## 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-GSM1606221.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606221.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606221.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 22:06:51 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	33938689	5204900	0	0	4462042	0	0.131474	117490488

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	27181477	27181477
2.0	1.749115	1577740	1577740
3.0	2.310287	352869	352869
4.0	2.73067	140722	140722
5.0	3.045585	71903	71903
6.0	3.281492	42101	42101
7.0	3.458214	26754	26754
8.0	3.590598	18040	18040
9.0	3.68977	12769	12769
10.0	3.76406	9434	9434
11.0	3.819713	7203	7203
12.0	3.861403	5519	5519
13.0	3.892633	4414	4414
14.0	3.916028	3588	3588
15.0	3.933554	2852	2852
16.0	3.946683	2420	2420
17.0	3.956518	2060	2060
18.0	3.963885	1636	1636
19.0	3.969404	1453	1453
20.0	3.973539	1161	1161
21.0	3.976636	1030	1030
22.0	3.978956	902	902
23.0	3.980694	794	794
24.0	3.981996	662	662
25.0	3.982971	588	588
26.0	3.983702	552	552
27.0	3.984249	521	521
28.0	3.984659	424	424
29.0	3.984967	392	392
30.0	3.985197	317	317
31.0	3.985369	303	303
32.0	3.985498	260	260
33.0	3.985595	275	275
34.0	3.985667	240	240
35.0	3.985722	226	226
36.0	3.985762	170	170
37.0	3.985793	181	181
38.0	3.985816	177	177
39.0	3.985833	142	142
40.0	3.985846	128	128
41.0	3.985855	138	138
42.0	3.985862	130	130
43.0	3.985868	93	93
44.0	3.985872	101	101
45.0	3.985875	91	91
46.0	3.985877	81	81
47.0	3.985879	95	95
48.0	3.98588	90	90
49.0	3.985881	81	81
50.0	3.985882	63	63
51.0	3.985882	64	64
52.0	3.985883	55	55
53.0	3.985883	44	44
54.0	3.985883	51	51
55.0	3.985883	46	46
56.0	3.985883	47	47
57.0	3.985883	40	40
58.0	3.985884	40	40
59.0	3.985884	50	50
60.0	3.985884	31	31
61.0	3.985884	34	34
62.0	3.985884	34	34
63.0	3.985884	37	37
64.0	3.985884	33	33
65.0	3.985884	31	31
66.0	3.985884	31	31
67.0	3.985884	33	33
68.0	3.985884	16	16
69.0	3.985884	16	16
70.0	3.985884	23	23
71.0	3.985884	15	15
72.0	3.985884	17	17
73.0	3.985884	14	14
74.0	3.985884	13	13
75.0	3.985884	19	19
76.0	3.985884	17	17
77.0	3.985884	9	9
78.0	3.985884	13	13
79.0	3.985884	17	17
80.0	3.985884	9	9
81.0	3.985884	13	13
82.0	3.985884	7	7
83.0	3.985884	7	7
84.0	3.985884	8	8
85.0	3.985884	8	8
86.0	3.985884	7	7
87.0	3.985884	14	14
88.0	3.985884	9	9
89.0	3.985884	5	5
90.0	3.985884	8	8
91.0	3.985884	9	9
92.0	3.985884	9	9
93.0	3.985884	9	9
94.0	3.985884	10	10
95.0	3.985884	7	7
96.0	3.985884	6	6
97.0	3.985884	8	8
98.0	3.985884	5	5
99.0	3.985884	2	2
100.0	3.985884	9	9
101.0	0	4	4
102.0	0	3	3
103.0	0	8	8
104.0	0	6	6
105.0	0	1	1
106.0	0	5	5
107.0	0	3	3
108.0	0	4	4
109.0	0	5	5
110.0	0	9	9
111.0	0	5	5
112.0	0	4	4
113.0	0	8	8
114.0	0	4	4
115.0	0	7	7
116.0	0	4	4
117.0	0	4	4
118.0	0	5	5
119.0	0	1	1
120.0	0	4	4
121.0	0	2	2
122.0	0	1	1
123.0	0	4	4
124.0	0	1	1
125.0	0	3	3
126.0	0	3	3
127.0	0	3	3
128.0	0	3	3
129.0	0	4	4
130.0	0	2	2
131.0	0	5	5
133.0	0	6	6
134.0	0	2	2
137.0	0	3	3
138.0	0	1	1
139.0	0	4	4
140.0	0	2	2
141.0	0	3	3
142.0	0	1	1
143.0	0	2	2
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
149.0	0	1	1
150.0	0	2	2
152.0	0	1	1
153.0	0	1	1
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
165.0	0	1	1
166.0	0	2	2
168.0	0	2	2
169.0	0	1	1
170.0	0	3	3
171.0	0	4	4
173.0	0	2	2
176.0	0	1	1
178.0	0	1	1
180.0	0	1	1
181.0	0	2	2
182.0	0	1	1
184.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	1	1
196.0	0	1	1
199.0	0	1	1
202.0	0	1	1
206.0	0	1	1
207.0	0	1	1
210.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
219.0	0	1	1
224.0	0	1	1
226.0	0	2	2
228.0	0	2	2
229.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
258.0	0	1	1
261.0	0	1	1
326.0	0	1	1
338.0	0	1	1
343.0	0	1	1
368.0	0	1	1
375.0	0	1	1
409.0	0	1	1
425.0	0	1	1
442.0	0	1	1
597.0	0	1	1
6260.0	0	1	1