## 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-GSM919928.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919928.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919928.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 15:44:48 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	9662954	1851666	0	0	1654518	0	0.171223	24895092

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7168853	7168853
2.0	1.678313	579650	579650
3.0	2.138421	126037	126037
4.0	2.450518	50700	50700
5.0	2.662217	26013	26013
6.0	2.805816	15449	15449
7.0	2.90322	9895	9895
8.0	2.969291	7041	7041
9.0	3.014108	4801	4801
10.0	3.044507	3551	3551
11.0	3.065128	2675	2675
12.0	3.079115	2107	2107
13.0	3.088603	1703	1703
14.0	3.095038	1414	1414
15.0	3.099404	1085	1085
16.0	3.102365	939	939
17.0	3.104373	707	707
18.0	3.105736	629	629
19.0	3.10666	524	524
20.0	3.107287	443	443
21.0	3.107712	385	385
22.0	3.108	350	350
23.0	3.108196	337	337
24.0	3.108329	254	254
25.0	3.108419	229	229
26.0	3.10848	224	224
27.0	3.108521	196	196
28.0	3.108549	166	166
29.0	3.108568	133	133
30.0	3.108581	159	159
31.0	3.10859	136	136
32.0	3.108596	118	118
33.0	3.1086	93	93
34.0	3.108603	93	93
35.0	3.108605	83	83
36.0	3.108606	68	68
37.0	3.108607	87	87
38.0	3.108607	69	69
39.0	3.108608	59	59
40.0	3.108608	56	56
41.0	3.108608	47	47
42.0	3.108608	45	45
43.0	3.108608	40	40
44.0	3.108608	42	42
45.0	3.108608	37	37
46.0	3.108608	37	37
47.0	3.108608	34	34
48.0	3.108608	32	32
49.0	3.108608	16	16
50.0	3.108608	25	25
51.0	3.108608	28	28
52.0	3.108608	16	16
53.0	3.108608	19	19
54.0	3.108608	26	26
55.0	3.108608	18	18
56.0	3.108608	19	19
57.0	3.108608	18	18
58.0	3.108608	22	22
59.0	3.108608	17	17
60.0	3.108608	9	9
61.0	3.108608	18	18
62.0	3.108608	12	12
63.0	3.108608	9	9
64.0	3.108608	10	10
65.0	3.108608	4	4
66.0	3.108608	9	9
67.0	3.108608	8	8
68.0	3.108608	10	10
69.0	3.108608	13	13
70.0	3.108608	11	11
71.0	3.108608	10	10
72.0	3.108608	11	11
73.0	3.108608	9	9
74.0	3.108608	3	3
75.0	3.108608	7	7
76.0	3.108608	12	12
77.0	3.108608	8	8
78.0	3.108608	6	6
79.0	3.108608	8	8
80.0	3.108608	4	4
81.0	3.108608	6	6
82.0	3.108608	5	5
83.0	3.108608	7	7
84.0	3.108608	2	2
85.0	3.108608	5	5
86.0	3.108608	3	3
87.0	3.108608	6	6
88.0	3.108608	4	4
89.0	3.108608	3	3
90.0	3.108608	2	2
91.0	3.108608	3	3
92.0	3.108608	4	4
93.0	3.108608	2	2
94.0	3.108608	5	5
95.0	3.108608	3	3
96.0	3.108608	3	3
97.0	3.108608	3	3
98.0	3.108608	1	1
99.0	3.108608	2	2
100.0	3.108608	3	3
101.0	0	1	1
102.0	0	4	4
103.0	0	5	5
104.0	0	2	2
105.0	0	7	7
106.0	0	3	3
107.0	0	5	5
108.0	0	7	7
109.0	0	3	3
110.0	0	2	2
111.0	0	2	2
112.0	0	2	2
113.0	0	2	2
114.0	0	2	2
117.0	0	1	1
118.0	0	2	2
119.0	0	1	1
120.0	0	1	1
121.0	0	1	1
123.0	0	4	4
124.0	0	2	2
126.0	0	2	2
127.0	0	1	1
128.0	0	4	4
130.0	0	2	2
132.0	0	2	2
133.0	0	1	1
136.0	0	1	1
137.0	0	1	1
139.0	0	1	1
140.0	0	3	3
141.0	0	2	2
142.0	0	1	1
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
159.0	0	2	2
164.0	0	1	1
165.0	0	2	2
167.0	0	3	3
175.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
189.0	0	1	1
190.0	0	3	3
191.0	0	1	1
193.0	0	1	1
197.0	0	1	1
209.0	0	1	1
213.0	0	1	1
225.0	0	1	1
226.0	0	1	1
229.0	0	1	1
234.0	0	1	1
239.0	0	1	1
241.0	0	1	1
270.0	0	1	1
274.0	0	1	1
303.0	0	1	1
309.0	0	1	1
311.0	0	1	1
326.0	0	1	1
356.0	0	1	1
456.0	0	1	1
463.0	0	1	1
584.0	0	1	1
643.0	0	1	1
644.0	0	1	1
725.0	0	1	1
905.0	0	1	1