## 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-Chipseq_DOM_H3K27ac.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/final_bam/hg38-Chipseq_DOM_H3K27ac.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/qc/markdup/hg38-Chipseq_DOM_H3K27ac.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 10:33:43 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	23068	25869771	0	0	6767	3724607	8987	0.144042	81151569

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000295	18889312	0	18895645
2.0	1.727543	2791455	8959	2787261
3.0	2.256276	381258	14	379544
4.0	2.640682	48050	0	47704
5.0	2.920158	5725	0	5656
6.0	3.123346	630	0	621
7.0	3.271071	62	0	61
8.0	3.378472	8	0	8
9.0	3.456556	1	0	1
10.0	3.513325	0	0	0
11.0	3.554598	0	0	0
12.0	3.584606	0	0	0
13.0	3.606422	0	0	0
14.0	3.622283	0	0	0
15.0	3.633814	0	0	0
16.0	3.642198	0	0	0
17.0	3.648293	0	0	0
18.0	3.652725	0	0	0
19.0	3.655947	0	0	0
20.0	3.658289	0	0	0
21.0	3.659992	0	0	0
22.0	3.66123	0	0	0
23.0	3.66213	0	0	0
24.0	3.662785	0	0	0
25.0	3.663261	0	0	0
26.0	3.663606	0	0	0
27.0	3.663858	0	0	0
28.0	3.664041	0	0	0
29.0	3.664174	0	0	0
30.0	3.66427	0	0	0
31.0	3.664341	0	0	0
32.0	3.664392	0	0	0
33.0	3.664429	0	0	0
34.0	3.664456	0	0	0
35.0	3.664476	0	0	0
36.0	3.66449	0	0	0
37.0	3.6645	0	0	0
38.0	3.664508	0	0	0
39.0	3.664513	0	0	0
40.0	3.664517	0	0	0
41.0	3.66452	0	0	0
42.0	3.664522	0	0	0
43.0	3.664524	0	0	0
44.0	3.664525	0	0	0
45.0	3.664526	0	0	0
46.0	3.664526	0	0	0
47.0	3.664527	0	0	0
48.0	3.664527	0	0	0
49.0	3.664527	0	0	0
50.0	3.664527	0	0	0
51.0	3.664527	0	0	0
52.0	3.664528	0	0	0
53.0	3.664528	0	0	0
54.0	3.664528	0	0	0
55.0	3.664528	0	0	0
56.0	3.664528	0	0	0
57.0	3.664528	0	0	0
58.0	3.664528	0	0	0
59.0	3.664528	0	0	0
60.0	3.664528	0	0	0
61.0	3.664528	0	0	0
62.0	3.664528	0	0	0
63.0	3.664528	0	0	0
64.0	3.664528	0	0	0
65.0	3.664528	0	0	0
66.0	3.664528	0	0	0
67.0	3.664528	0	0	0
68.0	3.664528	0	0	0
69.0	3.664528	0	0	0
70.0	3.664528	0	0	0
71.0	3.664528	0	0	0
72.0	3.664528	0	0	0
73.0	3.664528	0	0	0
74.0	3.664528	0	0	0
75.0	3.664528	0	0	0
76.0	3.664528	0	0	0
77.0	3.664528	0	0	0
78.0	3.664528	0	0	0
79.0	3.664528	0	0	0
80.0	3.664528	0	0	0
81.0	3.664528	0	0	0
82.0	3.664528	0	0	0
83.0	3.664528	0	0	0
84.0	3.664528	0	0	0
85.0	3.664528	0	0	0
86.0	3.664528	0	0	0
87.0	3.664528	0	0	0
88.0	3.664528	0	0	0
89.0	3.664528	0	0	0
90.0	3.664528	0	0	0
91.0	3.664528	0	0	0
92.0	3.664528	0	0	0
93.0	3.664528	0	0	0
94.0	3.664528	0	0	0
95.0	3.664528	0	0	0
96.0	3.664528	0	0	0
97.0	3.664528	0	0	0
98.0	3.664528	0	0	0
99.0	3.664528	0	0	0
100.0	3.664528	0	0	0