## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/bwa-mem2/hg38-GSM2400260.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-GSM2400260.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-GSM2400260.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/GZnl]    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 03:22:20 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	596005	128198943	0	0	168621	24674679	0	0.192682	288767495

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	82845057	82845057
2.0	1.641496	16829515	16829515
3.0	2.053013	2937822	2937822
4.0	2.317	475743	475743
5.0	2.486347	80363	80363
6.0	2.594982	18711	18711
7.0	2.664671	6729	6729
8.0	2.709376	3349	3349
9.0	2.738054	1914	1914
10.0	2.756451	1145	1145
11.0	2.768253	766	766
12.0	2.775823	533	533
13.0	2.78068	395	395
14.0	2.783795	250	250
15.0	2.785794	154	154
16.0	2.787076	147	147
17.0	2.787899	109	109
18.0	2.788426	73	73
19.0	2.788765	60	60
20.0	2.788982	40	40
21.0	2.789121	55	55
22.0	2.78921	24	24
23.0	2.789268	31	31
24.0	2.789304	18	18
25.0	2.789328	19	19
26.0	2.789343	10	10
27.0	2.789353	13	13
28.0	2.789359	8	8
29.0	2.789363	5	5
30.0	2.789366	6	6
31.0	2.789367	10	10
32.0	2.789368	3	3
33.0	2.789369	3	3
34.0	2.789369	1	1
35.0	2.78937	4	4
36.0	2.78937	3	3
37.0	2.78937	3	3
38.0	2.78937	3	3
39.0	2.78937	1	1
40.0	2.78937	3	3
41.0	2.78937	1	1
42.0	2.78937	2	2
43.0	2.78937	1	1
44.0	2.78937	0	0
45.0	2.78937	0	0
46.0	2.78937	1	1
47.0	2.78937	1	1
48.0	2.78937	1	1
49.0	2.78937	2	2
50.0	2.78937	0	0
51.0	2.78937	3	3
52.0	2.78937	0	0
53.0	2.78937	0	0
54.0	2.78937	1	1
55.0	2.78937	0	0
56.0	2.78937	0	0
57.0	2.78937	1	1
58.0	2.78937	2	2
59.0	2.78937	0	0
60.0	2.78937	0	0
61.0	2.78937	1	1
62.0	2.78937	0	0
63.0	2.78937	0	0
64.0	2.78937	2	2
65.0	2.78937	1	1
66.0	2.78937	0	0
67.0	2.78937	0	0
68.0	2.78937	1	1
69.0	2.78937	1	1
70.0	2.78937	0	0
71.0	2.78937	1	1
72.0	2.78937	0	0
73.0	2.78937	0	0
74.0	2.78937	0	0
75.0	2.78937	0	0
76.0	2.78937	0	0
77.0	2.78937	0	0
78.0	2.78937	0	0
79.0	2.78937	1	1
80.0	2.78937	0	0
81.0	2.78937	0	0
82.0	2.78937	0	0
83.0	2.78937	0	0
84.0	2.78937	0	0
85.0	2.78937	0	0
86.0	2.78937	0	0
87.0	2.78937	0	0
88.0	2.78937	0	0
89.0	2.78937	0	0
90.0	2.78937	0	0
91.0	2.78937	0	0
92.0	2.78937	0	0
93.0	2.78937	0	0
94.0	2.78937	0	0
95.0	2.78937	0	0
96.0	2.78937	0	0
97.0	2.78937	0	0
98.0	2.78937	0	0
99.0	2.78937	0	0
100.0	2.78937	0	0
112.0	0	1	1
124.0	0	1	1
203.0	0	1	1