## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/bwa-mem/hg38-GSM4728087.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/final_bam/hg38-GSM4728087.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/qc/markdup/hg38-GSM4728087.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 15:38:55 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	28001	13684152	0	0	829	1594971	0	0.116467	54046042

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	10630753	10630753
2.0	1.776317	1306520	1306520
3.0	2.378985	125767	125767
4.0	2.846847	10904	10904
5.0	3.210055	854	854
6.0	3.492021	64	64
7.0	3.710915	7	7
8.0	3.880846	5	5
9.0	4.012767	1	1
10.0	4.115179	1	1
11.0	4.194684	0	0
12.0	4.256404	0	0
13.0	4.304319	0	0
14.0	4.341516	1	1
15.0	4.370393	1	1
16.0	4.39281	0	0
17.0	4.410213	0	0
18.0	4.423723	0	0
19.0	4.434212	1	1
20.0	4.442354	1	1
21.0	4.448675	0	0
22.0	4.453582	0	0
23.0	4.457391	0	0
24.0	4.460349	0	0
25.0	4.462644	1	1
26.0	4.464427	2	2
27.0	4.46581	0	0
28.0	4.466884	0	0
29.0	4.467718	0	0
30.0	4.468366	1	1
31.0	4.468868	0	0
32.0	4.469258	1	1
33.0	4.469561	1	1
34.0	4.469796	0	0
35.0	4.469979	0	0
36.0	4.470121	0	0
37.0	4.470231	0	0
38.0	4.470316	0	0
39.0	4.470382	0	0
40.0	4.470434	0	0
41.0	4.470474	0	0
42.0	4.470505	0	0
43.0	4.470529	0	0
44.0	4.470547	0	0
45.0	4.470562	0	0
46.0	4.470573	0	0
47.0	4.470582	0	0
48.0	4.470589	0	0
49.0	4.470594	0	0
50.0	4.470598	1	1
51.0	4.470601	0	0
52.0	4.470604	0	0
53.0	4.470606	0	0
54.0	4.470607	0	0
55.0	4.470608	0	0
56.0	4.470609	0	0
57.0	4.47061	0	0
58.0	4.47061	0	0
59.0	4.470611	0	0
60.0	4.470611	0	0
61.0	4.470611	0	0
62.0	4.470612	0	0
63.0	4.470612	0	0
64.0	4.470612	0	0
65.0	4.470612	0	0
66.0	4.470612	0	0
67.0	4.470612	0	0
68.0	4.470612	0	0
69.0	4.470612	0	0
70.0	4.470612	0	0
71.0	4.470612	0	0
72.0	4.470612	0	0
73.0	4.470612	0	0
74.0	4.470612	0	0
75.0	4.470612	0	0
76.0	4.470612	0	0
77.0	4.470612	0	0
78.0	4.470612	0	0
79.0	4.470612	0	0
80.0	4.470612	0	0
81.0	4.470612	0	0
82.0	4.470612	0	0
83.0	4.470612	0	0
84.0	4.470612	0	0
85.0	4.470612	0	0
86.0	4.470612	0	0
87.0	4.470612	0	0
88.0	4.470612	0	0
89.0	4.470612	0	0
90.0	4.470612	0	0
91.0	4.470612	0	0
92.0	4.470612	0	0
93.0	4.470612	0	0
94.0	4.470612	0	0
95.0	4.470612	0	0
96.0	4.470612	0	0
97.0	4.470612	1	1
98.0	4.470612	0	0
99.0	4.470612	0	0
100.0	4.470612	0	0