## 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-GSM1606204.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606204.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606204.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 13:33:16 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	33810272	5905536	0	0	4913770	0	0.145334	104752959

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	26439011	26439011
2.0	1.724146	1671655	1671655
3.0	2.248534	383721	383721
4.0	2.628267	153252	153252
5.0	2.90325	78503	78503
6.0	3.102377	45940	45940
7.0	3.246575	29380	29380
8.0	3.350995	20095	20095
9.0	3.42661	14389	14389
10.0	3.481367	10621	10621
11.0	3.521018	8040	8040
12.0	3.549732	6384	6384
13.0	3.570525	5029	5029
14.0	3.585582	4005	4005
15.0	3.596486	3287	3287
16.0	3.604381	2720	2720
17.0	3.610099	2306	2306
18.0	3.61424	1951	1951
19.0	3.617238	1671	1671
20.0	3.619409	1318	1318
21.0	3.620981	1278	1278
22.0	3.62212	1088	1088
23.0	3.622944	902	902
24.0	3.623541	823	823
25.0	3.623974	758	758
26.0	3.624287	642	642
27.0	3.624513	570	570
28.0	3.624678	545	545
29.0	3.624797	483	483
30.0	3.624883	418	418
31.0	3.624945	402	402
32.0	3.62499	343	343
33.0	3.625023	353	353
34.0	3.625046	320	320
35.0	3.625064	267	267
36.0	3.625076	235	235
37.0	3.625085	255	255
38.0	3.625092	209	209
39.0	3.625096	199	199
40.0	3.6251	167	167
41.0	3.625102	163	163
42.0	3.625104	131	131
43.0	3.625105	139	139
44.0	3.625106	125	125
45.0	3.625107	111	111
46.0	3.625107	100	100
47.0	3.625108	114	114
48.0	3.625108	99	99
49.0	3.625108	85	85
50.0	3.625108	90	90
51.0	3.625108	70	70
52.0	3.625108	82	82
53.0	3.625109	73	73
54.0	3.625109	76	76
55.0	3.625109	63	63
56.0	3.625109	59	59
57.0	3.625109	66	66
58.0	3.625109	48	48
59.0	3.625109	63	63
60.0	3.625109	49	49
61.0	3.625109	44	44
62.0	3.625109	42	42
63.0	3.625109	53	53
64.0	3.625109	41	41
65.0	3.625109	36	36
66.0	3.625109	33	33
67.0	3.625109	37	37
68.0	3.625109	30	30
69.0	3.625109	16	16
70.0	3.625109	27	27
71.0	3.625109	34	34
72.0	3.625109	34	34
73.0	3.625109	24	24
74.0	3.625109	23	23
75.0	3.625109	25	25
76.0	3.625109	17	17
77.0	3.625109	16	16
78.0	3.625109	13	13
79.0	3.625109	21	21
80.0	3.625109	12	12
81.0	3.625109	11	11
82.0	3.625109	23	23
83.0	3.625109	21	21
84.0	3.625109	13	13
85.0	3.625109	10	10
86.0	3.625109	13	13
87.0	3.625109	14	14
88.0	3.625109	24	24
89.0	3.625109	12	12
90.0	3.625109	14	14
91.0	3.625109	17	17
92.0	3.625109	8	8
93.0	3.625109	19	19
94.0	3.625109	6	6
95.0	3.625109	11	11
96.0	3.625109	13	13
97.0	3.625109	16	16
98.0	3.625109	10	10
99.0	3.625109	4	4
100.0	3.625109	8	8
101.0	0	10	10
102.0	0	12	12
103.0	0	13	13
104.0	0	11	11
105.0	0	7	7
106.0	0	5	5
107.0	0	13	13
108.0	0	6	6
109.0	0	5	5
110.0	0	4	4
111.0	0	5	5
112.0	0	5	5
113.0	0	7	7
114.0	0	3	3
115.0	0	4	4
116.0	0	6	6
117.0	0	5	5
118.0	0	6	6
119.0	0	2	2
120.0	0	5	5
121.0	0	2	2
122.0	0	4	4
123.0	0	10	10
124.0	0	5	5
125.0	0	1	1
126.0	0	3	3
127.0	0	6	6
128.0	0	5	5
129.0	0	4	4
130.0	0	1	1
131.0	0	2	2
133.0	0	3	3
134.0	0	3	3
135.0	0	1	1
136.0	0	2	2
137.0	0	7	7
138.0	0	1	1
139.0	0	6	6
140.0	0	1	1
141.0	0	1	1
142.0	0	4	4
144.0	0	3	3
145.0	0	4	4
146.0	0	3	3
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
151.0	0	1	1
152.0	0	3	3
154.0	0	1	1
155.0	0	3	3
156.0	0	3	3
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	3	3
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
170.0	0	2	2
171.0	0	2	2
172.0	0	2	2
175.0	0	2	2
176.0	0	3	3
180.0	0	1	1
181.0	0	2	2
183.0	0	2	2
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
189.0	0	1	1
191.0	0	1	1
192.0	0	1	1
194.0	0	1	1
196.0	0	2	2
197.0	0	1	1
199.0	0	1	1
204.0	0	2	2
206.0	0	2	2
207.0	0	1	1
210.0	0	1	1
214.0	0	1	1
215.0	0	2	2
216.0	0	1	1
218.0	0	1	1
220.0	0	1	1
224.0	0	1	1
226.0	0	1	1
230.0	0	1	1
234.0	0	2	2
235.0	0	1	1
240.0	0	1	1
245.0	0	1	1
247.0	0	1	1
248.0	0	1	1
254.0	0	1	1
257.0	0	1	1
266.0	0	1	1
274.0	0	1	1
275.0	0	1	1
287.0	0	1	1
290.0	0	1	1
308.0	0	1	1
309.0	0	1	1
346.0	0	1	1
349.0	0	1	1
350.0	0	1	1
406.0	0	1	1
407.0	0	1	1
411.0	0	1	1
482.0	0	1	1
543.0	0	1	1
4537.0	0	1	1