## 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-GSM4728089.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/final_bam/hg38-GSM4728089.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/qc/markdup/hg38-GSM4728089.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 14:50:24 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	15638	19412715	0	0	1620	3592426	0	0.185023	45758115

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	12825620	12825620
2.0	1.654263	2458261	2458261
3.0	2.082322	428617	428617
4.0	2.362386	72243	72243
5.0	2.545621	11988	11988
6.0	2.665505	1925	1925
7.0	2.74394	349	349
8.0	2.795258	60	60
9.0	2.828833	8	8
10.0	2.8508	2	2
11.0	2.865172	0	0
12.0	2.874575	0	0
13.0	2.880727	0	0
14.0	2.884752	0	0
15.0	2.887386	1	1
16.0	2.889109	1	1
17.0	2.890236	0	0
18.0	2.890973	0	0
19.0	2.891456	0	0
20.0	2.891772	0	0
21.0	2.891978	0	0
22.0	2.892113	0	0
23.0	2.892202	0	0
24.0	2.89226	0	0
25.0	2.892297	0	0
26.0	2.892322	0	0
27.0	2.892338	0	0
28.0	2.892349	0	0
29.0	2.892356	0	0
30.0	2.892361	0	0
31.0	2.892363	0	0
32.0	2.892365	0	0
33.0	2.892367	0	0
34.0	2.892368	0	0
35.0	2.892368	0	0
36.0	2.892368	0	0
37.0	2.892369	0	0
38.0	2.892369	0	0
39.0	2.892369	0	0
40.0	2.892369	0	0
41.0	2.892369	0	0
42.0	2.892369	0	0
43.0	2.892369	0	0
44.0	2.892369	0	0
45.0	2.892369	0	0
46.0	2.892369	0	0
47.0	2.892369	0	0
48.0	2.892369	0	0
49.0	2.892369	0	0
50.0	2.892369	0	0
51.0	2.892369	0	0
52.0	2.892369	0	0
53.0	2.892369	0	0
54.0	2.892369	0	0
55.0	2.892369	0	0
56.0	2.892369	0	0
57.0	2.892369	0	0
58.0	2.892369	0	0
59.0	2.892369	0	0
60.0	2.892369	0	0
61.0	2.892369	0	0
62.0	2.892369	0	0
63.0	2.892369	0	0
64.0	2.892369	0	0
65.0	2.892369	0	0
66.0	2.892369	0	0
67.0	2.892369	0	0
68.0	2.892369	0	0
69.0	2.892369	0	0
70.0	2.892369	0	0
71.0	2.892369	0	0
72.0	2.892369	0	0
73.0	2.892369	0	0
74.0	2.892369	0	0
75.0	2.892369	0	0
76.0	2.892369	0	0
77.0	2.892369	0	0
78.0	2.892369	0	0
79.0	2.892369	0	0
80.0	2.892369	0	0
81.0	2.892369	0	0
82.0	2.892369	0	0
83.0	2.892369	0	0
84.0	2.892369	0	0
85.0	2.892369	0	0
86.0	2.892369	0	0
87.0	2.892369	0	0
88.0	2.892369	0	0
89.0	2.892369	0	0
90.0	2.892369	0	0
91.0	2.892369	0	0
92.0	2.892369	0	0
93.0	2.892369	0	0
94.0	2.892369	0	0
95.0	2.892369	0	0
96.0	2.892369	0	0
97.0	2.892369	0	0
98.0	2.892369	0	0
99.0	2.892369	0	0
100.0	2.892369	0	0