## 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-GSM919957.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919957.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919957.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 15:24:20 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	11239937	2437388	0	0	2739922	0	0.243767	19132119

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7466473	7466473
2.0	1.55572	627616	627616
3.0	1.864545	170355	170355
4.0	2.036165	76925	76925
5.0	2.131538	42832	42832
6.0	2.184539	26756	26756
7.0	2.213992	18318	18318
8.0	2.23036	12937	12937
9.0	2.239456	9539	9539
10.0	2.244511	7342	7342
11.0	2.24732	5768	5768
12.0	2.248881	4543	4543
13.0	2.249748	3648	3648
14.0	2.250231	3061	3061
15.0	2.250498	2505	2505
16.0	2.250647	2137	2137
17.0	2.25073	1808	1808
18.0	2.250776	1645	1645
19.0	2.250802	1365	1365
20.0	2.250816	1292	1292
21.0	2.250824	1080	1080
22.0	2.250828	1000	1000
23.0	2.250831	897	897
24.0	2.250832	741	741
25.0	2.250833	667	667
26.0	2.250833	602	602
27.0	2.250833	493	493
28.0	2.250833	456	456
29.0	2.250833	447	447
30.0	2.250834	422	422
31.0	2.250834	346	346
32.0	2.250834	284	284
33.0	2.250834	319	319
34.0	2.250834	304	304
35.0	2.250834	250	250
36.0	2.250834	259	259
37.0	2.250834	213	213
38.0	2.250834	210	210
39.0	2.250834	191	191
40.0	2.250834	189	189
41.0	2.250834	187	187
42.0	2.250834	153	153
43.0	2.250834	146	146
44.0	2.250834	144	144
45.0	2.250834	133	133
46.0	2.250834	126	126
47.0	2.250834	123	123
48.0	2.250834	95	95
49.0	2.250834	111	111
50.0	2.250834	101	101
51.0	2.250834	91	91
52.0	2.250834	107	107
53.0	2.250834	65	65
54.0	2.250834	67	67
55.0	2.250834	65	65
56.0	2.250834	61	61
57.0	2.250834	79	79
58.0	2.250834	61	61
59.0	2.250834	75	75
60.0	2.250834	59	59
61.0	2.250834	76	76
62.0	2.250834	55	55
63.0	2.250834	53	53
64.0	2.250834	55	55
65.0	2.250834	40	40
66.0	2.250834	58	58
67.0	2.250834	49	49
68.0	2.250834	47	47
69.0	2.250834	29	29
70.0	2.250834	39	39
71.0	2.250834	35	35
72.0	2.250834	42	42
73.0	2.250834	31	31
74.0	2.250834	33	33
75.0	2.250834	29	29
76.0	2.250834	31	31
77.0	2.250834	28	28
78.0	2.250834	25	25
79.0	2.250834	28	28
80.0	2.250834	21	21
81.0	2.250834	24	24
82.0	2.250834	23	23
83.0	2.250834	25	25
84.0	2.250834	25	25
85.0	2.250834	22	22
86.0	2.250834	16	16
87.0	2.250834	14	14
88.0	2.250834	18	18
89.0	2.250834	14	14
90.0	2.250834	16	16
91.0	2.250834	10	10
92.0	2.250834	8	8
93.0	2.250834	15	15
94.0	2.250834	14	14
95.0	2.250834	15	15
96.0	2.250834	13	13
97.0	2.250834	12	12
98.0	2.250834	26	26
99.0	2.250834	10	10
100.0	2.250834	13	13
101.0	0	17	17
102.0	0	7	7
103.0	0	8	8
104.0	0	12	12
105.0	0	9	9
106.0	0	8	8
107.0	0	12	12
108.0	0	7	7
109.0	0	17	17
110.0	0	16	16
111.0	0	8	8
112.0	0	4	4
113.0	0	10	10
114.0	0	12	12
115.0	0	5	5
116.0	0	6	6
117.0	0	8	8
118.0	0	6	6
119.0	0	6	6
120.0	0	7	7
121.0	0	9	9
122.0	0	7	7
123.0	0	5	5
124.0	0	8	8
125.0	0	8	8
126.0	0	9	9
127.0	0	6	6
128.0	0	10	10
129.0	0	10	10
130.0	0	9	9
131.0	0	10	10
132.0	0	2	2
133.0	0	6	6
134.0	0	8	8
135.0	0	5	5
136.0	0	6	6
137.0	0	6	6
138.0	0	3	3
139.0	0	3	3
140.0	0	5	5
141.0	0	2	2
142.0	0	6	6
143.0	0	3	3
144.0	0	5	5
145.0	0	7	7
146.0	0	3	3
147.0	0	3	3
148.0	0	4	4
149.0	0	7	7
150.0	0	5	5
151.0	0	2	2
152.0	0	4	4
153.0	0	10	10
154.0	0	2	2
155.0	0	2	2
156.0	0	2	2
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
160.0	0	1	1
161.0	0	2	2
162.0	0	7	7
163.0	0	3	3
164.0	0	1	1
165.0	0	8	8
166.0	0	6	6
167.0	0	5	5
169.0	0	2	2
170.0	0	3	3
171.0	0	1	1
172.0	0	2	2
173.0	0	1	1
175.0	0	1	1
176.0	0	3	3
177.0	0	3	3
178.0	0	3	3
179.0	0	2	2
180.0	0	3	3
181.0	0	1	1
183.0	0	2	2
184.0	0	5	5
186.0	0	3	3
187.0	0	2	2
188.0	0	2	2
189.0	0	3	3
192.0	0	2	2
193.0	0	2	2
194.0	0	2	2
198.0	0	3	3
199.0	0	1	1
200.0	0	4	4
201.0	0	1	1
202.0	0	1	1
204.0	0	1	1
206.0	0	1	1
207.0	0	2	2
208.0	0	3	3
209.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	2	2
213.0	0	1	1
215.0	0	1	1
217.0	0	1	1
219.0	0	1	1
221.0	0	1	1
222.0	0	2	2
223.0	0	1	1
225.0	0	1	1
227.0	0	2	2
228.0	0	1	1
229.0	0	2	2
230.0	0	1	1
231.0	0	1	1
236.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	2	2
242.0	0	1	1
247.0	0	3	3
248.0	0	1	1
250.0	0	1	1
252.0	0	1	1
254.0	0	1	1
256.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
263.0	0	1	1
264.0	0	1	1
268.0	0	1	1
270.0	0	1	1
271.0	0	1	1
273.0	0	1	1
274.0	0	1	1
276.0	0	2	2
277.0	0	1	1
279.0	0	2	2
281.0	0	1	1
283.0	0	2	2
285.0	0	1	1
286.0	0	1	1
288.0	0	2	2
289.0	0	2	2
297.0	0	1	1
300.0	0	1	1
301.0	0	1	1
306.0	0	1	1
309.0	0	1	1
316.0	0	1	1
323.0	0	1	1
327.0	0	1	1
328.0	0	2	2
330.0	0	2	2
333.0	0	1	1
344.0	0	1	1
358.0	0	1	1
359.0	0	1	1
360.0	0	1	1
361.0	0	1	1
362.0	0	1	1
364.0	0	2	2
365.0	0	1	1
368.0	0	1	1
372.0	0	1	1
387.0	0	1	1
405.0	0	1	1
409.0	0	1	1
421.0	0	1	1
427.0	0	1	1
442.0	0	1	1
444.0	0	1	1
452.0	0	1	1
455.0	0	1	1
478.0	0	1	1
488.0	0	1	1
521.0	0	1	1
524.0	0	1	1
537.0	0	1	1
541.0	0	1	1
555.0	0	1	1
684.0	0	1	1
691.0	0	1	1
754.0	0	1	1
839.0	0	1	1
926.0	0	1	1