## 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-GSM919947.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919947.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919947.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 15:55:49 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	8867925	1653068	0	0	1448073	0	0.163293	24109061

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6680664	6680664
2.0	1.692238	511150	511150
3.0	2.171432	113405	113405
4.0	2.503147	44457	44457
5.0	2.732774	22594	22594
6.0	2.89173	13048	13048
7.0	3.001766	8448	8448
8.0	3.077936	5520	5520
9.0	3.130665	3965	3965
10.0	3.167165	2902	2902
11.0	3.192432	2203	2203
12.0	3.209923	1732	1732
13.0	3.222031	1428	1428
14.0	3.230412	1052	1052
15.0	3.236214	911	911
16.0	3.240231	770	770
17.0	3.243011	615	615
18.0	3.244935	547	547
19.0	3.246268	463	463
20.0	3.24719	395	395
21.0	3.247828	332	332
22.0	3.24827	290	290
23.0	3.248576	259	259
24.0	3.248788	213	213
25.0	3.248935	195	195
26.0	3.249036	173	173
27.0	3.249106	172	172
28.0	3.249155	145	145
29.0	3.249189	131	131
30.0	3.249212	128	128
31.0	3.249228	109	109
32.0	3.249239	70	70
33.0	3.249247	81	81
34.0	3.249252	68	68
35.0	3.249256	71	71
36.0	3.249259	53	53
37.0	3.24926	55	55
38.0	3.249262	46	46
39.0	3.249262	68	68
40.0	3.249263	49	49
41.0	3.249263	33	33
42.0	3.249264	53	53
43.0	3.249264	43	43
44.0	3.249264	47	47
45.0	3.249264	34	34
46.0	3.249264	36	36
47.0	3.249264	24	24
48.0	3.249264	26	26
49.0	3.249264	29	29
50.0	3.249264	16	16
51.0	3.249264	18	18
52.0	3.249264	13	13
53.0	3.249264	16	16
54.0	3.249264	25	25
55.0	3.249264	22	22
56.0	3.249264	11	11
57.0	3.249264	15	15
58.0	3.249264	16	16
59.0	3.249264	11	11
60.0	3.249264	14	14
61.0	3.249264	7	7
62.0	3.249264	10	10
63.0	3.249264	16	16
64.0	3.249264	15	15
65.0	3.249264	9	9
66.0	3.249264	6	6
67.0	3.249264	8	8
68.0	3.249264	7	7
69.0	3.249264	7	7
70.0	3.249264	10	10
71.0	3.249264	9	9
72.0	3.249264	6	6
73.0	3.249264	7	7
74.0	3.249264	10	10
75.0	3.249264	7	7
76.0	3.249264	7	7
77.0	3.249264	5	5
78.0	3.249264	7	7
79.0	3.249264	8	8
80.0	3.249264	3	3
81.0	3.249264	2	2
82.0	3.249264	2	2
83.0	3.249264	8	8
84.0	3.249264	2	2
85.0	3.249264	1	1
86.0	3.249264	5	5
87.0	3.249264	6	6
88.0	3.249264	5	5
89.0	3.249264	5	5
90.0	3.249264	2	2
91.0	3.249264	2	2
92.0	3.249264	3	3
93.0	3.249264	4	4
94.0	3.249264	6	6
95.0	3.249264	3	3
96.0	3.249264	3	3
97.0	3.249264	1	1
98.0	3.249264	3	3
99.0	3.249264	3	3
100.0	3.249264	1	1
101.0	0	5	5
102.0	0	3	3
104.0	0	2	2
105.0	0	2	2
106.0	0	3	3
107.0	0	1	1
108.0	0	3	3
110.0	0	3	3
111.0	0	2	2
112.0	0	2	2
114.0	0	2	2
115.0	0	2	2
116.0	0	2	2
117.0	0	1	1
118.0	0	2	2
119.0	0	2	2
120.0	0	3	3
121.0	0	2	2
122.0	0	2	2
123.0	0	1	1
124.0	0	3	3
126.0	0	1	1
127.0	0	3	3
128.0	0	3	3
130.0	0	1	1
133.0	0	2	2
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	4	4
139.0	0	1	1
140.0	0	1	1
141.0	0	3	3
143.0	0	2	2
144.0	0	1	1
145.0	0	1	1
146.0	0	1	1
148.0	0	1	1
151.0	0	2	2
152.0	0	1	1
153.0	0	1	1
157.0	0	2	2
158.0	0	2	2
159.0	0	1	1
160.0	0	2	2
161.0	0	1	1
164.0	0	2	2
167.0	0	1	1
168.0	0	2	2
171.0	0	1	1
173.0	0	1	1
175.0	0	1	1
180.0	0	1	1
187.0	0	1	1
190.0	0	1	1
191.0	0	2	2
195.0	0	1	1
202.0	0	1	1
204.0	0	1	1
206.0	0	1	1
208.0	0	1	1
209.0	0	1	1
216.0	0	2	2
226.0	0	1	1
229.0	0	1	1
242.0	0	1	1
250.0	0	1	1
260.0	0	1	1
264.0	0	2	2
265.0	0	2	2
266.0	0	1	1
278.0	0	1	1
281.0	0	1	1
294.0	0	1	1
347.0	0	1	1
357.0	0	1	1
365.0	0	1	1
394.0	0	1	1
397.0	0	1	1
421.0	0	1	1
440.0	0	1	1
503.0	0	1	1
515.0	0	1	1
523.0	0	1	1
539.0	0	1	1
554.0	0	1	1
568.0	0	1	1
569.0	0	1	1
589.0	0	1	1
719.0	0	1	1
805.0	0	1	1
813.0	0	1	1
1418.0	0	1	1
2052.0	0	1	1