## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919943.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919943.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919943.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/siebrenf/tmp]    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 REMOVE_DUPLICATES=false 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: Tue Nov 02 15:32:11 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	0	10528340	1052438	0	0	1040114	0	0.098792	49714986

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8798588	8798588
2.0	1.809148	536772	536772
3.0	2.463867	91036	91036
4.0	2.993632	29132	29132
5.0	3.42229	12677	12677
6.0	3.769138	6406	6406
7.0	4.049789	3817	3817
8.0	4.276877	2422	2422
9.0	4.460624	1678	1678
10.0	4.609303	1144	1144
11.0	4.729607	838	838
12.0	4.82695	602	602
13.0	4.905715	478	478
14.0	4.969447	368	368
15.0	5.021016	310	310
16.0	5.062743	226	226
17.0	5.096506	222	222
18.0	5.123825	165	165
19.0	5.145931	146	146
20.0	5.163818	131	131
21.0	5.17829	118	118
22.0	5.190001	88	88
23.0	5.199477	94	94
24.0	5.207144	62	62
25.0	5.213348	57	57
26.0	5.218368	51	51
27.0	5.22243	41	41
28.0	5.225716	46	46
29.0	5.228376	38	38
30.0	5.230527	25	25
31.0	5.232268	24	24
32.0	5.233677	30	30
33.0	5.234817	30	30
34.0	5.23574	23	23
35.0	5.236486	15	15
36.0	5.23709	17	17
37.0	5.237579	17	17
38.0	5.237974	20	20
39.0	5.238294	15	15
40.0	5.238553	11	11
41.0	5.238762	18	18
42.0	5.238932	15	15
43.0	5.239069	9	9
44.0	5.23918	9	9
45.0	5.23927	8	8
46.0	5.239342	9	9
47.0	5.239401	10	10
48.0	5.239449	6	6
49.0	5.239487	5	5
50.0	5.239518	7	7
51.0	5.239543	6	6
52.0	5.239564	2	2
53.0	5.23958	3	3
54.0	5.239594	3	3
55.0	5.239604	5	5
56.0	5.239613	4	4
57.0	5.23962	2	2
58.0	5.239626	3	3
59.0	5.239631	5	5
60.0	5.239634	5	5
61.0	5.239637	2	2
62.0	5.23964	2	2
63.0	5.239642	2	2
64.0	5.239643	2	2
65.0	5.239645	9	9
66.0	5.239646	2	2
67.0	5.239647	3	3
68.0	5.239647	2	2
69.0	5.239648	4	4
70.0	5.239648	2	2
71.0	5.239649	1	1
72.0	5.239649	1	1
73.0	5.239649	3	3
74.0	5.239649	2	2
75.0	5.23965	1	1
76.0	5.23965	2	2
77.0	5.23965	1	1
78.0	5.23965	0	0
79.0	5.23965	3	3
80.0	5.23965	1	1
81.0	5.23965	3	3
82.0	5.23965	2	2
83.0	5.23965	0	0
84.0	5.23965	4	4
85.0	5.23965	2	2
86.0	5.23965	0	0
87.0	5.23965	0	0
88.0	5.23965	2	2
89.0	5.23965	0	0
90.0	5.23965	1	1
91.0	5.23965	0	0
92.0	5.23965	1	1
93.0	5.23965	1	1
94.0	5.23965	0	0
95.0	5.23965	1	1
96.0	5.23965	0	0
97.0	5.23965	1	1
98.0	5.23965	0	0
99.0	5.23965	0	0
100.0	5.23965	0	0
102.0	0	1	1
110.0	0	1	1
111.0	0	3	3
112.0	0	2	2
113.0	0	1	1
114.0	0	2	2
118.0	0	2	2
119.0	0	1	1
120.0	0	1	1
122.0	0	2	2
123.0	0	1	1
126.0	0	1	1
130.0	0	1	1
136.0	0	1	1
137.0	0	1	1
147.0	0	1	1
150.0	0	1	1
160.0	0	2	2
164.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
177.0	0	1	1
180.0	0	1	1
182.0	0	1	1
184.0	0	1	1
224.0	0	1	1
241.0	0	1	1
255.0	0	2	2
261.0	0	1	1
263.0	0	1	1
271.0	0	1	1
278.0	0	1	1
302.0	0	1	1
307.0	0	1	1
326.0	0	1	1
422.0	0	1	1
424.0	0	1	1
554.0	0	1	1
603.0	0	1	1
1293.0	0	1	1