## 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-PRIM_LSC_input.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/final_bam/hg38-PRIM_LSC_input.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/qc/markdup/hg38-PRIM_LSC_input.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 10:54:59 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	19930	31379764	0	0	1857	1274639	25946	0.040636	383114189

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000794	28807736	0	28831009
2.0	1.922883	1181088	25826	1160307
3.0	2.772457	44013	60	41693
4.0	3.555219	1740	0	1577
5.0	4.276422	68	0	59
6.0	4.940907	1	0	1
7.0	5.553137	2	0	2
8.0	6.117219	1	0	1
9.0	6.63694	0	0	0
10.0	7.115789	1	0	1
11.0	7.55698	0	0	0
12.0	7.963475	0	0	0
13.0	8.338002	0	0	0
14.0	8.683075	0	0	0
15.0	9.001011	0	0	0
16.0	9.293944	0	0	0
17.0	9.56384	0	0	0
18.0	9.81251	0	0	0
19.0	10.041625	0	0	0
20.0	10.252721	0	0	0
21.0	10.447216	0	0	0
22.0	10.626416	0	0	0
23.0	10.791523	0	0	0
24.0	10.943645	0	0	0
25.0	11.083804	0	0	0
26.0	11.212941	0	0	0
27.0	11.331922	0	0	0
28.0	11.441546	0	0	0
29.0	11.542549	0	0	0
30.0	11.635609	0	0	0
31.0	11.721351	0	0	0
32.0	11.800349	0	0	0
33.0	11.873135	0	0	0
34.0	11.940197	0	0	0
35.0	12.001985	0	0	0
36.0	12.058914	0	0	0
37.0	12.111366	0	0	0
38.0	12.159693	0	0	0
39.0	12.204219	0	0	0
40.0	12.245244	0	0	0
41.0	12.283042	0	0	0
42.0	12.317868	0	0	0
43.0	12.349955	0	0	0
44.0	12.379518	0	0	0
45.0	12.406757	0	0	0
46.0	12.431854	0	0	0
47.0	12.454977	0	0	0
48.0	12.476281	0	0	0
49.0	12.49591	0	0	0
50.0	12.513995	0	0	0
51.0	12.530658	0	0	0
52.0	12.546011	0	0	0
53.0	12.560156	0	0	0
54.0	12.573189	0	0	0
55.0	12.585197	0	0	0
56.0	12.596261	0	0	0
57.0	12.606454	0	0	0
58.0	12.615846	0	0	0
59.0	12.624499	0	0	0
60.0	12.632472	0	0	0
61.0	12.639818	0	0	0
62.0	12.646586	0	0	0
63.0	12.652822	0	0	0
64.0	12.658567	0	0	0
65.0	12.663861	0	0	0
66.0	12.668738	0	0	0
67.0	12.673232	0	0	0
68.0	12.677372	0	0	0
69.0	12.681187	0	0	0
70.0	12.684702	0	0	0
71.0	12.68794	0	0	0
72.0	12.690924	0	0	0
73.0	12.693673	0	0	0
74.0	12.696205	0	0	0
75.0	12.698539	0	0	0
76.0	12.700689	0	0	0
77.0	12.70267	0	0	0
78.0	12.704495	0	0	0
79.0	12.706177	0	0	0
80.0	12.707727	0	0	0
81.0	12.709154	0	0	0
82.0	12.710469	0	0	0
83.0	12.711681	0	0	0
84.0	12.712798	0	0	0
85.0	12.713827	0	0	0
86.0	12.714774	0	0	0
87.0	12.715648	0	0	0
88.0	12.716452	0	0	0
89.0	12.717194	0	0	0
90.0	12.717877	0	0	0
91.0	12.718506	0	0	0
92.0	12.719086	0	0	0
93.0	12.71962	0	0	0
94.0	12.720113	0	0	0
95.0	12.720566	0	0	0
96.0	12.720984	0	0	0
97.0	12.721369	0	0	0
98.0	12.721724	0	0	0
99.0	12.72205	0	0	0
100.0	12.722352	0	0	0