## 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-GSM1606356.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606356.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606356.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 22:36:26 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	30720967	4332214	0	0	4934036	0	0.160608	85098764

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23275908	23275908
2.0	1.696976	1739836	1739836
3.0	2.182753	377301	377301
4.0	2.521327	149668	149668
5.0	2.757306	76062	76062
6.0	2.921777	44991	44991
7.0	3.03641	29214	29214
8.0	3.116306	19651	19651
9.0	3.171992	14191	14191
10.0	3.210804	10396	10396
11.0	3.237854	8017	8017
12.0	3.256708	6317	6317
13.0	3.269849	4971	4971
14.0	3.279008	4046	4046
15.0	3.285391	3411	3411
16.0	3.28984	2716	2716
17.0	3.292941	2334	2334
18.0	3.295102	1887	1887
19.0	3.296609	1600	1600
20.0	3.297659	1377	1377
21.0	3.29839	1191	1191
22.0	3.2989	1053	1053
23.0	3.299256	949	949
24.0	3.299504	817	817
25.0	3.299676	792	792
26.0	3.299797	634	634
27.0	3.29988	592	592
28.0	3.299939	519	519
29.0	3.29998	487	487
30.0	3.300008	397	397
31.0	3.300028	360	360
32.0	3.300042	399	399
33.0	3.300051	310	310
34.0	3.300058	288	288
35.0	3.300063	306	306
36.0	3.300066	258	258
37.0	3.300068	235	235
38.0	3.30007	205	205
39.0	3.300071	174	174
40.0	3.300072	169	169
41.0	3.300072	158	158
42.0	3.300073	119	119
43.0	3.300073	149	149
44.0	3.300073	120	120
45.0	3.300073	98	98
46.0	3.300073	113	113
47.0	3.300073	104	104
48.0	3.300073	98	98
49.0	3.300073	93	93
50.0	3.300073	71	71
51.0	3.300073	90	90
52.0	3.300073	79	79
53.0	3.300073	80	80
54.0	3.300073	68	68
55.0	3.300073	45	45
56.0	3.300073	58	58
57.0	3.300073	53	53
58.0	3.300073	60	60
59.0	3.300073	37	37
60.0	3.300073	58	58
61.0	3.300073	37	37
62.0	3.300073	37	37
63.0	3.300073	38	38
64.0	3.300073	33	33
65.0	3.300073	32	32
66.0	3.300073	35	35
67.0	3.300073	35	35
68.0	3.300073	36	36
69.0	3.300073	37	37
70.0	3.300073	23	23
71.0	3.300073	34	34
72.0	3.300073	34	34
73.0	3.300073	33	33
74.0	3.300073	19	19
75.0	3.300073	22	22
76.0	3.300073	30	30
77.0	3.300073	18	18
78.0	3.300073	18	18
79.0	3.300073	16	16
80.0	3.300073	11	11
81.0	3.300073	23	23
82.0	3.300073	15	15
83.0	3.300073	13	13
84.0	3.300073	21	21
85.0	3.300073	15	15
86.0	3.300073	10	10
87.0	3.300073	20	20
88.0	3.300073	8	8
89.0	3.300073	12	12
90.0	3.300073	12	12
91.0	3.300073	12	12
92.0	3.300073	10	10
93.0	3.300073	13	13
94.0	3.300073	7	7
95.0	3.300073	17	17
96.0	3.300073	9	9
97.0	3.300073	3	3
98.0	3.300073	5	5
99.0	3.300073	16	16
100.0	3.300073	14	14
101.0	0	7	7
102.0	0	8	8
103.0	0	4	4
104.0	0	9	9
105.0	0	5	5
106.0	0	10	10
107.0	0	9	9
108.0	0	6	6
109.0	0	5	5
110.0	0	4	4
111.0	0	7	7
112.0	0	4	4
113.0	0	5	5
114.0	0	7	7
115.0	0	4	4
116.0	0	5	5
117.0	0	5	5
118.0	0	3	3
119.0	0	2	2
120.0	0	6	6
121.0	0	6	6
122.0	0	9	9
123.0	0	8	8
124.0	0	2	2
125.0	0	7	7
126.0	0	3	3
127.0	0	5	5
128.0	0	3	3
129.0	0	7	7
130.0	0	4	4
131.0	0	4	4
132.0	0	3	3
133.0	0	2	2
134.0	0	2	2
135.0	0	2	2
136.0	0	2	2
137.0	0	2	2
138.0	0	2	2
139.0	0	6	6
140.0	0	5	5
141.0	0	1	1
142.0	0	4	4
143.0	0	1	1
144.0	0	1	1
145.0	0	4	4
147.0	0	2	2
148.0	0	2	2
149.0	0	1	1
150.0	0	3	3
151.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	5	5
155.0	0	2	2
156.0	0	1	1
157.0	0	2	2
159.0	0	2	2
160.0	0	2	2
161.0	0	4	4
162.0	0	1	1
163.0	0	1	1
165.0	0	1	1
166.0	0	2	2
168.0	0	1	1
169.0	0	1	1
172.0	0	2	2
174.0	0	4	4
175.0	0	3	3
178.0	0	1	1
179.0	0	1	1
182.0	0	3	3
185.0	0	1	1
188.0	0	2	2
189.0	0	1	1
191.0	0	1	1
193.0	0	1	1
194.0	0	2	2
195.0	0	1	1
197.0	0	1	1
198.0	0	2	2
199.0	0	1	1
200.0	0	3	3
201.0	0	1	1
204.0	0	1	1
205.0	0	1	1
210.0	0	1	1
211.0	0	2	2
214.0	0	2	2
215.0	0	1	1
220.0	0	1	1
225.0	0	1	1
228.0	0	1	1
232.0	0	2	2
239.0	0	1	1
240.0	0	1	1
242.0	0	1	1
243.0	0	1	1
248.0	0	1	1
254.0	0	1	1
257.0	0	1	1
259.0	0	1	1
260.0	0	1	1
262.0	0	1	1
266.0	0	1	1
274.0	0	2	2
289.0	0	1	1
290.0	0	1	1
302.0	0	1	1
325.0	0	1	1
327.0	0	1	1
333.0	0	1	1
338.0	0	1	1
377.0	0	1	1
387.0	0	1	1
390.0	0	1	1
456.0	0	1	1
482.0	0	1	1
490.0	0	1	1
619.0	0	1	1
7645.0	0	1	1