## 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-GSM1606341.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606341.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606341.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 23:28:17 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	32695778	5034192	0	0	6117600	0	0.187107	76094710

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23489043	23489043
2.0	1.650722	2126515	2126515
3.0	2.074162	472421	472421
4.0	2.349704	185973	185973
5.0	2.529005	95508	95508
6.0	2.64568	55992	55992
7.0	2.721603	35937	35937
8.0	2.771008	24173	24173
9.0	2.803157	17447	17447
10.0	2.824077	12841	12841
11.0	2.83769	9930	9930
12.0	2.846549	7852	7852
13.0	2.852313	6214	6214
14.0	2.856064	5038	5038
15.0	2.858505	4103	4103
16.0	2.860093	3329	3329
17.0	2.861127	2815	2815
18.0	2.861799	2375	2375
19.0	2.862237	2110	2110
20.0	2.862522	1805	1805
21.0	2.862707	1567	1567
22.0	2.862827	1322	1322
23.0	2.862906	1191	1191
24.0	2.862957	1032	1032
25.0	2.86299	988	988
26.0	2.863012	807	807
27.0	2.863026	774	774
28.0	2.863035	663	663
29.0	2.863041	597	597
30.0	2.863045	547	547
31.0	2.863047	485	485
32.0	2.863049	448	448
33.0	2.86305	385	385
34.0	2.863051	389	389
35.0	2.863051	325	325
36.0	2.863052	314	314
37.0	2.863052	303	303
38.0	2.863052	251	251
39.0	2.863052	269	269
40.0	2.863052	241	241
41.0	2.863052	192	192
42.0	2.863052	208	208
43.0	2.863052	185	185
44.0	2.863052	176	176
45.0	2.863052	143	143
46.0	2.863052	151	151
47.0	2.863052	132	132
48.0	2.863052	136	136
49.0	2.863052	129	129
50.0	2.863052	107	107
51.0	2.863052	95	95
52.0	2.863052	89	89
53.0	2.863052	103	103
54.0	2.863052	93	93
55.0	2.863052	92	92
56.0	2.863052	84	84
57.0	2.863052	84	84
58.0	2.863052	65	65
59.0	2.863052	73	73
60.0	2.863052	70	70
61.0	2.863052	46	46
62.0	2.863052	50	50
63.0	2.863052	55	55
64.0	2.863052	47	47
65.0	2.863052	50	50
66.0	2.863052	43	43
67.0	2.863052	39	39
68.0	2.863052	37	37
69.0	2.863052	45	45
70.0	2.863052	33	33
71.0	2.863052	46	46
72.0	2.863052	37	37
73.0	2.863052	33	33
74.0	2.863052	30	30
75.0	2.863052	29	29
76.0	2.863052	36	36
77.0	2.863052	19	19
78.0	2.863052	23	23
79.0	2.863052	19	19
80.0	2.863052	34	34
81.0	2.863052	23	23
82.0	2.863052	15	15
83.0	2.863052	17	17
84.0	2.863052	22	22
85.0	2.863052	17	17
86.0	2.863052	15	15
87.0	2.863052	18	18
88.0	2.863052	14	14
89.0	2.863052	15	15
90.0	2.863052	22	22
91.0	2.863052	14	14
92.0	2.863052	12	12
93.0	2.863052	17	17
94.0	2.863052	17	17
95.0	2.863052	10	10
96.0	2.863052	9	9
97.0	2.863052	12	12
98.0	2.863052	9	9
99.0	2.863052	9	9
100.0	2.863052	8	8
101.0	0	9	9
102.0	0	19	19
103.0	0	9	9
104.0	0	5	5
105.0	0	9	9
106.0	0	4	4
107.0	0	5	5
108.0	0	7	7
109.0	0	10	10
110.0	0	7	7
111.0	0	8	8
112.0	0	10	10
113.0	0	11	11
114.0	0	4	4
115.0	0	5	5
116.0	0	9	9
117.0	0	8	8
118.0	0	6	6
119.0	0	5	5
120.0	0	6	6
121.0	0	3	3
122.0	0	3	3
123.0	0	7	7
124.0	0	3	3
125.0	0	7	7
126.0	0	10	10
127.0	0	5	5
128.0	0	4	4
129.0	0	6	6
130.0	0	10	10
131.0	0	3	3
132.0	0	4	4
133.0	0	6	6
134.0	0	6	6
135.0	0	6	6
136.0	0	6	6
137.0	0	6	6
138.0	0	2	2
139.0	0	5	5
140.0	0	4	4
141.0	0	1	1
143.0	0	3	3
144.0	0	2	2
145.0	0	2	2
146.0	0	4	4
147.0	0	3	3
148.0	0	3	3
149.0	0	3	3
150.0	0	2	2
151.0	0	2	2
152.0	0	2	2
153.0	0	4	4
154.0	0	2	2
155.0	0	2	2
156.0	0	4	4
157.0	0	3	3
158.0	0	3	3
160.0	0	2	2
161.0	0	6	6
162.0	0	1	1
163.0	0	4	4
164.0	0	2	2
165.0	0	1	1
167.0	0	2	2
168.0	0	2	2
170.0	0	1	1
171.0	0	2	2
172.0	0	2	2
173.0	0	1	1
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
178.0	0	2	2
180.0	0	1	1
181.0	0	1	1
182.0	0	2	2
183.0	0	1	1
184.0	0	1	1
186.0	0	1	1
188.0	0	1	1
190.0	0	1	1
191.0	0	1	1
194.0	0	1	1
196.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	2	2
204.0	0	1	1
205.0	0	5	5
207.0	0	1	1
208.0	0	1	1
209.0	0	2	2
210.0	0	2	2
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
224.0	0	1	1
225.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	3	3
237.0	0	1	1
242.0	0	1	1
243.0	0	2	2
250.0	0	1	1
251.0	0	1	1
256.0	0	1	1
267.0	0	1	1
269.0	0	2	2
270.0	0	1	1
279.0	0	1	1
281.0	0	2	2
282.0	0	1	1
301.0	0	1	1
310.0	0	1	1
314.0	0	1	1
322.0	0	1	1
325.0	0	2	2
350.0	0	1	1
355.0	0	1	1
415.0	0	1	1
453.0	0	1	1
507.0	0	1	1
6192.0	0	1	1