## 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-GSM4728090.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/final_bam/hg38-GSM4728090.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/qc/markdup/hg38-GSM4728090.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 13:51:14 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	10275	16062636	0	0	1053	3346651	0	0.208316	32983039

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	9990684	9990684
2.0	1.614469	2190589	2190589
3.0	1.992041	424719	424719
4.0	2.224047	78073	78073
5.0	2.366608	14167	14167
6.0	2.454207	2460	2460
7.0	2.508034	438	438
8.0	2.541109	84	84
9.0	2.561433	18	18
10.0	2.573921	5	5
11.0	2.581595	1	1
12.0	2.58631	2	2
13.0	2.589207	0	0
14.0	2.590987	0	0
15.0	2.592081	0	0
16.0	2.592754	0	0
17.0	2.593167	0	0
18.0	2.59342	0	0
19.0	2.593576	0	0
20.0	2.593672	0	0
21.0	2.593731	0	0
22.0	2.593767	0	0
23.0	2.59379	0	0
24.0	2.593803	0	0
25.0	2.593812	0	0
26.0	2.593817	0	0
27.0	2.59382	0	0
28.0	2.593822	0	0
29.0	2.593823	0	0
30.0	2.593824	0	0
31.0	2.593824	0	0
32.0	2.593824	0	0
33.0	2.593825	0	0
34.0	2.593825	0	0
35.0	2.593825	0	0
36.0	2.593825	0	0
37.0	2.593825	0	0
38.0	2.593825	0	0
39.0	2.593825	0	0
40.0	2.593825	0	0
41.0	2.593825	0	0
42.0	2.593825	0	0
43.0	2.593825	0	0
44.0	2.593825	0	0
45.0	2.593825	0	0
46.0	2.593825	0	0
47.0	2.593825	0	0
48.0	2.593825	0	0
49.0	2.593825	0	0
50.0	2.593825	0	0
51.0	2.593825	0	0
52.0	2.593825	0	0
53.0	2.593825	0	0
54.0	2.593825	0	0
55.0	2.593825	0	0
56.0	2.593825	0	0
57.0	2.593825	0	0
58.0	2.593825	0	0
59.0	2.593825	0	0
60.0	2.593825	0	0
61.0	2.593825	0	0
62.0	2.593825	0	0
63.0	2.593825	0	0
64.0	2.593825	0	0
65.0	2.593825	0	0
66.0	2.593825	0	0
67.0	2.593825	0	0
68.0	2.593825	0	0
69.0	2.593825	0	0
70.0	2.593825	0	0
71.0	2.593825	0	0
72.0	2.593825	0	0
73.0	2.593825	0	0
74.0	2.593825	0	0
75.0	2.593825	0	0
76.0	2.593825	0	0
77.0	2.593825	0	0
78.0	2.593825	0	0
79.0	2.593825	0	0
80.0	2.593825	0	0
81.0	2.593825	0	0
82.0	2.593825	0	0
83.0	2.593825	0	0
84.0	2.593825	0	0
85.0	2.593825	0	0
86.0	2.593825	0	0
87.0	2.593825	0	0
88.0	2.593825	0	0
89.0	2.593825	0	0
90.0	2.593825	0	0
91.0	2.593825	0	0
92.0	2.593825	0	0
93.0	2.593825	0	0
94.0	2.593825	0	0
95.0	2.593825	0	0
96.0	2.593825	0	0
97.0	2.593825	0	0
98.0	2.593825	0	0
99.0	2.593825	0	0
100.0	2.593825	0	0