## 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-GSM1606213.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606213.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606213.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 14:09:43 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	30406574	5079110	0	0	4011194	0	0.131919	104871871

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	24320907	24320907
2.0	1.748308	1435916	1435916
3.0	2.308274	316326	316326
4.0	2.7273	124876	124876
5.0	3.040861	63584	63584
6.0	3.275502	36863	36863
7.0	3.451085	23440	23440
8.0	3.582476	16017	16017
9.0	3.680796	11292	11292
10.0	3.75437	8213	8213
11.0	3.809426	6361	6361
12.0	3.850625	4947	4947
13.0	3.881455	3790	3790
14.0	3.904525	3125	3125
15.0	3.921788	2480	2480
16.0	3.934707	2079	2079
17.0	3.944374	1801	1801
18.0	3.951608	1491	1491
19.0	3.957021	1219	1219
20.0	3.961071	1071	1071
21.0	3.964103	919	919
22.0	3.966371	776	776
23.0	3.968068	684	684
24.0	3.969338	638	638
25.0	3.970289	564	564
26.0	3.971	486	486
27.0	3.971532	399	399
28.0	3.971931	366	366
29.0	3.972229	357	357
30.0	3.972452	294	294
31.0	3.972618	269	269
32.0	3.972743	285	285
33.0	3.972837	243	243
34.0	3.972907	208	208
35.0	3.972959	196	196
36.0	3.972998	190	190
37.0	3.973028	172	172
38.0	3.973049	145	145
39.0	3.973066	160	160
40.0	3.973078	111	111
41.0	3.973087	122	122
42.0	3.973094	97	97
43.0	3.973099	102	102
44.0	3.973103	100	100
45.0	3.973106	88	88
46.0	3.973108	91	91
47.0	3.97311	72	72
48.0	3.973111	79	79
49.0	3.973112	57	57
50.0	3.973113	55	55
51.0	3.973113	58	58
52.0	3.973114	48	48
53.0	3.973114	62	62
54.0	3.973114	44	44
55.0	3.973114	49	49
56.0	3.973114	43	43
57.0	3.973114	49	49
58.0	3.973114	41	41
59.0	3.973115	38	38
60.0	3.973115	30	30
61.0	3.973115	28	28
62.0	3.973115	32	32
63.0	3.973115	26	26
64.0	3.973115	27	27
65.0	3.973115	26	26
66.0	3.973115	16	16
67.0	3.973115	33	33
68.0	3.973115	20	20
69.0	3.973115	28	28
70.0	3.973115	17	17
71.0	3.973115	16	16
72.0	3.973115	22	22
73.0	3.973115	16	16
74.0	3.973115	15	15
75.0	3.973115	12	12
76.0	3.973115	17	17
77.0	3.973115	16	16
78.0	3.973115	18	18
79.0	3.973115	14	14
80.0	3.973115	15	15
81.0	3.973115	17	17
82.0	3.973115	13	13
83.0	3.973115	11	11
84.0	3.973115	10	10
85.0	3.973115	9	9
86.0	3.973115	11	11
87.0	3.973115	8	8
88.0	3.973115	9	9
89.0	3.973115	8	8
90.0	3.973115	13	13
91.0	3.973115	13	13
92.0	3.973115	5	5
93.0	3.973115	4	4
94.0	3.973115	7	7
95.0	3.973115	7	7
96.0	3.973115	5	5
97.0	3.973115	5	5
98.0	3.973115	5	5
99.0	3.973115	10	10
100.0	3.973115	3	3
101.0	0	6	6
102.0	0	2	2
103.0	0	3	3
104.0	0	7	7
105.0	0	4	4
106.0	0	4	4
107.0	0	9	9
108.0	0	1	1
109.0	0	3	3
110.0	0	3	3
111.0	0	4	4
112.0	0	5	5
113.0	0	4	4
115.0	0	1	1
116.0	0	3	3
117.0	0	7	7
118.0	0	3	3
119.0	0	1	1
120.0	0	1	1
121.0	0	4	4
122.0	0	7	7
123.0	0	3	3
124.0	0	2	2
125.0	0	2	2
126.0	0	3	3
127.0	0	2	2
128.0	0	1	1
129.0	0	2	2
130.0	0	3	3
131.0	0	1	1
133.0	0	3	3
134.0	0	1	1
135.0	0	1	1
136.0	0	2	2
138.0	0	3	3
139.0	0	3	3
141.0	0	1	1
143.0	0	2	2
144.0	0	1	1
145.0	0	4	4
146.0	0	4	4
147.0	0	2	2
151.0	0	3	3
152.0	0	1	1
154.0	0	1	1
155.0	0	1	1
156.0	0	2	2
159.0	0	2	2
160.0	0	1	1
161.0	0	2	2
162.0	0	3	3
163.0	0	2	2
164.0	0	2	2
165.0	0	1	1
167.0	0	1	1
168.0	0	2	2
169.0	0	3	3
171.0	0	2	2
172.0	0	1	1
173.0	0	1	1
175.0	0	1	1
176.0	0	1	1
182.0	0	1	1
184.0	0	1	1
186.0	0	1	1
188.0	0	1	1
192.0	0	1	1
195.0	0	1	1
198.0	0	1	1
199.0	0	1	1
203.0	0	1	1
207.0	0	1	1
208.0	0	1	1
210.0	0	1	1
215.0	0	1	1
218.0	0	1	1
222.0	0	1	1
223.0	0	2	2
224.0	0	1	1
234.0	0	1	1
236.0	0	1	1
240.0	0	1	1
244.0	0	1	1
250.0	0	1	1
254.0	0	1	1
261.0	0	1	1
276.0	0	1	1
278.0	0	1	1
280.0	0	1	1
295.0	0	1	1
300.0	0	2	2
310.0	0	1	1
312.0	0	1	1
320.0	0	2	2
329.0	0	1	1
331.0	0	1	1
363.0	0	1	1
364.0	0	1	1
440.0	0	1	1
445.0	0	1	1
520.0	0	1	1
599.0	0	1	1
636.0	0	1	1
1093.0	0	1	1
1198.0	0	1	1
8751.0	0	1	1