## 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-GSM1606198.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606198.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606198.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 22:07:50 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	38382235	6578432	0	0	6429728	0	0.167518	101374026

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28696054	28696054
2.0	1.684806	2224761	2224761
3.0	2.153765	507460	507460
4.0	2.474911	200596	200596
5.0	2.694833	102849	102849
6.0	2.845437	60280	60280
7.0	2.948572	38226	38226
8.0	3.019199	26043	26043
9.0	3.067565	18746	18746
10.0	3.100686	13613	13613
11.0	3.123368	10416	10416
12.0	3.1389	7937	7937
13.0	3.149537	6522	6522
14.0	3.156821	5061	5061
15.0	3.161809	4145	4145
16.0	3.165225	3613	3613
17.0	3.167565	2995	2995
18.0	3.169167	2489	2489
19.0	3.170264	2169	2169
20.0	3.171015	1900	1900
21.0	3.171529	1595	1595
22.0	3.171882	1366	1366
23.0	3.172123	1225	1225
24.0	3.172288	1055	1055
25.0	3.172401	961	961
26.0	3.172479	792	792
27.0	3.172532	727	727
28.0	3.172568	686	686
29.0	3.172593	598	598
30.0	3.17261	508	508
31.0	3.172622	525	525
32.0	3.17263	425	425
33.0	3.172635	404	404
34.0	3.172639	358	358
35.0	3.172641	336	336
36.0	3.172643	348	348
37.0	3.172644	299	299
38.0	3.172645	262	262
39.0	3.172646	273	273
40.0	3.172646	230	230
41.0	3.172646	197	197
42.0	3.172647	184	184
43.0	3.172647	150	150
44.0	3.172647	163	163
45.0	3.172647	154	154
46.0	3.172647	148	148
47.0	3.172647	149	149
48.0	3.172647	135	135
49.0	3.172647	109	109
50.0	3.172647	105	105
51.0	3.172647	99	99
52.0	3.172647	94	94
53.0	3.172647	90	90
54.0	3.172647	102	102
55.0	3.172647	74	74
56.0	3.172647	71	71
57.0	3.172647	65	65
58.0	3.172647	78	78
59.0	3.172647	62	62
60.0	3.172647	74	74
61.0	3.172647	48	48
62.0	3.172647	64	64
63.0	3.172647	50	50
64.0	3.172647	38	38
65.0	3.172647	47	47
66.0	3.172647	41	41
67.0	3.172647	49	49
68.0	3.172647	45	45
69.0	3.172647	43	43
70.0	3.172647	31	31
71.0	3.172647	33	33
72.0	3.172647	32	32
73.0	3.172647	38	38
74.0	3.172647	25	25
75.0	3.172647	31	31
76.0	3.172647	23	23
77.0	3.172647	22	22
78.0	3.172647	25	25
79.0	3.172647	20	20
80.0	3.172647	22	22
81.0	3.172647	22	22
82.0	3.172647	19	19
83.0	3.172647	19	19
84.0	3.172647	14	14
85.0	3.172647	19	19
86.0	3.172647	25	25
87.0	3.172647	12	12
88.0	3.172647	18	18
89.0	3.172647	15	15
90.0	3.172647	20	20
91.0	3.172647	13	13
92.0	3.172647	15	15
93.0	3.172647	11	11
94.0	3.172647	11	11
95.0	3.172647	9	9
96.0	3.172647	17	17
97.0	3.172647	7	7
98.0	3.172647	9	9
99.0	3.172647	13	13
100.0	3.172647	10	10
101.0	0	11	11
102.0	0	7	7
103.0	0	5	5
104.0	0	9	9
105.0	0	11	11
106.0	0	3	3
107.0	0	8	8
108.0	0	5	5
109.0	0	8	8
110.0	0	10	10
111.0	0	11	11
112.0	0	7	7
113.0	0	10	10
114.0	0	7	7
115.0	0	4	4
116.0	0	3	3
117.0	0	5	5
118.0	0	5	5
119.0	0	6	6
120.0	0	5	5
121.0	0	6	6
122.0	0	7	7
123.0	0	7	7
124.0	0	6	6
125.0	0	4	4
126.0	0	3	3
127.0	0	2	2
128.0	0	5	5
129.0	0	3	3
130.0	0	1	1
131.0	0	4	4
132.0	0	9	9
133.0	0	1	1
134.0	0	3	3
135.0	0	3	3
136.0	0	3	3
137.0	0	3	3
138.0	0	1	1
139.0	0	3	3
140.0	0	4	4
141.0	0	1	1
142.0	0	1	1
143.0	0	2	2
144.0	0	3	3
145.0	0	3	3
146.0	0	3	3
147.0	0	2	2
148.0	0	5	5
149.0	0	1	1
150.0	0	3	3
151.0	0	2	2
152.0	0	2	2
153.0	0	1	1
154.0	0	1	1
156.0	0	1	1
157.0	0	2	2
158.0	0	2	2
159.0	0	1	1
160.0	0	1	1
162.0	0	1	1
164.0	0	3	3
165.0	0	3	3
168.0	0	2	2
169.0	0	1	1
170.0	0	3	3
172.0	0	2	2
173.0	0	1	1
176.0	0	1	1
177.0	0	2	2
179.0	0	2	2
182.0	0	1	1
187.0	0	2	2
191.0	0	1	1
192.0	0	1	1
195.0	0	2	2
197.0	0	1	1
199.0	0	2	2
200.0	0	1	1
203.0	0	4	4
215.0	0	1	1
218.0	0	1	1
219.0	0	2	2
222.0	0	1	1
224.0	0	2	2
225.0	0	1	1
228.0	0	1	1
231.0	0	1	1
233.0	0	1	1
236.0	0	1	1
237.0	0	1	1
240.0	0	1	1
242.0	0	1	1
243.0	0	1	1
245.0	0	1	1
250.0	0	1	1
251.0	0	1	1
255.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	1	1
270.0	0	1	1
271.0	0	1	1
281.0	0	1	1
282.0	0	1	1
295.0	0	1	1
303.0	0	1	1
315.0	0	1	1
320.0	0	1	1
330.0	0	1	1
342.0	0	1	1
392.0	0	1	1
405.0	0	1	1
408.0	0	1	1
473.0	0	1	1
484.0	0	1	1
591.0	0	1	1
4114.0	0	1	1