## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-10-20/ES_Ler_Gim_1_2014-10-20.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-10-20/ES_Ler_Gim_1_2014-10-20.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Ler_Gim_1_2014-10-20/ES_Ler_Gim_1_2014-10-20.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 08:48:51 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	6192384	21279182	0	0	1242715	672238	0	0.05307	329657101

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	19562699	19562699
2.0	1.93749	462378	462378
3.0	2.816377	10470	10470
4.0	3.640324	1168	1168
5.0	4.412767	573	573
6.0	5.136924	395	395
7.0	5.815813	292	292
8.0	6.452266	205	205
9.0	7.048933	192	192
10.0	7.608302	167	167
11.0	8.132706	130	130
12.0	8.624328	108	108
13.0	9.085219	91	91
14.0	9.5173	110	110
15.0	9.922371	86	86
16.0	10.302122	51	51
17.0	10.658134	66	66
18.0	10.991891	58	58
19.0	11.304785	55	55
20.0	11.598121	55	55
21.0	11.873119	43	43
22.0	12.130928	52	52
23.0	12.372621	40	40
24.0	12.599205	50	50
25.0	12.811626	33	33
26.0	13.010768	34	34
27.0	13.197462	31	31
28.0	13.372485	26	26
29.0	13.536568	32	32
30.0	13.690394	24	24
31.0	13.834604	31	31
32.0	13.9698	24	24
33.0	14.096544	22	22
34.0	14.215366	27	27
35.0	14.32676	20	20
36.0	14.431191	22	22
37.0	14.529094	20	20
38.0	14.620877	10	10
39.0	14.706922	21	21
40.0	14.787589	27	27
41.0	14.863213	16	16
42.0	14.93411	24	24
43.0	15.000575	15	15
44.0	15.062886	7	7
45.0	15.121301	12	12
46.0	15.176065	14	14
47.0	15.227406	12	12
48.0	15.275537	15	15
49.0	15.320659	13	13
50.0	15.362961	14	14
51.0	15.402619	6	6
52.0	15.439798	14	14
53.0	15.474652	8	8
54.0	15.507328	17	17
55.0	15.537961	8	8
56.0	15.56668	10	10
57.0	15.593603	10	10
58.0	15.618843	9	9
59.0	15.642505	10	10
60.0	15.664689	9	9
61.0	15.685485	13	13
62.0	15.704982	9	9
63.0	15.72326	8	8
64.0	15.740395	13	13
65.0	15.756459	13	13
66.0	15.771519	11	11
67.0	15.785638	7	7
68.0	15.798874	5	5
69.0	15.811282	10	10
70.0	15.822915	13	13
71.0	15.833821	5	5
72.0	15.844045	7	7
73.0	15.85363	8	8
74.0	15.862616	7	7
75.0	15.87104	4	4
76.0	15.878937	2	2
77.0	15.886341	9	9
78.0	15.893282	4	4
79.0	15.899789	4	4
80.0	15.90589	4	4
81.0	15.911609	6	6
82.0	15.91697	12	12
83.0	15.921997	9	9
84.0	15.926709	4	4
85.0	15.931127	4	4
86.0	15.935268	6	6
87.0	15.939151	5	5
88.0	15.942791	4	4
89.0	15.946203	3	3
90.0	15.949402	5	5
91.0	15.952401	2	2
92.0	15.955213	3	3
93.0	15.957849	3	3
94.0	15.96032	2	2
95.0	15.962636	5	5
96.0	15.964808	5	5
97.0	15.966844	10	10
98.0	15.968753	4	4
99.0	15.970542	7	7
100.0	15.97222	3	3
101.0	0	8	8
102.0	0	4	4
103.0	0	5	5
104.0	0	3	3
105.0	0	4	4
106.0	0	1	1
107.0	0	4	4
108.0	0	5	5
109.0	0	1	1
110.0	0	3	3
111.0	0	3	3
112.0	0	2	2
113.0	0	6	6
114.0	0	2	2
115.0	0	4	4
116.0	0	1	1
117.0	0	7	7
118.0	0	2	2
119.0	0	4	4
120.0	0	4	4
121.0	0	6	6
122.0	0	3	3
123.0	0	4	4
124.0	0	2	2
125.0	0	4	4
126.0	0	3	3
127.0	0	4	4
128.0	0	1	1
132.0	0	5	5
133.0	0	3	3
135.0	0	6	6
137.0	0	5	5
138.0	0	4	4
139.0	0	2	2
140.0	0	2	2
141.0	0	1	1
142.0	0	3	3
143.0	0	5	5
144.0	0	2	2
145.0	0	4	4
146.0	0	2	2
148.0	0	2	2
149.0	0	2	2
151.0	0	1	1
152.0	0	6	6
153.0	0	2	2
154.0	0	1	1
156.0	0	3	3
157.0	0	1	1
158.0	0	4	4
159.0	0	1	1
160.0	0	3	3
162.0	0	2	2
163.0	0	3	3
164.0	0	3	3
165.0	0	1	1
166.0	0	3	3
167.0	0	3	3
168.0	0	1	1
169.0	0	1	1
171.0	0	5	5
173.0	0	1	1
174.0	0	2	2
175.0	0	1	1
176.0	0	4	4
179.0	0	1	1
180.0	0	2	2
181.0	0	2	2
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	3	3
186.0	0	1	1
188.0	0	4	4
189.0	0	3	3
190.0	0	3	3
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
194.0	0	3	3
195.0	0	1	1
196.0	0	3	3
197.0	0	6	6
198.0	0	4	4
200.0	0	3	3
202.0	0	5	5
203.0	0	1	1
204.0	0	3	3
205.0	0	1	1
206.0	0	1	1
207.0	0	2	2
208.0	0	1	1
209.0	0	1	1
210.0	0	3	3
211.0	0	2	2
212.0	0	1	1
214.0	0	2	2
217.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	6	6
223.0	0	1	1
224.0	0	2	2
227.0	0	1	1
228.0	0	2	2
229.0	0	2	2
230.0	0	1	1
231.0	0	3	3
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	3	3
236.0	0	4	4
237.0	0	1	1
238.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	2	2
243.0	0	2	2
244.0	0	2	2
247.0	0	2	2
248.0	0	1	1
249.0	0	2	2
251.0	0	1	1
253.0	0	2	2
254.0	0	2	2
257.0	0	2	2
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	1	1
265.0	0	1	1
266.0	0	2	2
268.0	0	1	1
270.0	0	1	1
271.0	0	2	2
275.0	0	1	1
278.0	0	3	3
280.0	0	1	1
281.0	0	2	2
282.0	0	2	2
283.0	0	1	1
284.0	0	1	1
287.0	0	1	1
289.0	0	1	1
291.0	0	1	1
293.0	0	1	1
295.0	0	1	1
297.0	0	1	1
300.0	0	3	3
303.0	0	1	1
311.0	0	2	2
312.0	0	1	1
313.0	0	1	1
314.0	0	2	2
316.0	0	2	2
317.0	0	1	1
320.0	0	2	2
321.0	0	2	2
324.0	0	1	1
326.0	0	2	2
327.0	0	1	1
328.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	2	2
333.0	0	1	1
334.0	0	1	1
337.0	0	1	1
338.0	0	2	2
339.0	0	2	2
340.0	0	1	1
343.0	0	1	1
346.0	0	1	1
351.0	0	1	1
355.0	0	1	1
357.0	0	2	2
358.0	0	2	2
359.0	0	2	2
381.0	0	1	1
382.0	0	2	2
384.0	0	2	2
386.0	0	1	1
387.0	0	2	2
388.0	0	1	1
394.0	0	1	1
395.0	0	1	1
399.0	0	1	1
405.0	0	1	1
408.0	0	1	1
412.0	0	1	1
417.0	0	1	1
419.0	0	1	1
424.0	0	1	1
425.0	0	1	1
429.0	0	1	1
431.0	0	1	1
433.0	0	4	4
440.0	0	1	1
441.0	0	2	2
457.0	0	2	2
466.0	0	1	1
478.0	0	2	2
490.0	0	1	1
497.0	0	1	1
503.0	0	1	1
506.0	0	1	1
508.0	0	1	1
516.0	0	1	1
518.0	0	1	1
525.0	0	1	1
531.0	0	1	1
535.0	0	1	1
539.0	0	1	1
548.0	0	1	1
554.0	0	2	2
559.0	0	1	1
575.0	0	1	1
590.0	0	1	1
598.0	0	2	2
609.0	0	2	2
613.0	0	1	1
614.0	0	1	1
615.0	0	1	1
622.0	0	1	1
624.0	0	1	1
636.0	0	1	1
638.0	0	1	1
651.0	0	1	1
691.0	0	1	1
699.0	0	1	1
711.0	0	1	1
712.0	0	1	1
721.0	0	1	1
747.0	0	1	1
760.0	0	1	1
765.0	0	1	1
766.0	0	1	1
863.0	0	1	1
903.0	0	1	1
931.0	0	1	1
941.0	0	1	1
981.0	0	1	1