## 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-GSM919952.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919952.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919952.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 15:50:17 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	9321052	1626660	0	0	2059265	0	0.220926	17858115

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6407630	6407630
2.0	1.593362	550077	550077
3.0	1.945441	136609	136609
4.0	2.154351	58275	58275
5.0	2.27831	31289	31289
6.0	2.351863	19078	19078
7.0	2.395506	12752	12752
8.0	2.421402	8789	8789
9.0	2.436768	6417	6417
10.0	2.445886	4901	4901
11.0	2.451296	3707	3707
12.0	2.454506	3002	3002
13.0	2.456411	2359	2359
14.0	2.457541	1974	1974
15.0	2.458212	1646	1646
16.0	2.458609	1345	1345
17.0	2.458846	1136	1136
18.0	2.458986	1060	1060
19.0	2.459069	901	901
20.0	2.459118	720	720
21.0	2.459147	657	657
22.0	2.459165	596	596
23.0	2.459175	495	495
24.0	2.459181	475	475
25.0	2.459185	390	390
26.0	2.459187	355	355
27.0	2.459188	337	337
28.0	2.459189	323	323
29.0	2.459189	264	264
30.0	2.45919	242	242
31.0	2.45919	227	227
32.0	2.45919	227	227
33.0	2.45919	205	205
34.0	2.45919	173	173
35.0	2.45919	170	170
36.0	2.45919	153	153
37.0	2.45919	131	131
38.0	2.45919	128	128
39.0	2.45919	124	124
40.0	2.45919	112	112
41.0	2.45919	100	100
42.0	2.45919	109	109
43.0	2.45919	96	96
44.0	2.45919	89	89
45.0	2.45919	84	84
46.0	2.45919	73	73
47.0	2.45919	63	63
48.0	2.45919	62	62
49.0	2.45919	68	68
50.0	2.45919	60	60
51.0	2.45919	58	58
52.0	2.45919	53	53
53.0	2.45919	56	56
54.0	2.45919	51	51
55.0	2.45919	30	30
56.0	2.45919	36	36
57.0	2.45919	49	49
58.0	2.45919	40	40
59.0	2.45919	32	32
60.0	2.45919	25	25
61.0	2.45919	39	39
62.0	2.45919	34	34
63.0	2.45919	37	37
64.0	2.45919	23	23
65.0	2.45919	23	23
66.0	2.45919	25	25
67.0	2.45919	19	19
68.0	2.45919	22	22
69.0	2.45919	20	20
70.0	2.45919	24	24
71.0	2.45919	25	25
72.0	2.45919	27	27
73.0	2.45919	22	22
74.0	2.45919	20	20
75.0	2.45919	13	13
76.0	2.45919	11	11
77.0	2.45919	19	19
78.0	2.45919	17	17
79.0	2.45919	18	18
80.0	2.45919	15	15
81.0	2.45919	16	16
82.0	2.45919	13	13
83.0	2.45919	11	11
84.0	2.45919	10	10
85.0	2.45919	14	14
86.0	2.45919	12	12
87.0	2.45919	13	13
88.0	2.45919	12	12
89.0	2.45919	11	11
90.0	2.45919	7	7
91.0	2.45919	11	11
92.0	2.45919	11	11
93.0	2.45919	7	7
94.0	2.45919	7	7
95.0	2.45919	8	8
96.0	2.45919	8	8
97.0	2.45919	7	7
98.0	2.45919	10	10
99.0	2.45919	4	4
100.0	2.45919	14	14
101.0	0	7	7
102.0	0	10	10
103.0	0	7	7
104.0	0	6	6
105.0	0	7	7
106.0	0	5	5
107.0	0	11	11
108.0	0	7	7
109.0	0	4	4
110.0	0	5	5
111.0	0	9	9
112.0	0	3	3
113.0	0	6	6
114.0	0	5	5
115.0	0	6	6
116.0	0	4	4
117.0	0	6	6
118.0	0	3	3
119.0	0	9	9
120.0	0	6	6
121.0	0	8	8
122.0	0	4	4
123.0	0	5	5
124.0	0	5	5
125.0	0	4	4
126.0	0	9	9
127.0	0	6	6
128.0	0	6	6
129.0	0	2	2
130.0	0	4	4
131.0	0	1	1
132.0	0	3	3
133.0	0	4	4
134.0	0	3	3
135.0	0	3	3
136.0	0	5	5
137.0	0	1	1
139.0	0	2	2
140.0	0	4	4
141.0	0	5	5
142.0	0	2	2
143.0	0	2	2
144.0	0	4	4
145.0	0	4	4
146.0	0	4	4
147.0	0	5	5
148.0	0	1	1
149.0	0	2	2
150.0	0	3	3
151.0	0	4	4
152.0	0	1	1
153.0	0	2	2
155.0	0	3	3
156.0	0	1	1
157.0	0	2	2
159.0	0	2	2
160.0	0	3	3
161.0	0	1	1
162.0	0	1	1
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
166.0	0	5	5
167.0	0	2	2
168.0	0	3	3
169.0	0	2	2
170.0	0	2	2
171.0	0	3	3
174.0	0	1	1
175.0	0	2	2
176.0	0	4	4
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
185.0	0	1	1
186.0	0	2	2
188.0	0	4	4
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
193.0	0	3	3
194.0	0	2	2
196.0	0	1	1
197.0	0	2	2
199.0	0	2	2
201.0	0	2	2
202.0	0	1	1
203.0	0	1	1
206.0	0	2	2
207.0	0	1	1
208.0	0	3	3
209.0	0	2	2
210.0	0	1	1
212.0	0	1	1
213.0	0	1	1
214.0	0	3	3
216.0	0	2	2
217.0	0	1	1
218.0	0	2	2
219.0	0	2	2
222.0	0	2	2
224.0	0	3	3
227.0	0	1	1
228.0	0	1	1
229.0	0	1	1
230.0	0	1	1
232.0	0	1	1
234.0	0	2	2
236.0	0	1	1
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
242.0	0	1	1
244.0	0	1	1
246.0	0	1	1
258.0	0	3	3
259.0	0	1	1
261.0	0	1	1
264.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
286.0	0	1	1
287.0	0	1	1
289.0	0	1	1
293.0	0	1	1
298.0	0	1	1
300.0	0	1	1
302.0	0	1	1
304.0	0	1	1
307.0	0	1	1
311.0	0	1	1
312.0	0	1	1
313.0	0	1	1
320.0	0	1	1
322.0	0	1	1
327.0	0	1	1
331.0	0	2	2
332.0	0	1	1
334.0	0	1	1
343.0	0	1	1
344.0	0	1	1
355.0	0	1	1
366.0	0	1	1
388.0	0	1	1
389.0	0	1	1
394.0	0	1	1
410.0	0	1	1
424.0	0	1	1
428.0	0	1	1
431.0	0	1	1
432.0	0	1	1
434.0	0	1	1
435.0	0	1	1
448.0	0	1	1
453.0	0	1	1
474.0	0	1	1
485.0	0	1	1
488.0	0	1	1
499.0	0	1	1
506.0	0	1	1
508.0	0	1	1
516.0	0	1	1
521.0	0	1	1
546.0	0	1	1
568.0	0	1	1
596.0	0	1	1
612.0	0	1	1
620.0	0	1	1
647.0	0	1	1
673.0	0	1	1
702.0	0	1	1
724.0	0	1	1
751.0	0	1	1
790.0	0	1	1
800.0	0	1	1
810.0	0	1	1
827.0	0	1	1
873.0	0	1	1
907.0	0	1	1
952.0	0	1	1
1115.0	0	1	1
1196.0	0	1	1
1210.0	0	1	1
1232.0	0	1	1
1312.0	0	1	1
1378.0	0	1	1
1382.0	0	1	1
1386.0	0	1	1
1511.0	0	1	1
1554.0	0	1	1
1574.0	0	1	1
2313.0	0	1	1
2407.0	0	1	1
4384.0	0	1	1
5937.0	0	1	1