## 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-GSM919934.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919934.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919934.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 15:38:05 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	10288694	1789956	0	0	1681142	0	0.163397	27951615

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7844711	7844711
2.0	1.692055	483843	483843
3.0	2.170996	129109	129109
4.0	2.502449	55782	55782
5.0	2.731833	29288	29288
6.0	2.89058	17452	17452
7.0	3.000441	11231	11231
8.0	3.076471	7718	7718
9.0	3.129088	5600	5600
10.0	3.165502	4133	4133
11.0	3.190702	3048	3048
12.0	3.208142	2387	2387
13.0	3.220212	1884	1884
14.0	3.228565	1553	1553
15.0	3.234345	1292	1292
16.0	3.238346	1041	1041
17.0	3.241114	871	871
18.0	3.24303	733	733
19.0	3.244356	586	586
20.0	3.245274	511	511
21.0	3.245909	477	477
22.0	3.246348	357	357
23.0	3.246653	314	314
24.0	3.246863	308	308
25.0	3.247009	266	266
26.0	3.24711	242	242
27.0	3.247179	222	222
28.0	3.247228	167	167
29.0	3.247261	136	136
30.0	3.247284	149	149
31.0	3.2473	140	140
32.0	3.247311	124	124
33.0	3.247319	114	114
34.0	3.247324	108	108
35.0	3.247328	100	100
36.0	3.24733	86	86
37.0	3.247332	77	77
38.0	3.247333	73	73
39.0	3.247334	59	59
40.0	3.247335	67	67
41.0	3.247335	58	58
42.0	3.247336	69	69
43.0	3.247336	44	44
44.0	3.247336	38	38
45.0	3.247336	45	45
46.0	3.247336	40	40
47.0	3.247336	45	45
48.0	3.247336	46	46
49.0	3.247336	27	27
50.0	3.247336	29	29
51.0	3.247336	23	23
52.0	3.247336	22	22
53.0	3.247336	26	26
54.0	3.247336	20	20
55.0	3.247336	27	27
56.0	3.247336	25	25
57.0	3.247336	28	28
58.0	3.247336	18	18
59.0	3.247336	26	26
60.0	3.247336	13	13
61.0	3.247336	29	29
62.0	3.247336	18	18
63.0	3.247336	14	14
64.0	3.247336	20	20
65.0	3.247336	14	14
66.0	3.247336	13	13
67.0	3.247336	10	10
68.0	3.247336	9	9
69.0	3.247336	14	14
70.0	3.247336	13	13
71.0	3.247336	14	14
72.0	3.247336	11	11
73.0	3.247336	14	14
74.0	3.247336	6	6
75.0	3.247336	14	14
76.0	3.247336	4	4
77.0	3.247336	15	15
78.0	3.247336	2	2
79.0	3.247336	9	9
80.0	3.247336	5	5
81.0	3.247336	3	3
82.0	3.247336	6	6
83.0	3.247336	8	8
84.0	3.247336	8	8
85.0	3.247336	6	6
86.0	3.247336	9	9
87.0	3.247336	8	8
88.0	3.247336	5	5
89.0	3.247336	9	9
90.0	3.247336	6	6
91.0	3.247336	6	6
92.0	3.247336	2	2
93.0	3.247336	5	5
94.0	3.247336	5	5
95.0	3.247336	2	2
96.0	3.247336	2	2
97.0	3.247336	7	7
98.0	3.247336	4	4
99.0	3.247336	2	2
100.0	3.247336	1	1
101.0	0	4	4
102.0	0	4	4
103.0	0	3	3
104.0	0	3	3
105.0	0	2	2
106.0	0	5	5
108.0	0	1	1
109.0	0	4	4
110.0	0	2	2
111.0	0	1	1
112.0	0	3	3
113.0	0	3	3
114.0	0	2	2
115.0	0	5	5
116.0	0	1	1
117.0	0	1	1
118.0	0	6	6
120.0	0	2	2
121.0	0	2	2
122.0	0	5	5
123.0	0	4	4
124.0	0	2	2
125.0	0	2	2
126.0	0	2	2
127.0	0	2	2
129.0	0	7	7
130.0	0	1	1
131.0	0	1	1
132.0	0	1	1
134.0	0	3	3
136.0	0	2	2
139.0	0	1	1
142.0	0	2	2
144.0	0	1	1
145.0	0	2	2
146.0	0	1	1
147.0	0	1	1
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
153.0	0	1	1
154.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	2	2
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	3	3
174.0	0	2	2
175.0	0	1	1
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
182.0	0	1	1
186.0	0	2	2
189.0	0	1	1
191.0	0	1	1
192.0	0	2	2
196.0	0	1	1
197.0	0	1	1
204.0	0	1	1
206.0	0	1	1
207.0	0	1	1
212.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	2	2
227.0	0	2	2
229.0	0	1	1
233.0	0	1	1
238.0	0	1	1
239.0	0	1	1
245.0	0	1	1
246.0	0	1	1
249.0	0	1	1
252.0	0	1	1
257.0	0	1	1
258.0	0	1	1
260.0	0	1	1
267.0	0	2	2
268.0	0	1	1
280.0	0	1	1
281.0	0	1	1
318.0	0	1	1
321.0	0	1	1
349.0	0	1	1
350.0	0	1	1
353.0	0	1	1
374.0	0	1	1
388.0	0	1	1
394.0	0	1	1
398.0	0	1	1
428.0	0	1	1
438.0	0	1	1
449.0	0	1	1
495.0	0	1	1
503.0	0	1	1
556.0	0	1	1
666.0	0	1	1
683.0	0	1	1
932.0	0	1	1
1279.0	0	1	1