## 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-GSM919932.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919932.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919932.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 15:23:51 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	11411866	2151520	0	0	1827478	0	0.160138	31716055

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8743405	8743405
2.0	1.697806	539937	539937
3.0	2.18474	139765	139765
4.0	2.524526	59565	59565
5.0	2.76163	31506	31506
6.0	2.927083	18868	18868
7.0	3.042538	12113	12113
8.0	3.123102	8514	8514
9.0	3.179321	5867	5867
10.0	3.218551	4460	4460
11.0	3.245925	3336	3336
12.0	3.265027	2567	2567
13.0	3.278357	2037	2037
14.0	3.287659	1759	1759
15.0	3.294149	1334	1334
16.0	3.298679	1138	1138
17.0	3.301839	926	926
18.0	3.304045	848	848
19.0	3.305584	670	670
20.0	3.306657	585	585
21.0	3.307407	456	456
22.0	3.30793	438	438
23.0	3.308295	407	407
24.0	3.308549	313	313
25.0	3.308727	281	281
26.0	3.308851	266	266
27.0	3.308937	236	236
28.0	3.308998	202	202
29.0	3.30904	180	180
30.0	3.309069	172	172
31.0	3.30909	150	150
32.0	3.309104	131	131
33.0	3.309114	127	127
34.0	3.309121	106	106
35.0	3.309126	108	108
36.0	3.309129	86	86
37.0	3.309132	83	83
38.0	3.309133	70	70
39.0	3.309135	77	77
40.0	3.309135	56	56
41.0	3.309136	64	64
42.0	3.309136	61	61
43.0	3.309137	53	53
44.0	3.309137	51	51
45.0	3.309137	53	53
46.0	3.309137	27	27
47.0	3.309137	36	36
48.0	3.309137	36	36
49.0	3.309137	42	42
50.0	3.309137	40	40
51.0	3.309137	33	33
52.0	3.309137	34	34
53.0	3.309137	29	29
54.0	3.309137	27	27
55.0	3.309137	31	31
56.0	3.309137	33	33
57.0	3.309137	17	17
58.0	3.309137	17	17
59.0	3.309137	15	15
60.0	3.309137	21	21
61.0	3.309137	10	10
62.0	3.309137	26	26
63.0	3.309137	14	14
64.0	3.309137	14	14
65.0	3.309137	16	16
66.0	3.309137	13	13
67.0	3.309137	21	21
68.0	3.309137	15	15
69.0	3.309137	13	13
70.0	3.309137	6	6
71.0	3.309137	9	9
72.0	3.309137	7	7
73.0	3.309137	12	12
74.0	3.309137	18	18
75.0	3.309137	6	6
76.0	3.309137	14	14
77.0	3.309137	6	6
78.0	3.309137	8	8
79.0	3.309137	10	10
80.0	3.309137	4	4
81.0	3.309137	2	2
82.0	3.309137	5	5
83.0	3.309137	2	2
84.0	3.309137	6	6
85.0	3.309137	6	6
86.0	3.309137	8	8
87.0	3.309137	2	2
88.0	3.309137	6	6
89.0	3.309137	5	5
90.0	3.309137	4	4
91.0	3.309137	4	4
92.0	3.309137	7	7
93.0	3.309137	6	6
94.0	3.309137	6	6
95.0	3.309137	6	6
96.0	3.309137	6	6
97.0	3.309137	6	6
98.0	3.309137	7	7
99.0	3.309137	5	5
100.0	3.309137	1	1
101.0	0	3	3
102.0	0	1	1
103.0	0	3	3
104.0	0	4	4
105.0	0	2	2
106.0	0	4	4
107.0	0	2	2
108.0	0	3	3
109.0	0	3	3
110.0	0	4	4
111.0	0	2	2
112.0	0	5	5
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
116.0	0	1	1
117.0	0	2	2
118.0	0	1	1
119.0	0	6	6
120.0	0	7	7
121.0	0	3	3
122.0	0	1	1
124.0	0	1	1
125.0	0	1	1
127.0	0	2	2
129.0	0	3	3
131.0	0	3	3
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	2	2
136.0	0	1	1
137.0	0	3	3
138.0	0	2	2
139.0	0	2	2
140.0	0	3	3
141.0	0	2	2
142.0	0	3	3
143.0	0	1	1
144.0	0	4	4
145.0	0	1	1
146.0	0	2	2
149.0	0	1	1
150.0	0	5	5
151.0	0	1	1
152.0	0	2	2
153.0	0	1	1
154.0	0	1	1
155.0	0	2	2
156.0	0	4	4
157.0	0	1	1
158.0	0	1	1
164.0	0	1	1
166.0	0	2	2
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
171.0	0	2	2
172.0	0	1	1
173.0	0	3	3
174.0	0	1	1
176.0	0	1	1
177.0	0	3	3
178.0	0	1	1
179.0	0	2	2
182.0	0	1	1
183.0	0	1	1
188.0	0	1	1
189.0	0	1	1
196.0	0	1	1
205.0	0	2	2
212.0	0	2	2
214.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
223.0	0	1	1
225.0	0	1	1
228.0	0	1	1
234.0	0	1	1
236.0	0	1	1
241.0	0	1	1
242.0	0	1	1
247.0	0	1	1
249.0	0	1	1
250.0	0	1	1
261.0	0	2	2
266.0	0	1	1
285.0	0	1	1
289.0	0	1	1
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
354.0	0	1	1
369.0	0	1	1
406.0	0	1	1
426.0	0	1	1
434.0	0	1	1
568.0	0	2	2
833.0	0	1	1