663	143	143
23.0	5.635046	132	132
24.0	5.646907	133	133
25.0	5.656689	103	103
26.0	5.664755	96	96
27.0	5.671406	83	83
28.0	5.676892	98	98
29.0	5.681415	60	60
30.0	5.685145	67	67
31.0	5.688221	72	72
32.0	5.690758	59	59
33.0	5.69285	52	52
34.0	5.694575	47	47
35.0	5.695997	47	47
36.0	5.69717	51	51
37.0	5.698138	50	50
38.0	5.698936	49	49
39.0	5.699593	52	52
40.0	5.700136	39	39
41.0	5.700583	40	40
42.0	5.700952	35	35
43.0	5.701256	26	26
44.0	5.701507	38	38
45.0	5.701714	47	47
46.0	5.701885	28	28
47.0	5.702025	28	28
48.0	5.702141	27	27
49.0	5.702237	40	40
50.0	5.702316	23	23
51.0	5.702381	27	27
52.0	5.702435	25	25
53.0	5.702479	28	28
54.0	5.702516	23	23
55.0	5.702546	22	22
56.0	5.70257	21	21
57.0	5.702591	29	29
58.0	5.702608	16	16
59.0	5.702622	13	13
60.0	5.702633	19	19
61.0	5.702643	12	12
62.0	5.70265	10	10
63.0	5.702657	17	17
64.0	5.702662	20	20
65.0	5.702667	16	16
66.0	5.70267	22	22
67.0	5.702673	11	11
68.0	5.702676	12	12
69.0	5.702678	21	21
70.0	5.702679	14	14
71.0	5.702681	17	17
72.0	5.702682	16	16
73.0	5.702683	16	16
74.0	5.702683	10	10
75.0	5.702684	10	10
76.0	5.702685	22	22
77.0	5.702685	10	10
78.0	5.702685	9	9
79.0	5.702686	10	10
80.0	5.702686	10	10
81.0	5.702686	17	17
82.0	5.702686	7	7
83.0	5.702686	10	10
84.0	5.702687	9	9
85.0	5.702687	15	15
86.0	5.702687	9	9
87.0	5.702687	11	11
88.0	5.702687	6	6
89.0	5.702687	13	13
90.0	5.702687	13	13
91.0	5.702687	11	11
92.0	5.702687	7	7
93.0	5.702687	7	7
94.0	5.702687	6	6
95.0	5.702687	4	4
96.0	5.702687	4	4
97.0	5.702687	4	4
98.0	5.702687	5	5
99.0	5.702687	8	8
100.0	5.702687	4	4
101.0	0	2	2
102.0	0	4	4
103.0	0	7	7
104.0	0	5	5
105.0	0	6	6
106.0	0	7	7
107.0	0	7	7
108.0	0	8	8
109.0	0	7	7
110.0	0	6	6
111.0	0	2	2
112.0	0	5	5
113.0	0	4	4
114.0	0	10	10
115.0	0	6	6
116.0	0	4	4
117.0	0	5	5
118.0	0	4	4
119.0	0	5	5
120.0	0	1	1
121.0	0	2	2
122.0	0	4	4
123.0	0	2	2
124.0	0	5	5
125.0	0	2	2
126.0	0	5	5
127.0	0	4	4
128.0	0	2	2
129.0	0	4	4
130.0	0	1	1
131.0	0	5	5
132.0	0	1	1
133.0	0	6	6
134.0	0	2	2
135.0	0	5	5
136.0	0	6	6
137.0	0	5	5
138.0	0	3	3
139.0	0	2	2
140.0	0	2	2
141.0	0	2	2
142.0	0	3	3
143.0	0	3	3
144.0	0	3	3
145.0	0	2	2
146.0	0	3	3
147.0	0	3	3
148.0	0	4	4
149.0	0	1	1
150.0	0	5	5
151.0	0	1	1
152.0	0	2	2
153.0	0	2	2
154.0	0	4	4
155.0	0	3	3
156.0	0	1	1
157.0	0	3	3
158.0	0	1	1
159.0	0	3	3
160.0	0	2	2
161.0	0	2	2
163.0	0	3	3
164.0	0	1	1
166.0	0	1	1
167.0	0	3	3
168.0	0	5	5
169.0	0	3	3
172.0	0	4	4
173.0	0	1	1
174.0	0	1	1
175.0	0	2	2
177.0	0	2	2
178.0	0	1	1
179.0	0	1	1
180.0	0	2	2
181.0	0	2	2
183.0	0	3	3
184.0	0	2	2
186.0	0	3	3
187.0	0	2	2
190.0	0	1	1
191.0	0	2	2
192.0	0	1	1
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	2	2
205.0	0	2	2
207.0	0	1	1
209.0	0	2	2
210.0	0	2	2
212.0	0	3	3
215.0	0	1	1
218.0	0	1	1
223.0	0	1	1
224.0	0	2	2
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
237.0	0	2	2
239.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
249.0	0	2	2
250.0	0	1	1
251.0	0	1	1
252.0	0	1	1
253.0	0	2	2
254.0	0	1	1
255.0	0	1	1
256.0	0	1	1
260.0	0	2	2
261.0	0	1	1
266.0	0	1	1
267.0	0	1	1
269.0	0	3	3
270.0	0	1	1
271.0	0	1	1
272.0	0	2	2
275.0	0	1	1
277.0	0	1	1
279.0	0	2	2
280.0	0	1	1
281.0	0	2	2
286.0	0	1	1
287.0	0	1	1
288.0	0	1	1
290.0	0	3	3
292.0	0	1	1
293.0	0	1	1
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
300.0	0	2	2
301.0	0	1	1
302.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
309.0	0	1	1
312.0	0	1	1
314.0	0	1	1
316.0	0	1	1
317.0	0	1	1
318.0	0	1	1
320.0	0	1	1
321.0	0	1	1
322.0	0	2	2
324.0	0	1	1
326.0	0	1	1
328.0	0	1	1
331.0	0	1	1
337.0	0	1	1
339.0	0	1	1
341.0	0	1	1
342.0	0	1	1
344.0	0	1	1
348.0	0	2	2
351.0	0	1	1
352.0	0	1	1
363.0	0	1	1
364.0	0	1	1
366.0	0	2	2
368.0	0	2	2
371.0	0	2	2
373.0	0	1	1
380.0	0	1	1
384.0	0	2	2
386.0	0	2	2
387.0	0	1	1
390.0	0	2	2
394.0	0	1	1
399.0	0	1	1
400.0	0	1	1
402.0	0	1	1
406.0	0	1	1
410.0	0	1	1
413.0	0	1	1
414.0	0	1	1
423.0	0	1	1
425.0	0	1	1
432.0	0	1	1
436.0	0	1	1
437.0	0	1	1
451.0	0	1	1
454.0	0	1	1
456.0	0	1	1
459.0	0	1	1
460.0	0	1	1
471.0	0	1	1
473.0	0	1	1
476.0	0	1	1
482.0	0	1	1
486.0	0	1	1
490.0	0	2	2
506.0	0	1	1
518.0	0	1	1
520.0	0	1	1
523.0	0	1	1
551.0	0	1	1
559.0	0	1	1
562.0	0	1	1
570.0	0	1	1
579.0	0	1	1
600.0	0	1	1
605.0	0	1	1
609.0	0	1	1
622.0	0	1	1
662.0	0	1	1
669.0	0	1	1
711.0	0	1	1
819.0	0	1	1