## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606344.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606344.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606344.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp]    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 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 REMOVE_DUPLICATES=false 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 VALIDATION_STRINGENCY=STRICT 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: Mon Nov 01 21:14:21 CET 2021

## 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
Unknown Library	0	36848174	5428618	0	0	7470611	0	0.20274	78125512

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25879483	25879483
2.0	1.62397	2333510	2333510
3.0	2.013308	549911	549911
4.0	2.256243	224106	224106
5.0	2.407827	117440	117440
6.0	2.502411	70436	70436
7.0	2.561429	45514	45514
8.0	2.598254	31542	31542
9.0	2.621231	22674	22674
10.0	2.635569	16779	16779
11.0	2.644515	13160	13160
12.0	2.650097	10347	10347
13.0	2.65358	8098	8098
14.0	2.655754	6777	6777
15.0	2.65711	5678	5678
16.0	2.657956	4747	4747
17.0	2.658484	3961	3961
18.0	2.658813	3319	3319
19.0	2.659019	2703	2703
20.0	2.659147	2508	2508
21.0	2.659227	2194	2194
22.0	2.659277	1914	1914
23.0	2.659308	1789	1789
24.0	2.659328	1534	1534
25.0	2.65934	1328	1328
26.0	2.659347	1213	1213
27.0	2.659352	1129	1129
28.0	2.659355	996	996
29.0	2.659357	896	896
30.0	2.659358	755	755
31.0	2.659359	694	694
32.0	2.659359	697	697
33.0	2.659359	624	624
34.0	2.65936	564	564
35.0	2.65936	466	466
36.0	2.65936	452	452
37.0	2.65936	410	410
38.0	2.65936	426	426
39.0	2.65936	343	343
40.0	2.65936	311	311
41.0	2.65936	314	314
42.0	2.65936	296	296
43.0	2.65936	269	269
44.0	2.65936	287	287
45.0	2.65936	250	250
46.0	2.65936	199	199
47.0	2.65936	195	195
48.0	2.65936	203	203
49.0	2.65936	188	188
50.0	2.65936	163	163
51.0	2.65936	177	177
52.0	2.65936	134	134
53.0	2.65936	147	147
54.0	2.65936	144	144
55.0	2.65936	138	138
56.0	2.65936	115	115
57.0	2.65936	106	106
58.0	2.65936	99	99
59.0	2.65936	104	104
60.0	2.65936	96	96
61.0	2.65936	83	83
62.0	2.65936	100	100
63.0	2.65936	81	81
64.0	2.65936	89	89
65.0	2.65936	84	84
66.0	2.65936	77	77
67.0	2.65936	77	77
68.0	2.65936	61	61
69.0	2.65936	58	58
70.0	2.65936	51	51
71.0	2.65936	73	73
72.0	2.65936	55	55
73.0	2.65936	51	51
74.0	2.65936	56	56
75.0	2.65936	49	49
76.0	2.65936	41	41
77.0	2.65936	51	51
78.0	2.65936	43	43
79.0	2.65936	37	37
80.0	2.65936	34	34
81.0	2.65936	25	25
82.0	2.65936	36	36
83.0	2.65936	29	29
84.0	2.65936	35	35
85.0	2.65936	28	28
86.0	2.65936	29	29
87.0	2.65936	39	39
88.0	2.65936	25	25
89.0	2.65936	21	21
90.0	2.65936	28	28
91.0	2.65936	26	26
92.0	2.65936	24	24
93.0	2.65936	22	22
94.0	2.65936	23	23
95.0	2.65936	29	29
96.0	2.65936	22	22
97.0	2.65936	18	18
98.0	2.65936	21	21
99.0	2.65936	11	11
100.0	2.65936	15	15
101.0	0	21	21
102.0	0	14	14
103.0	0	21	21
104.0	0	16	16
105.0	0	16	16
106.0	0	29	29
107.0	0	14	14
108.0	0	23	23
109.0	0	23	23
110.0	0	20	20
111.0	0	12	12
112.0	0	13	13
113.0	0	17	17
114.0	0	13	13
115.0	0	14	14
116.0	0	9	9
117.0	0	10	10
118.0	0	9	9
119.0	0	7	7
120.0	0	9	9
121.0	0	9	9
122.0	0	6	6
123.0	0	7	7
124.0	0	8	8
125.0	0	2	2
126.0	0	11	11
127.0	0	5	5
128.0	0	7	7
129.0	0	6	6
130.0	0	6	6
131.0	0	8	8
132.0	0	6	6
133.0	0	2	2
134.0	0	10	10
135.0	0	6	6
136.0	0	11	11
137.0	0	6	6
138.0	0	11	11
139.0	0	9	9
140.0	0	6	6
141.0	0	6	6
142.0	0	4	4
143.0	0	10	10
144.0	0	3	3
145.0	0	6	6
146.0	0	3	3
147.0	0	7	7
148.0	0	2	2
149.0	0	6	6
150.0	0	2	2
151.0	0	3	3
152.0	0	3	3
153.0	0	8	8
154.0	0	7	7
155.0	0	8	8
156.0	0	3	3
157.0	0	1	1
158.0	0	2	2
159.0	0	3	3
160.0	0	4	4
161.0	0	6	6
162.0	0	5	5
163.0	0	2	2
164.0	0	5	5
165.0	0	3	3
166.0	0	5	5
168.0	0	3	3
169.0	0	4	4
170.0	0	2	2
171.0	0	5	5
172.0	0	4	4
173.0	0	3	3
174.0	0	2	2
175.0	0	1	1
176.0	0	3	3
177.0	0	3	3
178.0	0	2	2
179.0	0	2	2
181.0	0	1	1
182.0	0	5	5
183.0	0	6	6
184.0	0	1	1
185.0	0	3	3
186.0	0	2	2
187.0	0	4	4
189.0	0	3	3
190.0	0	2	2
191.0	0	3	3
192.0	0	2	2
193.0	0	3	3
197.0	0	3	3
200.0	0	3	3
201.0	0	1	1
202.0	0	5	5
203.0	0	3	3
204.0	0	2	2
205.0	0	1	1
206.0	0	2	2
208.0	0	1	1
209.0	0	1	1
211.0	0	2	2
212.0	0	3	3
213.0	0	2	2
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
224.0	0	1	1
225.0	0	2	2
226.0	0	2	2
227.0	0	1	1
229.0	0	2	2
230.0	0	1	1
232.0	0	1	1
233.0	0	3	3
234.0	0	1	1
236.0	0	1	1
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	2	2
247.0	0	1	1
248.0	0	4	4
252.0	0	1	1
255.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	2	2
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
280.0	0	1	1
283.0	0	1	1
286.0	0	1	1
290.0	0	1	1
292.0	0	1	1
298.0	0	1	1
299.0	0	1	1
301.0	0	1	1
304.0	0	1	1
306.0	0	1	1
307.0	0	2	2
309.0	0	1	1
314.0	0	1	1
321.0	0	1	1
326.0	0	1	1
330.0	0	1	1
333.0	0	1	1
359.0	0	1	1
360.0	0	1	1
363.0	0	1	1
373.0	0	1	1
379.0	0	1	1
405.0	0	1	1
406.0	0	2	2
411.0	0	1	1
416.0	0	1	1
456.0	0	1	1
488.0	0	1	1
494.0	0	1	1
496.0	0	1	1
513.0	0	1	1
520.0	0	1	1
604.0	0	1	1
659.0	0	1	1
713.0	0	1	1
11352.0	0	1	1