## 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-GSM919927.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919927.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919927.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 15:46:33 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	8980130	1718580	0	0	1393340	0	0.155158	25860702

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6823327	6823327
2.0	1.706629	546550	546550
3.0	2.205953	109788	109788
4.0	2.558789	42133	42133
5.0	2.808114	21253	21253
6.0	2.984293	12393	12393
7.0	3.108787	7930	7930
8.0	3.196758	5243	5243
9.0	3.258921	3610	3610
10.0	3.302847	2681	2681
11.0	3.333886	2015	2015
12.0	3.355819	1604	1604
13.0	3.371318	1247	1247
14.0	3.38227	1004	1004
15.0	3.390009	799	799
16.0	3.395477	638	638
17.0	3.399341	585	585
18.0	3.402072	462	462
19.0	3.404001	379	379
20.0	3.405365	312	312
21.0	3.406328	306	306
22.0	3.407009	226	226
23.0	3.40749	229	229
24.0	3.40783	187	187
25.0	3.40807	150	150
26.0	3.40824	141	141
27.0	3.40836	146	146
28.0	3.408445	118	118
29.0	3.408504	102	102
30.0	3.408547	84	84
31.0	3.408577	65	65
32.0	3.408598	57	57
33.0	3.408613	63	63
34.0	3.408623	70	70
35.0	3.408631	52	52
36.0	3.408636	65	65
37.0	3.40864	49	49
38.0	3.408642	44	44
39.0	3.408644	25	25
40.0	3.408646	46	46
41.0	3.408646	31	31
42.0	3.408647	33	33
43.0	3.408648	30	30
44.0	3.408648	20	20
45.0	3.408648	30	30
46.0	3.408648	23	23
47.0	3.408648	17	17
48.0	3.408649	23	23
49.0	3.408649	23	23
50.0	3.408649	19	19
51.0	3.408649	13	13
52.0	3.408649	13	13
53.0	3.408649	19	19
54.0	3.408649	15	15
55.0	3.408649	13	13
56.0	3.408649	7	7
57.0	3.408649	12	12
58.0	3.408649	2	2
59.0	3.408649	15	15
60.0	3.408649	9	9
61.0	3.408649	6	6
62.0	3.408649	11	11
63.0	3.408649	9	9
64.0	3.408649	6	6
65.0	3.408649	8	8
66.0	3.408649	7	7
67.0	3.408649	9	9
68.0	3.408649	2	2
69.0	3.408649	5	5
70.0	3.408649	5	5
71.0	3.408649	8	8
72.0	3.408649	8	8
73.0	3.408649	5	5
74.0	3.408649	3	3
75.0	3.408649	6	6
76.0	3.408649	4	4
77.0	3.408649	5	5
78.0	3.408649	9	9
79.0	3.408649	5	5
80.0	3.408649	2	2
81.0	3.408649	7	7
82.0	3.408649	0	0
83.0	3.408649	6	6
84.0	3.408649	1	1
85.0	3.408649	4	4
86.0	3.408649	4	4
87.0	3.408649	3	3
88.0	3.408649	3	3
89.0	3.408649	3	3
90.0	3.408649	1	1
91.0	3.408649	2	2
92.0	3.408649	3	3
93.0	3.408649	3	3
94.0	3.408649	5	5
95.0	3.408649	5	5
96.0	3.408649	1	1
97.0	3.408649	4	4
98.0	3.408649	2	2
99.0	3.408649	2	2
100.0	3.408649	1	1
101.0	0	2	2
103.0	0	2	2
104.0	0	1	1
105.0	0	1	1
107.0	0	3	3
108.0	0	3	3
110.0	0	1	1
111.0	0	1	1
112.0	0	1	1
113.0	0	2	2
114.0	0	1	1
116.0	0	3	3
118.0	0	2	2
120.0	0	2	2
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
129.0	0	1	1
131.0	0	1	1
136.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	1	1
147.0	0	2	2
151.0	0	3	3
156.0	0	1	1
168.0	0	1	1
171.0	0	1	1
173.0	0	3	3
174.0	0	1	1
176.0	0	1	1
183.0	0	1	1
189.0	0	1	1
200.0	0	1	1
204.0	0	1	1
213.0	0	1	1
230.0	0	2	2
260.0	0	1	1
393.0	0	1	1
415.0	0	1	1
418.0	0	1	1
424.0	0	1	1
567.0	0	1	1
592.0	0	1	1
617.0	0	1	1