## 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-GSM919935.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919935.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919935.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 15:23:39 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	11742705	2181960	0	0	2025440	0	0.172485	30001317

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8810093	8810093
2.0	1.676105	565811	565811
3.0	2.133224	156037	156037
4.0	2.442284	68333	68333
5.0	2.651241	36436	36436
6.0	2.792519	21947	21947
7.0	2.888037	13820	13820
8.0	2.952617	9614	9614
9.0	2.99628	6849	6849
10.0	3.025801	5037	5037
11.0	3.045761	3785	3785
12.0	3.059255	3079	3079
13.0	3.068379	2399	2399
14.0	3.074547	1952	1952
15.0	3.078718	1517	1517
16.0	3.081538	1338	1338
17.0	3.083444	1112	1112
18.0	3.084733	906	906
19.0	3.085605	792	792
20.0	3.086194	608	608
21.0	3.086592	558	558
22.0	3.086862	487	487
23.0	3.087044	415	415
24.0	3.087167	374	374
25.0	3.08725	303	303
26.0	3.087307	292	292
27.0	3.087345	258	258
28.0	3.08737	225	225
29.0	3.087388	201	201
30.0	3.087399	192	192
31.0	3.087407	192	192
32.0	3.087413	164	164
33.0	3.087416	146	146
34.0	3.087419	122	122
35.0	3.087421	124	124
36.0	3.087422	104	104
37.0	3.087422	92	92
38.0	3.087423	99	99
39.0	3.087423	75	75
40.0	3.087423	81	81
41.0	3.087424	73	73
42.0	3.087424	56	56
43.0	3.087424	51	51
44.0	3.087424	51	51
45.0	3.087424	47	47
46.0	3.087424	43	43
47.0	3.087424	48	48
48.0	3.087424	45	45
49.0	3.087424	34	34
50.0	3.087424	31	31
51.0	3.087424	29	29
52.0	3.087424	35	35
53.0	3.087424	30	30
54.0	3.087424	33	33
55.0	3.087424	31	31
56.0	3.087424	26	26
57.0	3.087424	24	24
58.0	3.087424	17	17
59.0	3.087424	20	20
60.0	3.087424	32	32
61.0	3.087424	21	21
62.0	3.087424	18	18
63.0	3.087424	14	14
64.0	3.087424	17	17
65.0	3.087424	16	16
66.0	3.087424	10	10
67.0	3.087424	16	16
68.0	3.087424	15	15
69.0	3.087424	14	14
70.0	3.087424	10	10
71.0	3.087424	12	12
72.0	3.087424	13	13
73.0	3.087424	8	8
74.0	3.087424	14	14
75.0	3.087424	8	8
76.0	3.087424	7	7
77.0	3.087424	13	13
78.0	3.087424	5	5
79.0	3.087424	9	9
80.0	3.087424	5	5
81.0	3.087424	7	7
82.0	3.087424	3	3
83.0	3.087424	13	13
84.0	3.087424	7	7
85.0	3.087424	9	9
86.0	3.087424	6	6
87.0	3.087424	5	5
88.0	3.087424	3	3
89.0	3.087424	7	7
90.0	3.087424	3	3
91.0	3.087424	4	4
92.0	3.087424	8	8
93.0	3.087424	14	14
94.0	3.087424	7	7
95.0	3.087424	7	7
96.0	3.087424	5	5
97.0	3.087424	6	6
98.0	3.087424	7	7
99.0	3.087424	2	2
100.0	3.087424	3	3
101.0	0	1	1
102.0	0	4	4
103.0	0	4	4
104.0	0	7	7
105.0	0	6	6
106.0	0	3	3
107.0	0	1	1
108.0	0	3	3
109.0	0	1	1
110.0	0	3	3
111.0	0	6	6
112.0	0	3	3
113.0	0	4	4
114.0	0	5	5
115.0	0	5	5
116.0	0	4	4
117.0	0	4	4
118.0	0	3	3
119.0	0	1	1
120.0	0	3	3
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
129.0	0	2	2
130.0	0	2	2
132.0	0	3	3
134.0	0	5	5
135.0	0	2	2
136.0	0	3	3
137.0	0	1	1
138.0	0	2	2
139.0	0	2	2
140.0	0	1	1
141.0	0	1	1
144.0	0	1	1
145.0	0	1	1
147.0	0	1	1
148.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	2	2
155.0	0	2	2
156.0	0	1	1
158.0	0	1	1
159.0	0	2	2
162.0	0	3	3
164.0	0	1	1
165.0	0	1	1
169.0	0	1	1
171.0	0	1	1
173.0	0	1	1
175.0	0	1	1
179.0	0	1	1
181.0	0	1	1
183.0	0	2	2
185.0	0	3	3
188.0	0	1	1
189.0	0	1	1
190.0	0	1	1
200.0	0	1	1
204.0	0	1	1
206.0	0	1	1
208.0	0	1	1
209.0	0	1	1
211.0	0	1	1
217.0	0	2	2
219.0	0	1	1
222.0	0	1	1
224.0	0	1	1
230.0	0	1	1
237.0	0	1	1
255.0	0	1	1
256.0	0	1	1
265.0	0	1	1
271.0	0	1	1
277.0	0	1	1
289.0	0	1	1
309.0	0	2	2
311.0	0	1	1
313.0	0	1	1
334.0	0	1	1
347.0	0	2	2
356.0	0	1	1
419.0	0	1	1
425.0	0	1	1
516.0	0	1	1
568.0	0	1	1
604.0	0	1	1
645.0	0	1	1
1160.0	0	1	1