## 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-GSM919926.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919926.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919926.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 15:31:13 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	10349993	2245014	0	0	1485444	0	0.143521	32517836

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8124890	8124890
2.0	1.727394	496732	496732
3.0	2.256497	117418	117418
4.0	2.641363	48442	48442
5.0	2.921312	24635	24635
6.0	3.124946	14572	14572
7.0	3.273067	9348	9348
8.0	3.38081	6290	6290
9.0	3.459182	4562	4562
10.0	3.516189	3285	3285
11.0	3.557656	2524	2524
12.0	3.587818	1843	1843
13.0	3.609758	1485	1485
14.0	3.625718	1231	1231
15.0	3.637326	948	948
16.0	3.64577	774	774
17.0	3.651912	700	700
18.0	3.65638	529	529
19.0	3.65963	452	452
20.0	3.661994	388	388
21.0	3.663713	348	348
22.0	3.664964	277	277
23.0	3.665874	266	266
24.0	3.666535	228	228
25.0	3.667017	175	175
26.0	3.667367	177	177
27.0	3.667622	179	179
28.0	3.667807	145	145
29.0	3.667942	109	109
30.0	3.66804	112	112
31.0	3.668111	86	86
32.0	3.668163	78	78
33.0	3.668201	87	87
34.0	3.668228	111	111
35.0	3.668248	55	55
36.0	3.668262	60	60
37.0	3.668273	54	54
38.0	3.668281	44	44
39.0	3.668286	61	61
40.0	3.66829	64	64
41.0	3.668293	42	42
42.0	3.668295	37	37
43.0	3.668297	39	39
44.0	3.668298	33	33
45.0	3.668299	35	35
46.0	3.6683	24	24
47.0	3.6683	21	21
48.0	3.6683	24	24
49.0	3.668301	13	13
50.0	3.668301	18	18
51.0	3.668301	13	13
52.0	3.668301	27	27
53.0	3.668301	17	17
54.0	3.668301	13	13
55.0	3.668301	16	16
56.0	3.668301	20	20
57.0	3.668301	17	17
58.0	3.668301	14	14
59.0	3.668301	13	13
60.0	3.668301	15	15
61.0	3.668301	6	6
62.0	3.668301	11	11
63.0	3.668301	14	14
64.0	3.668301	5	5
65.0	3.668301	8	8
66.0	3.668301	14	14
67.0	3.668301	9	9
68.0	3.668301	3	3
69.0	3.668301	10	10
70.0	3.668301	9	9
71.0	3.668301	9	9
72.0	3.668301	8	8
73.0	3.668301	6	6
74.0	3.668301	4	4
75.0	3.668301	6	6
76.0	3.668301	8	8
77.0	3.668301	3	3
78.0	3.668301	3	3
79.0	3.668301	4	4
80.0	3.668301	3	3
81.0	3.668301	4	4
82.0	3.668301	7	7
83.0	3.668301	1	1
84.0	3.668301	4	4
85.0	3.668301	2	2
86.0	3.668301	2	2
87.0	3.668301	8	8
88.0	3.668301	5	5
89.0	3.668301	5	5
90.0	3.668301	2	2
91.0	3.668301	4	4
92.0	3.668301	3	3
93.0	3.668301	5	5
94.0	3.668301	3	3
95.0	3.668301	4	4
96.0	3.668301	3	3
97.0	3.668301	3	3
98.0	3.668301	6	6
99.0	3.668301	6	6
100.0	3.668301	2	2
102.0	0	1	1
103.0	0	1	1
104.0	0	2	2
105.0	0	3	3
106.0	0	4	4
107.0	0	1	1
108.0	0	2	2
110.0	0	2	2
112.0	0	3	3
113.0	0	2	2
114.0	0	2	2
115.0	0	3	3
116.0	0	2	2
118.0	0	3	3
120.0	0	1	1
121.0	0	1	1
122.0	0	3	3
123.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
132.0	0	1	1
133.0	0	2	2
135.0	0	1	1
136.0	0	1	1
137.0	0	3	3
139.0	0	2	2
140.0	0	1	1
141.0	0	2	2
146.0	0	1	1
149.0	0	1	1
150.0	0	1	1
151.0	0	1	1
153.0	0	2	2
155.0	0	4	4
156.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	2	2
162.0	0	1	1
167.0	0	1	1
170.0	0	2	2
174.0	0	1	1
184.0	0	1	1
188.0	0	1	1
194.0	0	1	1
195.0	0	1	1
198.0	0	1	1
200.0	0	1	1
204.0	0	2	2
205.0	0	1	1
209.0	0	2	2
216.0	0	1	1
219.0	0	1	1
224.0	0	2	2
226.0	0	1	1
250.0	0	1	1
265.0	0	2	2
269.0	0	1	1
274.0	0	1	1
289.0	0	1	1
298.0	0	1	1
302.0	0	1	1
322.0	0	1	1
329.0	0	1	1
372.0	0	1	1
381.0	0	1	1
410.0	0	1	1
416.0	0	1	1
438.0	0	1	1
592.0	0	1	1
597.0	0	1	1
629.0	0	1	1
662.0	0	1	1
1292.0	0	1	1