## 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-GSM919954.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919954.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919954.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 15:44:31 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	10258870	1919620	0	0	2238641	0	0.218215	19945336

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7077508	7077508
2.0	1.597889	603213	603213
3.0	1.955361	151199	151199
4.0	2.16909	65214	65214
5.0	2.296876	35010	35010
6.0	2.373278	21771	21771
7.0	2.418958	14403	14403
8.0	2.44627	10141	10141
9.0	2.462599	7339	7339
10.0	2.472362	5430	5430
11.0	2.478199	4184	4184
12.0	2.481689	3458	3458
13.0	2.483776	2797	2797
14.0	2.485024	2238	2238
15.0	2.48577	1752	1752
16.0	2.486216	1632	1632
17.0	2.486482	1317	1317
18.0	2.486642	1166	1166
19.0	2.486737	1010	1010
20.0	2.486794	836	836
21.0	2.486828	676	676
22.0	2.486848	643	643
23.0	2.486861	563	563
24.0	2.486868	513	513
25.0	2.486872	444	444
26.0	2.486875	395	395
27.0	2.486876	350	350
28.0	2.486877	352	352
29.0	2.486878	307	307
30.0	2.486878	254	254
31.0	2.486878	255	255
32.0	2.486878	240	240
33.0	2.486879	212	212
34.0	2.486879	179	179
35.0	2.486879	173	173
36.0	2.486879	160	160
37.0	2.486879	146	146
38.0	2.486879	133	133
39.0	2.486879	136	136
40.0	2.486879	140	140
41.0	2.486879	111	111
42.0	2.486879	118	118
43.0	2.486879	86	86
44.0	2.486879	103	103
45.0	2.486879	93	93
46.0	2.486879	76	76
47.0	2.486879	74	74
48.0	2.486879	67	67
49.0	2.486879	55	55
50.0	2.486879	58	58
51.0	2.486879	52	52
52.0	2.486879	49	49
53.0	2.486879	53	53
54.0	2.486879	37	37
55.0	2.486879	49	49
56.0	2.486879	46	46
57.0	2.486879	42	42
58.0	2.486879	48	48
59.0	2.486879	40	40
60.0	2.486879	34	34
61.0	2.486879	43	43
62.0	2.486879	26	26
63.0	2.486879	29	29
64.0	2.486879	23	23
65.0	2.486879	32	32
66.0	2.486879	43	43
67.0	2.486879	22	22
68.0	2.486879	24	24
69.0	2.486879	25	25
70.0	2.486879	24	24
71.0	2.486879	16	16
72.0	2.486879	21	21
73.0	2.486879	16	16
74.0	2.486879	22	22
75.0	2.486879	18	18
76.0	2.486879	18	18
77.0	2.486879	19	19
78.0	2.486879	15	15
79.0	2.486879	12	12
80.0	2.486879	13	13
81.0	2.486879	11	11
82.0	2.486879	18	18
83.0	2.486879	18	18
84.0	2.486879	17	17
85.0	2.486879	7	7
86.0	2.486879	15	15
87.0	2.486879	8	8
88.0	2.486879	10	10
89.0	2.486879	12	12
90.0	2.486879	9	9
91.0	2.486879	15	15
92.0	2.486879	7	7
93.0	2.486879	6	6
94.0	2.486879	7	7
95.0	2.486879	7	7
96.0	2.486879	5	5
97.0	2.486879	9	9
98.0	2.486879	10	10
99.0	2.486879	6	6
100.0	2.486879	6	6
101.0	0	6	6
102.0	0	5	5
103.0	0	7	7
104.0	0	7	7
105.0	0	11	11
106.0	0	9	9
107.0	0	3	3
108.0	0	7	7
109.0	0	7	7
110.0	0	13	13
111.0	0	5	5
112.0	0	7	7
113.0	0	3	3
114.0	0	1	1
115.0	0	9	9
116.0	0	3	3
117.0	0	10	10
118.0	0	4	4
119.0	0	4	4
120.0	0	5	5
121.0	0	8	8
122.0	0	3	3
123.0	0	3	3
124.0	0	2	2
125.0	0	7	7
126.0	0	2	2
127.0	0	6	6
128.0	0	8	8
129.0	0	7	7
130.0	0	3	3
131.0	0	3	3
132.0	0	1	1
133.0	0	4	4
134.0	0	6	6
135.0	0	2	2
136.0	0	2	2
137.0	0	2	2
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
141.0	0	4	4
142.0	0	2	2
143.0	0	1	1
144.0	0	1	1
145.0	0	1	1
146.0	0	4	4
147.0	0	2	2
149.0	0	2	2
150.0	0	4	4
151.0	0	1	1
152.0	0	3	3
153.0	0	2	2
154.0	0	1	1
155.0	0	3	3
156.0	0	3	3
158.0	0	1	1
159.0	0	3	3
160.0	0	4	4
161.0	0	5	5
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
170.0	0	2	2
171.0	0	3	3
173.0	0	5	5
174.0	0	1	1
175.0	0	3	3
176.0	0	3	3
177.0	0	2	2
178.0	0	1	1
179.0	0	1	1
182.0	0	2	2
183.0	0	4	4
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	2	2
193.0	0	2	2
194.0	0	1	1
196.0	0	2	2
197.0	0	1	1
198.0	0	2	2
200.0	0	1	1
202.0	0	1	1
204.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
210.0	0	1	1
212.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	2	2
219.0	0	1	1
221.0	0	1	1
222.0	0	1	1
225.0	0	1	1
229.0	0	1	1
230.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
236.0	0	2	2
241.0	0	1	1
242.0	0	1	1
247.0	0	1	1
255.0	0	1	1
257.0	0	1	1
261.0	0	3	3
265.0	0	1	1
267.0	0	1	1
270.0	0	1	1
271.0	0	1	1
273.0	0	1	1
275.0	0	1	1
287.0	0	2	2
290.0	0	1	1
296.0	0	1	1
306.0	0	1	1
312.0	0	1	1
326.0	0	1	1
328.0	0	1	1
334.0	0	1	1
337.0	0	2	2
349.0	0	1	1
361.0	0	1	1
374.0	0	1	1
387.0	0	2	2
391.0	0	1	1
404.0	0	1	1
405.0	0	1	1
426.0	0	1	1
478.0	0	1	1
488.0	0	1	1
503.0	0	1	1
515.0	0	1	1
524.0	0	1	1
532.0	0	1	1
535.0	0	1	1
542.0	0	1	1
551.0	0	1	1
679.0	0	1	1
680.0	0	1	1
728.0	0	1	1
750.0	0	1	1
761.0	0	1	1
817.0	0	1	1
840.0	0	1	1
879.0	0	1	1
906.0	0	1	1
923.0	0	1	1
932.0	0	1	1
945.0	0	1	1
959.0	0	1	1
1305.0	0	1	1
1386.0	0	1	1
2773.0	0	1	1
3709.0	0	1	1