## 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-GSM919951.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919951.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919951.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 15:37:13 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	10517375	1942728	0	0	2281934	0	0.216968	20587387

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7270713	7270713
2.0	1.599976	628826	628826
3.0	1.959948	152380	152380
4.0	2.175923	63921	63921
5.0	2.305502	34258	34258
6.0	2.383247	20876	20876
7.0	2.429892	13727	13727
8.0	2.457878	9656	9656
9.0	2.474669	7061	7061
10.0	2.484743	5345	5345
11.0	2.490787	4156	4156
12.0	2.494413	3293	3293
13.0	2.496589	2605	2605
14.0	2.497894	2160	2160
15.0	2.498678	1818	1818
16.0	2.499148	1514	1514
17.0	2.49943	1311	1311
18.0	2.499599	1083	1083
19.0	2.4997	958	958
20.0	2.499761	822	822
21.0	2.499798	711	711
22.0	2.49982	645	645
23.0	2.499833	573	573
24.0	2.499841	515	515
25.0	2.499845	458	458
26.0	2.499848	375	375
27.0	2.49985	404	404
28.0	2.499851	326	326
29.0	2.499851	279	279
30.0	2.499852	300	300
31.0	2.499852	262	262
32.0	2.499852	234	234
33.0	2.499852	215	215
34.0	2.499852	194	194
35.0	2.499852	168	168
36.0	2.499852	164	164
37.0	2.499852	147	147
38.0	2.499852	139	139
39.0	2.499852	140	140
40.0	2.499852	115	115
41.0	2.499852	138	138
42.0	2.499852	119	119
43.0	2.499852	107	107
44.0	2.499852	89	89
45.0	2.499852	98	98
46.0	2.499852	73	73
47.0	2.499852	77	77
48.0	2.499852	69	69
49.0	2.499852	67	67
50.0	2.499852	57	57
51.0	2.499852	59	59
52.0	2.499852	55	55
53.0	2.499852	57	57
54.0	2.499852	59	59
55.0	2.499852	48	48
56.0	2.499852	47	47
57.0	2.499852	50	50
58.0	2.499852	42	42
59.0	2.499852	44	44
60.0	2.499852	31	31
61.0	2.499852	42	42
62.0	2.499852	34	34
63.0	2.499852	31	31
64.0	2.499852	48	48
65.0	2.499852	25	25
66.0	2.499852	33	33
67.0	2.499852	33	33
68.0	2.499852	18	18
69.0	2.499852	25	25
70.0	2.499852	19	19
71.0	2.499852	25	25
72.0	2.499852	17	17
73.0	2.499852	20	20
74.0	2.499852	23	23
75.0	2.499852	22	22
76.0	2.499852	30	30
77.0	2.499852	14	14
78.0	2.499852	17	17
79.0	2.499852	10	10
80.0	2.499852	20	20
81.0	2.499852	12	12
82.0	2.499852	13	13
83.0	2.499852	16	16
84.0	2.499852	17	17
85.0	2.499852	17	17
86.0	2.499852	17	17
87.0	2.499852	10	10
88.0	2.499852	17	17
89.0	2.499852	8	8
90.0	2.499852	13	13
91.0	2.499852	13	13
92.0	2.499852	3	3
93.0	2.499852	18	18
94.0	2.499852	11	11
95.0	2.499852	14	14
96.0	2.499852	5	5
97.0	2.499852	10	10
98.0	2.499852	8	8
99.0	2.499852	7	7
100.0	2.499852	16	16
101.0	0	11	11
102.0	0	8	8
103.0	0	10	10
104.0	0	4	4
105.0	0	6	6
106.0	0	1	1
107.0	0	9	9
108.0	0	7	7
109.0	0	7	7
110.0	0	6	6
111.0	0	4	4
112.0	0	11	11
113.0	0	9	9
114.0	0	5	5
115.0	0	5	5
116.0	0	6	6
117.0	0	5	5
118.0	0	7	7
119.0	0	6	6
120.0	0	6	6
121.0	0	4	4
122.0	0	3	3
123.0	0	6	6
124.0	0	2	2
125.0	0	3	3
126.0	0	1	1
127.0	0	6	6
128.0	0	1	1
129.0	0	4	4
130.0	0	6	6
131.0	0	7	7
132.0	0	4	4
133.0	0	2	2
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
137.0	0	2	2
139.0	0	4	4
140.0	0	6	6
141.0	0	1	1
142.0	0	3	3
143.0	0	6	6
144.0	0	3	3
145.0	0	2	2
146.0	0	4	4
147.0	0	4	4
148.0	0	2	2
150.0	0	3	3
151.0	0	1	1
152.0	0	3	3
153.0	0	1	1
154.0	0	1	1
155.0	0	2	2
156.0	0	3	3
157.0	0	4	4
158.0	0	7	7
160.0	0	3	3
163.0	0	1	1
164.0	0	2	2
165.0	0	3	3
167.0	0	2	2
169.0	0	3	3
170.0	0	1	1
171.0	0	1	1
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	3	3
177.0	0	4	4
178.0	0	4	4
179.0	0	1	1
180.0	0	3	3
181.0	0	3	3
182.0	0	1	1
183.0	0	1	1
184.0	0	3	3
185.0	0	4	4
186.0	0	3	3
190.0	0	1	1
191.0	0	2	2
192.0	0	4	4
193.0	0	1	1
194.0	0	1	1
196.0	0	4	4
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	1	1
204.0	0	1	1
206.0	0	2	2
208.0	0	1	1
211.0	0	3	3
213.0	0	1	1
214.0	0	3	3
215.0	0	1	1
217.0	0	1	1
218.0	0	3	3
219.0	0	1	1
220.0	0	2	2
222.0	0	1	1
223.0	0	3	3
224.0	0	5	5
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	2	2
230.0	0	1	1
236.0	0	1	1
240.0	0	1	1
244.0	0	1	1
248.0	0	1	1
249.0	0	1	1
251.0	0	1	1
252.0	0	1	1
254.0	0	3	3
259.0	0	1	1
263.0	0	2	2
267.0	0	2	2
268.0	0	3	3
270.0	0	1	1
275.0	0	1	1
276.0	0	1	1
279.0	0	1	1
281.0	0	1	1
286.0	0	1	1
296.0	0	2	2
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
320.0	0	1	1
323.0	0	1	1
326.0	0	1	1
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
335.0	0	1	1
345.0	0	1	1
369.0	0	1	1
378.0	0	1	1
381.0	0	1	1
386.0	0	2	2
393.0	0	1	1
413.0	0	1	1
415.0	0	1	1
417.0	0	1	1
423.0	0	1	1
437.0	0	1	1
453.0	0	1	1
454.0	0	1	1
476.0	0	1	1
478.0	0	2	2
479.0	0	1	1
491.0	0	1	1
493.0	0	1	1
529.0	0	1	1
544.0	0	1	1
547.0	0	1	1
557.0	0	1	1
566.0	0	1	1
588.0	0	1	1
606.0	0	1	1
624.0	0	1	1
653.0	0	1	1
682.0	0	1	1
720.0	0	1	1
764.0	0	1	1
776.0	0	1	1
787.0	0	1	1
797.0	0	1	1
932.0	0	1	1
971.0	0	1	1
978.0	0	2	2
1050.0	0	1	1
1106.0	0	1	1
1110.0	0	1	1
1215.0	0	1	1
1216.0	0	1	1
1309.0	0	1	1
1332.0	0	1	1
1363.0	0	1	1
1371.0	0	1	1
1410.0	0	1	1
2120.0	0	1	1
2215.0	0	1	1
4099.0	0	1	1
5636.0	0	1	1