## 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-GSM919955.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919955.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919955.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 15:41:54 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	10274837	1914418	0	0	2484409	0	0.241795	17662690

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6820182	6820182
2.0	1.558933	609209	609209
3.0	1.871339	156401	156401
4.0	2.045953	68566	68566
5.0	2.143551	37579	37579
6.0	2.198102	23588	23588
7.0	2.228592	15598	15598
8.0	2.245634	10948	10948
9.0	2.255159	8133	8133
10.0	2.260483	6128	6128
11.0	2.263459	4750	4750
12.0	2.265122	3813	3813
13.0	2.266052	3211	3211
14.0	2.266571	2531	2531
15.0	2.266862	2167	2167
16.0	2.267024	1770	1770
17.0	2.267115	1536	1536
18.0	2.267165	1302	1302
19.0	2.267194	1114	1114
20.0	2.26721	1004	1004
21.0	2.267219	920	920
22.0	2.267223	784	784
23.0	2.267226	693	693
24.0	2.267228	591	591
25.0	2.267229	534	534
26.0	2.267229	527	527
27.0	2.267229	466	466
28.0	2.26723	400	400
29.0	2.26723	348	348
30.0	2.26723	318	318
31.0	2.26723	304	304
32.0	2.26723	278	278
33.0	2.26723	254	254
34.0	2.26723	265	265
35.0	2.26723	226	226
36.0	2.26723	190	190
37.0	2.26723	188	188
38.0	2.26723	171	171
39.0	2.26723	147	147
40.0	2.26723	148	148
41.0	2.26723	163	163
42.0	2.26723	115	115
43.0	2.26723	125	125
44.0	2.26723	122	122
45.0	2.26723	91	91
46.0	2.26723	108	108
47.0	2.26723	110	110
48.0	2.26723	96	96
49.0	2.26723	83	83
50.0	2.26723	78	78
51.0	2.26723	67	67
52.0	2.26723	70	70
53.0	2.26723	69	69
54.0	2.26723	58	58
55.0	2.26723	70	70
56.0	2.26723	58	58
57.0	2.26723	59	59
58.0	2.26723	44	44
59.0	2.26723	61	61
60.0	2.26723	48	48
61.0	2.26723	54	54
62.0	2.26723	45	45
63.0	2.26723	41	41
64.0	2.26723	36	36
65.0	2.26723	41	41
66.0	2.26723	35	35
67.0	2.26723	23	23
68.0	2.26723	31	31
69.0	2.26723	32	32
70.0	2.26723	32	32
71.0	2.26723	24	24
72.0	2.26723	14	14
73.0	2.26723	18	18
74.0	2.26723	23	23
75.0	2.26723	26	26
76.0	2.26723	24	24
77.0	2.26723	26	26
78.0	2.26723	26	26
79.0	2.26723	23	23
80.0	2.26723	20	20
81.0	2.26723	13	13
82.0	2.26723	16	16
83.0	2.26723	21	21
84.0	2.26723	17	17
85.0	2.26723	18	18
86.0	2.26723	8	8
87.0	2.26723	25	25
88.0	2.26723	18	18
89.0	2.26723	13	13
90.0	2.26723	14	14
91.0	2.26723	12	12
92.0	2.26723	10	10
93.0	2.26723	9	9
94.0	2.26723	11	11
95.0	2.26723	9	9
96.0	2.26723	13	13
97.0	2.26723	13	13
98.0	2.26723	13	13
99.0	2.26723	16	16
100.0	2.26723	9	9
101.0	0	10	10
102.0	0	8	8
103.0	0	9	9
104.0	0	12	12
105.0	0	13	13
106.0	0	10	10
107.0	0	7	7
108.0	0	8	8
109.0	0	12	12
110.0	0	9	9
111.0	0	9	9
112.0	0	4	4
113.0	0	9	9
114.0	0	10	10
115.0	0	5	5
116.0	0	9	9
117.0	0	7	7
118.0	0	7	7
119.0	0	6	6
120.0	0	8	8
121.0	0	4	4
122.0	0	9	9
123.0	0	5	5
124.0	0	2	2
125.0	0	6	6
126.0	0	6	6
127.0	0	6	6
128.0	0	6	6
129.0	0	10	10
130.0	0	6	6
131.0	0	3	3
132.0	0	4	4
133.0	0	3	3
134.0	0	5	5
135.0	0	6	6
136.0	0	4	4
137.0	0	6	6
138.0	0	6	6
139.0	0	4	4
140.0	0	3	3
141.0	0	1	1
142.0	0	2	2
143.0	0	4	4
144.0	0	7	7
145.0	0	4	4
146.0	0	3	3
147.0	0	2	2
148.0	0	3	3
149.0	0	2	2
150.0	0	2	2
151.0	0	1	1
152.0	0	3	3
153.0	0	4	4
155.0	0	6	6
156.0	0	2	2
157.0	0	3	3
158.0	0	5	5
160.0	0	1	1
162.0	0	4	4
163.0	0	6	6
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	2	2
169.0	0	2	2
170.0	0	3	3
171.0	0	2	2
172.0	0	2	2
173.0	0	3	3
174.0	0	2	2
175.0	0	2	2
176.0	0	5	5
178.0	0	3	3
181.0	0	2	2
182.0	0	3	3
183.0	0	6	6
184.0	0	3	3
185.0	0	2	2
186.0	0	1	1
187.0	0	2	2
189.0	0	2	2
191.0	0	2	2
192.0	0	3	3
193.0	0	4	4
194.0	0	4	4
195.0	0	1	1
196.0	0	2	2
197.0	0	3	3
198.0	0	2	2
199.0	0	2	2
201.0	0	5	5
202.0	0	4	4
203.0	0	1	1
204.0	0	2	2
205.0	0	1	1
206.0	0	2	2
207.0	0	2	2
208.0	0	1	1
210.0	0	1	1
212.0	0	3	3
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	1	1
222.0	0	1	1
223.0	0	3	3
224.0	0	1	1
227.0	0	1	1
228.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	2	2
233.0	0	2	2
236.0	0	2	2
237.0	0	2	2
239.0	0	2	2
241.0	0	1	1
245.0	0	1	1
250.0	0	2	2
252.0	0	3	3
256.0	0	2	2
257.0	0	1	1
259.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	1	1
265.0	0	1	1
270.0	0	1	1
271.0	0	3	3
279.0	0	1	1
284.0	0	2	2
287.0	0	1	1
294.0	0	1	1
296.0	0	1	1
298.0	0	2	2
300.0	0	1	1
302.0	0	3	3
308.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
317.0	0	1	1
321.0	0	1	1
323.0	0	1	1
326.0	0	1	1
332.0	0	1	1
336.0	0	1	1
341.0	0	2	2
345.0	0	2	2
348.0	0	2	2
349.0	0	1	1
352.0	0	1	1
354.0	0	1	1
356.0	0	1	1
359.0	0	2	2
361.0	0	1	1
368.0	0	2	2
372.0	0	1	1
373.0	0	1	1
375.0	0	1	1
376.0	0	1	1
378.0	0	1	1
383.0	0	1	1
384.0	0	1	1
390.0	0	1	1
432.0	0	1	1
457.0	0	1	1
462.0	0	1	1
466.0	0	1	1
467.0	0	1	1
482.0	0	1	1
506.0	0	1	1
529.0	0	1	1
541.0	0	1	1
544.0	0	1	1
546.0	0	1	1
567.0	0	1	1
568.0	0	1	1
597.0	0	1	1
617.0	0	1	1
622.0	0	1	1
631.0	0	1	1
637.0	0	1	1
649.0	0	1	1
655.0	0	1	1
672.0	0	1	1
691.0	0	1	1
703.0	0	1	1
710.0	0	2	2
745.0	0	1	1
755.0	0	1	1
771.0	0	1	1
807.0	0	1	1
812.0	0	1	1
843.0	0	1	1
928.0	0	1	1
934.0	0	1	1
946.0	0	1	1
1029.0	0	1	1
1118.0	0	1	1
1148.0	0	1	1
1214.0	0	1	1
1226.0	0	1	1
1258.0	0	1	1
1520.0	0	1	1
1663.0	0	1	1
1686.0	0	1	1
1719.0	0	1	1
1737.0	0	1	1
1824.0	0	1	1
1938.0	0	1	1
2304.0	0	1	1
2985.0	0	1	1
5089.0	0	1	1
6465.0	0	1	1