## 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-GSM4728088.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/final_bam/hg38-GSM4728088.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/TF_chipseq/results/qc/markdup/hg38-GSM4728088.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 15:16:32 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	8166	19450368	0	0	811	2753376	0	0.14155	62051348

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14276963	14276963
2.0	1.730917	2081179	2081179
3.0	2.265156	273292	273292
4.0	2.65564	34829	34829
5.0	2.941051	4454	4454
6.0	3.149663	557	557
7.0	3.302141	74	74
8.0	3.413589	9	9
9.0	3.495049	1	1
10.0	3.554589	0	0
11.0	3.598108	1	1
12.0	3.629916	0	0
13.0	3.653166	0	0
14.0	3.670159	0	0
15.0	3.68258	0	0
16.0	3.691659	0	0
17.0	3.698294	0	0
18.0	3.703144	0	0
19.0	3.70669	0	0
20.0	3.709281	0	0
21.0	3.711175	0	0
22.0	3.712559	0	0
23.0	3.713571	0	0
24.0	3.71431	0	0
25.0	3.714851	0	0
26.0	3.715246	0	0
27.0	3.715535	0	0
28.0	3.715746	0	0
29.0	3.7159	0	0
30.0	3.716013	0	0
31.0	3.716095	0	0
32.0	3.716155	0	0
33.0	3.716199	0	0
34.0	3.716232	0	0
35.0	3.716255	0	0
36.0	3.716272	0	0
37.0	3.716285	0	0
38.0	3.716294	0	0
39.0	3.716301	0	0
40.0	3.716306	0	0
41.0	3.716309	0	0
42.0	3.716312	0	0
43.0	3.716314	0	0
44.0	3.716315	0	0
45.0	3.716316	0	0
46.0	3.716317	0	0
47.0	3.716317	0	0
48.0	3.716318	0	0
49.0	3.716318	0	0
50.0	3.716318	0	0
51.0	3.716319	0	0
52.0	3.716319	0	0
53.0	3.716319	0	0
54.0	3.716319	0	0
55.0	3.716319	0	0
56.0	3.716319	0	0
57.0	3.716319	0	0
58.0	3.716319	0	0
59.0	3.716319	0	0
60.0	3.716319	0	0
61.0	3.716319	0	0
62.0	3.716319	0	0
63.0	3.716319	0	0
64.0	3.716319	0	0
65.0	3.716319	0	0
66.0	3.716319	0	0
67.0	3.716319	0	0
68.0	3.716319	0	0
69.0	3.716319	0	0
70.0	3.716319	0	0
71.0	3.716319	0	0
72.0	3.716319	0	0
73.0	3.716319	0	0
74.0	3.716319	0	0
75.0	3.716319	0	0
76.0	3.716319	0	0
77.0	3.716319	0	0
78.0	3.716319	0	0
79.0	3.716319	0	0
80.0	3.716319	0	0
81.0	3.716319	0	0
82.0	3.716319	0	0
83.0	3.716319	0	0
84.0	3.716319	0	0
85.0	3.716319	0	0
86.0	3.716319	0	0
87.0	3.716319	0	0
88.0	3.716319	0	0
89.0	3.716319	0	0
90.0	3.716319	0	0
91.0	3.716319	0	0
92.0	3.716319	0	0
93.0	3.716319	0	0
94.0	3.716319	0	0
95.0	3.716319	0	0
96.0	3.716319	0	0
97.0	3.716319	0	0
98.0	3.716319	0	0
99.0	3.716319	0	0
100.0	3.716319	0	0