## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/bwa-mem2/hg38-GSM4728063.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/final_bam/hg38-GSM4728063.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/qc/markdup/hg38-GSM4728063.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/RaLG]    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 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: Fri Feb 19 10:18:48 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	5374	23883935	0	0	1174	3459902	0	0.144871	74266214

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17383904	17383904
2.0	1.724989	2617678	2617678
3.0	2.250598	344734	344734
4.0	2.631658	42709	42709
5.0	2.907923	5232	5232
6.0	3.108212	613	613
7.0	3.253419	94	94
8.0	3.358693	8	8
9.0	3.435015	2	2
10.0	3.490348	0	0
11.0	3.530463	0	0
12.0	3.559547	0	0
13.0	3.580632	0	0
14.0	3.595918	0	0
15.0	3.607001	0	0
16.0	3.615036	0	0
17.0	3.620861	0	0
18.0	3.625084	0	0
19.0	3.628146	0	0
20.0	3.630365	0	0
21.0	3.631975	0	0
22.0	3.633141	0	0
23.0	3.633987	0	0
24.0	3.6346	0	0
25.0	3.635045	0	0
26.0	3.635367	0	0
27.0	3.635601	0	0
28.0	3.63577	0	0
29.0	3.635893	0	0
30.0	3.635982	0	0
31.0	3.636047	0	0
32.0	3.636094	0	0
33.0	3.636127	0	0
34.0	3.636152	0	0
35.0	3.63617	0	0
36.0	3.636183	0	0
37.0	3.636192	0	0
38.0	3.636199	0	0
39.0	3.636204	0	0
40.0	3.636207	0	0
41.0	3.63621	0	0
42.0	3.636212	0	0
43.0	3.636213	0	0
44.0	3.636214	0	0
45.0	3.636215	0	0
46.0	3.636216	0	0
47.0	3.636216	0	0
48.0	3.636216	0	0
49.0	3.636216	0	0
50.0	3.636217	0	0
51.0	3.636217	0	0
52.0	3.636217	0	0
53.0	3.636217	0	0
54.0	3.636217	0	0
55.0	3.636217	0	0
56.0	3.636217	0	0
57.0	3.636217	0	0
58.0	3.636217	0	0
59.0	3.636217	0	0
60.0	3.636217	0	0
61.0	3.636217	0	0
62.0	3.636217	0	0
63.0	3.636217	0	0
64.0	3.636217	0	0
65.0	3.636217	0	0
66.0	3.636217	0	0
67.0	3.636217	0	0
68.0	3.636217	0	0
69.0	3.636217	0	0
70.0	3.636217	0	0
71.0	3.636217	0	0
72.0	3.636217	0	0
73.0	3.636217	0	0
74.0	3.636217	0	0
75.0	3.636217	0	0
76.0	3.636217	0	0
77.0	3.636217	0	0
78.0	3.636217	0	0
79.0	3.636217	0	0
80.0	3.636217	0	0
81.0	3.636217	0	0
82.0	3.636217	0	0
83.0	3.636217	0	0
84.0	3.636217	0	0
85.0	3.636217	0	0
86.0	3.636217	0	0
87.0	3.636217	0	0
88.0	3.636217	0	0
89.0	3.636217	0	0
90.0	3.636217	0	0
91.0	3.636217	0	0
92.0	3.636217	0	0
93.0	3.636217	0	0
94.0	3.636217	0	0
95.0	3.636217	0	0
96.0	3.636217	0	0
97.0	3.636217	0	0
98.0	3.636217	0	0
99.0	3.636217	0	0
100.0	3.636217	0	0