## 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_1.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-Dombi-23_ATAC_1.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-Dombi-23_ATAC_1.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 17:16:47 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	33306	5096445	0	0	7202	1099133	1286	0.215668	10055848

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000194	3104470	0	3105290
2.0	1.602722	705864	1284	705374
3.0	1.965693	145840	1	145611
4.0	2.18435	26341	0	26269
5.0	2.316072	4574	0	4551
6.0	2.395423	683	0	677
7.0	2.443225	119	0	119
8.0	2.472021	12	0	12
9.0	2.489368	6	0	6
10.0	2.499819	1	0	1
11.0	2.506114	0	0	0
12.0	2.509906	0	0	0
13.0	2.512191	0	0	0
14.0	2.513567	0	0	0
15.0	2.514396	0	0	0
16.0	2.514896	0	0	0
17.0	2.515197	0	0	0
18.0	2.515378	0	0	0
19.0	2.515487	0	0	0
20.0	2.515553	0	0	0
21.0	2.515592	0	0	0
22.0	2.515616	0	0	0
23.0	2.515631	0	0	0
24.0	2.515639	0	0	0
25.0	2.515645	0	0	0
26.0	2.515648	0	0	0
27.0	2.51565	0	0	0
28.0	2.515651	0	0	0
29.0	2.515651	0	0	0
30.0	2.515652	0	0	0
31.0	2.515652	0	0	0
32.0	2.515652	0	0	0
33.0	2.515652	0	0	0
34.0	2.515652	0	0	0
35.0	2.515652	0	0	0
36.0	2.515652	0	0	0
37.0	2.515653	0	0	0
38.0	2.515653	0	0	0
39.0	2.515653	0	0	0
40.0	2.515653	0	0	0
41.0	2.515653	0	0	0
42.0	2.515653	0	0	0
43.0	2.515653	0	0	0
44.0	2.515653	0	0	0
45.0	2.515653	0	0	0
46.0	2.515653	0	0	0
47.0	2.515653	0	0	0
48.0	2.515653	0	0	0
49.0	2.515653	0	0	0
50.0	2.515653	0	0	0
51.0	2.515653	0	0	0
52.0	2.515653	0	0	0
53.0	2.515653	0	0	0
54.0	2.515653	0	0	0
55.0	2.515653	0	0	0
56.0	2.515653	0	0	0
57.0	2.515653	0	0	0
58.0	2.515653	0	0	0
59.0	2.515653	0	0	0
60.0	2.515653	0	0	0
61.0	2.515653	0	0	0
62.0	2.515653	0	0	0
63.0	2.515653	0	0	0
64.0	2.515653	0	0	0
65.0	2.515653	0	0	0
66.0	2.515653	0	0	0
67.0	2.515653	0	0	0
68.0	2.515653	0	0	0
69.0	2.515653	0	0	0
70.0	2.515653	0	0	0
71.0	2.515653	0	0	0
72.0	2.515653	0	0	0
73.0	2.515653	0	0	0
74.0	2.515653	0	0	0
75.0	2.515653	0	0	0
76.0	2.515653	0	0	0
77.0	2.515653	0	0	0
78.0	2.515653	0	0	0
79.0	2.515653	0	0	0
80.0	2.515653	0	0	0
81.0	2.515653	0	0	0
82.0	2.515653	0	0	0
83.0	2.515653	0	0	0
84.0	2.515653	0	0	0
85.0	2.515653	0	0	0
86.0	2.515653	0	0	0
87.0	2.515653	0	0	0
88.0	2.515653	0	0	0
89.0	2.515653	0	0	0
90.0	2.515653	0	0	0
91.0	2.515653	0	0	0
92.0	2.515653	0	0	0
93.0	2.515653	0	0	0
94.0	2.515653	0	0	0
95.0	2.515653	0	0	0
96.0	2.515653	0	0	0
97.0	2.515653	0	0	0
98.0	2.515653	0	0	0
99.0	2.515653	0	0	0
100.0	2.515653	0	0	0