## 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-GSM4728064.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/final_bam/hg38-GSM4728064.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/H3K27ac/results/qc/markdup/hg38-GSM4728064.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 10:18:10 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	6071	19381371	0	0	1205	3207810	0	0.165515	51894086

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	13411360	13411360
2.0	1.688335	2337392	2337392
3.0	2.16214	348740	348740
4.0	2.488277	47549	47549
5.0	2.712769	6394	6394
6.0	2.867294	814	814
7.0	2.973659	93	93
8.0	3.046874	10	10
9.0	3.097271	1	1
10.0	3.13196	1	1
11.0	3.155839	0	0
12.0	3.172275	0	0
13.0	3.183588	0	0
14.0	3.191376	0	0
15.0	3.196736	0	0
16.0	3.200426	0	0
17.0	3.202966	0	0
18.0	3.204714	0	0
19.0	3.205917	0	0
20.0	3.206746	0	0
21.0	3.207316	0	0
22.0	3.207708	0	0
23.0	3.207979	0	0
24.0	3.208164	0	0
25.0	3.208292	0	0
26.0	3.208381	0	0
27.0	3.208441	0	0
28.0	3.208483	0	0
29.0	3.208512	0	0
30.0	3.208531	0	0
31.0	3.208545	0	0
32.0	3.208554	0	0
33.0	3.208561	0	0
34.0	3.208565	0	0
35.0	3.208568	0	0
36.0	3.208571	0	0
37.0	3.208572	0	0
38.0	3.208573	0	0
39.0	3.208574	0	0
40.0	3.208574	0	0
41.0	3.208574	0	0
42.0	3.208575	0	0
43.0	3.208575	0	0
44.0	3.208575	0	0
45.0	3.208575	0	0
46.0	3.208575	0	0
47.0	3.208575	0	0
48.0	3.208575	0	0
49.0	3.208575	0	0
50.0	3.208575	0	0
51.0	3.208575	0	0
52.0	3.208575	0	0
53.0	3.208575	0	0
54.0	3.208575	0	0
55.0	3.208575	0	0
56.0	3.208575	0	0
57.0	3.208575	0	0
58.0	3.208575	0	0
59.0	3.208575	0	0
60.0	3.208575	0	0
61.0	3.208575	0	0
62.0	3.208575	0	0
63.0	3.208575	0	0
64.0	3.208575	0	0
65.0	3.208575	0	0
66.0	3.208575	0	0
67.0	3.208575	0	0
68.0	3.208575	0	0
69.0	3.208575	0	0
70.0	3.208575	0	0
71.0	3.208575	0	0
72.0	3.208575	0	0
73.0	3.208575	0	0
74.0	3.208575	0	0
75.0	3.208575	0	0
76.0	3.208575	0	0
77.0	3.208575	0	0
78.0	3.208575	0	0
79.0	3.208575	0	0
80.0	3.208575	0	0
81.0	3.208575	0	0
82.0	3.208575	0	0
83.0	3.208575	0	0
84.0	3.208575	0	0
85.0	3.208575	0	0
86.0	3.208575	0	0
87.0	3.208575	0	0
88.0	3.208575	0	0
89.0	3.208575	0	0
90.0	3.208575	0	0
91.0	3.208575	0	0
92.0	3.208575	0	0
93.0	3.208575	0	0
94.0	3.208575	0	0
95.0	3.208575	0	0
96.0	3.208575	0	0
97.0	3.208575	0	0
98.0	3.208575	0	0
99.0	3.208575	0	0
100.0	3.208575	0	0