## 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-GSM1606184.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606184.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606184.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 00:20:38 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	37322248	2783424	0	0	2930544	0	0.07852	225049931

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32211972	32211972
2.0	1.847182	1763870	1763870
3.0	2.564899	270839	270839
4.0	3.172936	77160	77160
5.0	3.688054	30306	30306
6.0	4.124453	14720	14720
7.0	4.494162	7845	7845
8.0	4.807372	4721	4721
9.0	5.072719	2925	2925
10.0	5.297515	1934	1934
11.0	5.487959	1255	1255
12.0	5.6493	899	899
13.0	5.785984	702	702
14.0	5.901781	533	533
15.0	5.999882	384	384
16.0	6.082992	279	279
17.0	6.1534	255	255
18.0	6.213049	178	178
19.0	6.263583	144	144
20.0	6.306394	127	127
21.0	6.342663	104	104
22.0	6.373389	84	84
23.0	6.39942	66	66
24.0	6.421473	59	59
25.0	6.440155	39	39
26.0	6.455983	29	29
27.0	6.469392	35	35
28.0	6.480752	30	30
29.0	6.490376	26	26
30.0	6.498529	21	21
31.0	6.505436	27	27
32.0	6.511287	15	15
33.0	6.516245	16	16
34.0	6.520445	15	15
35.0	6.524003	7	7
36.0	6.527017	10	10
37.0	6.529571	4	4
38.0	6.531734	10	10
39.0	6.533567	7	7
40.0	6.535119	2	2
41.0	6.536435	5	5
42.0	6.537549	3	3
43.0	6.538493	4	4
44.0	6.539293	4	4
45.0	6.539971	3	3
46.0	6.540545	2	2
47.0	6.541031	8	8
48.0	6.541443	1	1
49.0	6.541792	2	2
50.0	6.542088	0	0
51.0	6.542338	2	2
52.0	6.542551	1	1
53.0	6.542731	1	1
54.0	6.542883	1	1
55.0	6.543012	0	0
56.0	6.543121	0	0
57.0	6.543214	2	2
58.0	6.543292	0	0
59.0	6.543359	0	0
60.0	6.543415	1	1
61.0	6.543463	0	0
62.0	6.543503	1	1
63.0	6.543537	1	1
64.0	6.543566	1	1
65.0	6.543591	0	0
66.0	6.543612	0	0
67.0	6.543629	0	0
68.0	6.543644	1	1
69.0	6.543657	1	1
70.0	6.543668	0	0
71.0	6.543677	0	0
72.0	6.543685	1	1
73.0	6.543691	2	2
74.0	6.543697	0	0
75.0	6.543701	0	0
76.0	6.543705	0	0
77.0	6.543709	0	0
78.0	6.543711	0	0
79.0	6.543714	0	0
80.0	6.543716	0	0
81.0	6.543718	0	0
82.0	6.543719	0	0
83.0	6.54372	0	0
84.0	6.543721	0	0
85.0	6.543722	0	0
86.0	6.543723	0	0
87.0	6.543724	0	0
88.0	6.543724	0	0
89.0	6.543725	0	0
90.0	6.543725	0	0
91.0	6.543725	0	0
92.0	6.543726	0	0
93.0	6.543726	0	0
94.0	6.543726	0	0
95.0	6.543726	0	0
96.0	6.543726	0	0
97.0	6.543727	0	0
98.0	6.543727	0	0
99.0	6.543727	0	0
100.0	6.543727	0	0
124.0	0	1	1
725.0	0	1	1