## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/bwa-mem2/hg38-Dombi-23_ATAC_2.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-Dombi-23_ATAC_2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-Dombi-23_ATAC_2.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/GZnl]    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: Thu Feb 18 17:13:35 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	7204	481517	0	0	248	2315	19	0.005028	50327248

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000039	476164	0	476183
2.0	1.990556	2287	19	2268
3.0	2.971641	14	0	14
4.0	3.943384	0	0	0
5.0	4.905874	0	0	0
6.0	5.859199	0	0	0
7.0	6.803447	0	0	0
8.0	7.738703	0	0	0
9.0	8.665053	0	0	0
10.0	9.582583	0	0	0
11.0	10.491376	0	0	0
12.0	11.391516	0	0	0
13.0	12.283084	0	0	0
14.0	13.166162	0	0	0
15.0	14.040832	0	0	0
16.0	14.907173	0	0	0
17.0	15.765265	0	0	0
18.0	16.615186	0	0	0
19.0	17.457014	0	0	0
20.0	18.290826	0	0	0
21.0	19.116698	0	0	0
22.0	19.934706	0	0	0
23.0	20.744926	0	0	0
24.0	21.54743	0	0	0
25.0	22.342292	0	0	0
26.0	23.129586	0	0	0
27.0	23.909383	0	0	0
28.0	24.681755	0	0	0
29.0	25.446772	0	0	0
30.0	26.204505	0	0	0
31.0	26.955023	0	0	0
32.0	27.698394	0	0	0
33.0	28.434686	0	0	0
34.0	29.163968	0	0	0
35.0	29.886305	0	0	0
36.0	30.601764	0	0	0
37.0	31.31041	0	0	0
38.0	32.012309	0	0	0
39.0	32.707524	0	0	0
40.0	33.396119	0	0	0
41.0	34.078157	0	0	0
42.0	34.753701	0	0	0
43.0	35.422812	0	0	0
44.0	36.085552	0	0	0
45.0	36.741981	0	0	0
46.0	37.39216	0	0	0
47.0	38.036148	0	0	0
48.0	38.674003	0	0	0
49.0	39.305785	0	0	0
50.0	39.931551	0	0	0
51.0	40.551358	0	0	0
52.0	41.165263	0	0	0
53.0	41.773323	0	0	0
54.0	42.375593	0	0	0
55.0	42.972128	0	0	0
56.0	43.562982	0	0	0
57.0	44.148211	0	0	0
58.0	44.727867	0	0	0
59.0	45.302003	0	0	0
60.0	45.870672	0	0	0
61.0	46.433927	0	0	0
62.0	46.991818	0	0	0
63.0	47.544396	0	0	0
64.0	48.091713	0	0	0
65.0	48.633819	0	0	0
66.0	49.170762	0	0	0
67.0	49.702593	0	0	0
68.0	50.229359	0	0	0
69.0	50.75111	0	0	0
70.0	51.267892	0	0	0
71.0	51.779754	0	0	0
72.0	52.286741	0	0	0
73.0	52.788901	0	0	0
74.0	53.28628	0	0	0
75.0	53.778922	0	0	0
76.0	54.266873	0	0	0
77.0	54.750178	0	0	0
78.0	55.228881	0	0	0
79.0	55.703026	0	0	0
80.0	56.172656	0	0	0
81.0	56.637814	0	0	0
82.0	57.098542	0	0	0
83.0	57.554884	0	0	0
84.0	58.00688	0	0	0
85.0	58.454572	0	0	0
86.0	58.898002	0	0	0
87.0	59.337208	0	0	0
88.0	59.772233	0	0	0
89.0	60.203116	0	0	0
90.0	60.629895	0	0	0
91.0	61.052611	0	0	0
92.0	61.471301	0	0	0
93.0	61.886005	0	0	0
94.0	62.29676	0	0	0
95.0	62.703604	0	0	0
96.0	63.106573	0	0	0
97.0	63.505706	0	0	0
98.0	63.901038	0	0	0
99.0	64.292605	0	0	0
100.0	64.680444	0	0	0