## 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-GSM919929.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919929.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919929.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 15:25:38 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	10917658	2248632	0	0	1600271	0	0.146576	33506374

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8539271	8539271
2.0	1.721922	513285	513285
3.0	2.243093	126205	126205
4.0	2.619338	52363	52363
5.0	2.890958	27515	27515
6.0	3.087046	16144	16144
7.0	3.228606	10285	10285
8.0	3.330802	7023	7023
9.0	3.404579	5186	5186
10.0	3.45784	3682	3682
11.0	3.496291	2805	2805
12.0	3.524049	2164	2164
13.0	3.544088	1681	1681
14.0	3.558555	1419	1419
15.0	3.568999	1061	1061
16.0	3.576539	874	874
17.0	3.581982	732	732
18.0	3.585911	622	622
19.0	3.588748	566	566
20.0	3.590796	473	473
21.0	3.592275	401	401
22.0	3.593342	328	328
23.0	3.594112	319	319
24.0	3.594669	273	273
25.0	3.59507	245	245
26.0	3.59536	212	212
27.0	3.595569	151	151
28.0	3.59572	155	155
29.0	3.59583	131	131
30.0	3.595908	140	140
31.0	3.595965	129	129
32.0	3.596006	87	87
33.0	3.596036	90	90
34.0	3.596057	93	93
35.0	3.596073	77	77
36.0	3.596084	69	69
37.0	3.596092	77	77
38.0	3.596098	50	50
39.0	3.596102	54	54
40.0	3.596105	46	46
41.0	3.596107	51	51
42.0	3.596109	49	49
43.0	3.59611	46	46
44.0	3.596111	37	37
45.0	3.596111	51	51
46.0	3.596112	45	45
47.0	3.596112	21	21
48.0	3.596112	33	33
49.0	3.596112	31	31
50.0	3.596112	20	20
51.0	3.596113	18	18
52.0	3.596113	23	23
53.0	3.596113	18	18
54.0	3.596113	20	20
55.0	3.596113	16	16
56.0	3.596113	18	18
57.0	3.596113	17	17
58.0	3.596113	16	16
59.0	3.596113	8	8
60.0	3.596113	15	15
61.0	3.596113	14	14
62.0	3.596113	13	13
63.0	3.596113	15	15
64.0	3.596113	16	16
65.0	3.596113	14	14
66.0	3.596113	11	11
67.0	3.596113	9	9
68.0	3.596113	8	8
69.0	3.596113	15	15
70.0	3.596113	9	9
71.0	3.596113	11	11
72.0	3.596113	9	9
73.0	3.596113	6	6
74.0	3.596113	11	11
75.0	3.596113	5	5
76.0	3.596113	6	6
77.0	3.596113	3	3
78.0	3.596113	8	8
79.0	3.596113	10	10
80.0	3.596113	1	1
81.0	3.596113	4	4
82.0	3.596113	6	6
83.0	3.596113	3	3
84.0	3.596113	1	1
85.0	3.596113	3	3
86.0	3.596113	2	2
87.0	3.596113	2	2
88.0	3.596113	5	5
89.0	3.596113	4	4
90.0	3.596113	6	6
91.0	3.596113	4	4
92.0	3.596113	1	1
93.0	3.596113	4	4
94.0	3.596113	2	2
95.0	3.596113	2	2
96.0	3.596113	2	2
97.0	3.596113	3	3
98.0	3.596113	3	3
99.0	3.596113	3	3
100.0	3.596113	2	2
101.0	0	1	1
102.0	0	1	1
103.0	0	3	3
104.0	0	3	3
105.0	0	2	2
106.0	0	4	4
107.0	0	3	3
108.0	0	1	1
110.0	0	2	2
111.0	0	2	2
112.0	0	2	2
113.0	0	3	3
114.0	0	1	1
115.0	0	1	1
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
120.0	0	3	3
123.0	0	2	2
124.0	0	3	3
126.0	0	3	3
127.0	0	1	1
128.0	0	1	1
130.0	0	2	2
133.0	0	5	5
134.0	0	2	2
135.0	0	1	1
139.0	0	1	1
144.0	0	1	1
147.0	0	2	2
150.0	0	1	1
153.0	0	2	2
154.0	0	1	1
156.0	0	1	1
160.0	0	1	1
166.0	0	2	2
169.0	0	1	1
170.0	0	1	1
172.0	0	2	2
182.0	0	1	1
187.0	0	1	1
201.0	0	1	1
202.0	0	1	1
206.0	0	1	1
207.0	0	1	1
212.0	0	1	1
220.0	0	1	1
221.0	0	1	1
224.0	0	1	1
230.0	0	1	1
235.0	0	1	1
247.0	0	1	1
259.0	0	1	1
268.0	0	1	1
271.0	0	1	1
283.0	0	1	1
302.0	0	1	1
308.0	0	1	1
310.0	0	1	1
367.0	0	1	1
638.0	0	1	1
749.0	0	1	1