## 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-GSM919949.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919949.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919949.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: Tue Nov 02 15:23:10 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	11724029	2288090	0	0	2345415	0	0.200052	25248067

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8319479	8319479
2.0	1.628541	692055	692055
3.0	2.023605	169055	169055
4.0	2.27192	70784	70784
5.0	2.427995	38068	38068
6.0	2.526095	22632	22632
7.0	2.587755	14902	14902
8.0	2.626511	10317	10317
9.0	2.650871	7388	7388
10.0	2.666182	5823	5823
11.0	2.675805	4430	4430
12.0	2.681854	3308	3308
13.0	2.685656	2630	2630
14.0	2.688046	2157	2157
15.0	2.689548	1845	1845
16.0	2.690492	1581	1581
17.0	2.691085	1283	1283
18.0	2.691458	1063	1063
19.0	2.691693	984	984
20.0	2.69184	858	858
21.0	2.691933	660	660
22.0	2.691991	665	665
23.0	2.692027	550	550
24.0	2.69205	489	489
25.0	2.692065	449	449
26.0	2.692074	369	369
27.0	2.69208	355	355
28.0	2.692083	306	306
29.0	2.692086	292	292
30.0	2.692087	248	248
31.0	2.692088	258	258
32.0	2.692088	187	187
33.0	2.692089	201	201
34.0	2.692089	172	172
35.0	2.692089	175	175
36.0	2.692089	145	145
37.0	2.692089	128	128
38.0	2.692089	141	141
39.0	2.692089	120	120
40.0	2.692089	110	110
41.0	2.692089	104	104
42.0	2.692089	80	80
43.0	2.692089	91	91
44.0	2.692089	68	68
45.0	2.692089	76	76
46.0	2.692089	71	71
47.0	2.692089	54	54
48.0	2.692089	55	55
49.0	2.692089	61	61
50.0	2.692089	59	59
51.0	2.692089	46	46
52.0	2.692089	57	57
53.0	2.692089	51	51
54.0	2.692089	51	51
55.0	2.692089	49	49
56.0	2.692089	38	38
57.0	2.692089	37	37
58.0	2.692089	32	32
59.0	2.692089	30	30
60.0	2.692089	42	42
61.0	2.692089	23	23
62.0	2.692089	27	27
63.0	2.692089	23	23
64.0	2.692089	26	26
65.0	2.692089	17	17
66.0	2.692089	27	27
67.0	2.692089	24	24
68.0	2.692089	22	22
69.0	2.692089	17	17
70.0	2.692089	20	20
71.0	2.692089	20	20
72.0	2.692089	17	17
73.0	2.692089	29	29
74.0	2.692089	15	15
75.0	2.692089	18	18
76.0	2.692089	10	10
77.0	2.692089	18	18
78.0	2.692089	11	11
79.0	2.692089	13	13
80.0	2.692089	12	12
81.0	2.692089	13	13
82.0	2.692089	16	16
83.0	2.692089	8	8
84.0	2.692089	6	6
85.0	2.692089	5	5
86.0	2.692089	6	6
87.0	2.692089	3	3
88.0	2.692089	7	7
89.0	2.692089	8	8
90.0	2.692089	8	8
91.0	2.692089	9	9
92.0	2.692089	10	10
93.0	2.692089	2	2
94.0	2.692089	5	5
95.0	2.692089	7	7
96.0	2.692089	8	8
97.0	2.692089	10	10
98.0	2.692089	5	5
99.0	2.692089	5	5
100.0	2.692089	6	6
101.0	0	4	4
102.0	0	7	7
103.0	0	2	2
104.0	0	4	4
105.0	0	4	4
106.0	0	8	8
107.0	0	6	6
108.0	0	5	5
109.0	0	3	3
110.0	0	3	3
111.0	0	3	3
112.0	0	1	1
113.0	0	3	3
114.0	0	6	6
115.0	0	4	4
116.0	0	5	5
117.0	0	7	7
118.0	0	6	6
119.0	0	4	4
120.0	0	3	3
121.0	0	5	5
122.0	0	6	6
123.0	0	2	2
124.0	0	2	2
125.0	0	2	2
126.0	0	2	2
127.0	0	1	1
129.0	0	2	2
130.0	0	2	2
131.0	0	2	2
133.0	0	3	3
134.0	0	3	3
135.0	0	3	3
136.0	0	5	5
137.0	0	2	2
138.0	0	2	2
139.0	0	3	3
140.0	0	1	1
141.0	0	3	3
142.0	0	1	1
143.0	0	4	4
144.0	0	3	3
145.0	0	2	2
146.0	0	4	4
147.0	0	1	1
149.0	0	2	2
150.0	0	2	2
151.0	0	4	4
152.0	0	2	2
153.0	0	1	1
154.0	0	1	1
155.0	0	3	3
156.0	0	1	1
157.0	0	2	2
158.0	0	5	5
159.0	0	2	2
161.0	0	1	1
163.0	0	2	2
164.0	0	2	2
166.0	0	1	1
167.0	0	2	2
168.0	0	2	2
170.0	0	2	2
172.0	0	1	1
173.0	0	1	1
176.0	0	1	1
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
184.0	0	1	1
188.0	0	1	1
192.0	0	2	2
194.0	0	1	1
198.0	0	1	1
200.0	0	1	1
204.0	0	1	1
208.0	0	3	3
214.0	0	1	1
217.0	0	2	2
222.0	0	2	2
224.0	0	1	1
225.0	0	1	1
226.0	0	1	1
229.0	0	1	1
232.0	0	2	2
233.0	0	2	2
235.0	0	1	1
241.0	0	1	1
242.0	0	1	1
245.0	0	1	1
250.0	0	1	1
254.0	0	1	1
257.0	0	1	1
258.0	0	1	1
261.0	0	1	1
266.0	0	2	2
278.0	0	2	2
280.0	0	1	1
281.0	0	1	1
298.0	0	1	1
303.0	0	1	1
319.0	0	1	1
340.0	0	1	1
350.0	0	1	1
357.0	0	1	1
361.0	0	1	1
375.0	0	1	1
378.0	0	1	1
399.0	0	1	1
400.0	0	1	1
406.0	0	1	1
411.0	0	1	1
417.0	0	1	1
423.0	0	1	1
441.0	0	1	1
509.0	0	1	1
644.0	0	1	1
646.0	0	1	1
783.0	0	1	1
1106.0	0	1	1
1107.0	0	1	1
1367.0	0	1	1
1497.0	0	1	1