## 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-GSM1606211.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606211.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606211.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 13:55:39 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	32095297	5537684	0	0	4496499	0	0.140098	103576721

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25328562	25328562
2.0	1.733542	1559160	1559160
3.0	2.271627	348315	348315
4.0	2.666335	139329	139329
5.0	2.95587	71064	71064
6.0	3.168256	41252	41252
7.0	3.32405	26380	26380
8.0	3.438332	17845	17845
9.0	3.522163	12841	12841
10.0	3.583656	9523	9523
11.0	3.628764	7221	7221
12.0	3.661852	5437	5437
13.0	3.686124	4482	4482
14.0	3.703929	3569	3569
15.0	3.716989	3038	3038
16.0	3.726569	2458	2458
17.0	3.733597	2069	2069
18.0	3.738752	1701	1701
19.0	3.742533	1488	1488
20.0	3.745307	1261	1261
21.0	3.747342	1111	1111
22.0	3.748834	965	965
23.0	3.749929	845	845
24.0	3.750732	732	732
25.0	3.751321	652	652
26.0	3.751754	606	606
27.0	3.752071	520	520
28.0	3.752303	487	487
29.0	3.752474	381	381
30.0	3.752599	343	343
31.0	3.752691	337	337
32.0	3.752758	321	321
33.0	3.752807	273	273
34.0	3.752843	247	247
35.0	3.75287	265	265
36.0	3.75289	241	241
37.0	3.752904	213	213
38.0	3.752914	173	173
39.0	3.752922	169	169
40.0	3.752928	160	160
41.0	3.752932	162	162
42.0	3.752935	141	141
43.0	3.752937	115	115
44.0	3.752939	118	118
45.0	3.75294	107	107
46.0	3.752941	94	94
47.0	3.752941	93	93
48.0	3.752942	92	92
49.0	3.752942	79	79
50.0	3.752942	70	70
51.0	3.752943	64	64
52.0	3.752943	69	69
53.0	3.752943	80	80
54.0	3.752943	41	41
55.0	3.752943	66	66
56.0	3.752943	64	64
57.0	3.752943	59	59
58.0	3.752943	41	41
59.0	3.752943	50	50
60.0	3.752943	50	50
61.0	3.752943	37	37
62.0	3.752943	41	41
63.0	3.752943	36	36
64.0	3.752943	30	30
65.0	3.752943	43	43
66.0	3.752943	33	33
67.0	3.752943	36	36
68.0	3.752943	29	29
69.0	3.752943	31	31
70.0	3.752943	22	22
71.0	3.752943	26	26
72.0	3.752943	36	36
73.0	3.752943	24	24
74.0	3.752943	25	25
75.0	3.752943	19	19
76.0	3.752943	20	20
77.0	3.752943	13	13
78.0	3.752943	16	16
79.0	3.752943	12	12
80.0	3.752943	12	12
81.0	3.752943	15	15
82.0	3.752943	14	14
83.0	3.752943	14	14
84.0	3.752943	16	16
85.0	3.752943	13	13
86.0	3.752943	14	14
87.0	3.752943	14	14
88.0	3.752943	13	13
89.0	3.752943	11	11
90.0	3.752943	15	15
91.0	3.752943	14	14
92.0	3.752943	6	6
93.0	3.752943	13	13
94.0	3.752943	17	17
95.0	3.752943	12	12
96.0	3.752943	7	7
97.0	3.752943	9	9
98.0	3.752943	12	12
99.0	3.752943	7	7
100.0	3.752943	7	7
101.0	0	17	17
102.0	0	9	9
103.0	0	12	12
104.0	0	4	4
105.0	0	7	7
106.0	0	8	8
107.0	0	2	2
108.0	0	8	8
109.0	0	4	4
110.0	0	12	12
111.0	0	6	6
112.0	0	3	3
113.0	0	5	5
114.0	0	3	3
115.0	0	3	3
116.0	0	3	3
117.0	0	4	4
118.0	0	8	8
119.0	0	4	4
120.0	0	4	4
121.0	0	3	3
122.0	0	4	4
123.0	0	2	2
124.0	0	2	2
125.0	0	5	5
126.0	0	4	4
127.0	0	5	5
128.0	0	3	3
129.0	0	5	5
131.0	0	4	4
132.0	0	2	2
133.0	0	1	1
134.0	0	1	1
135.0	0	3	3
136.0	0	3	3
137.0	0	3	3
138.0	0	3	3
139.0	0	1	1
140.0	0	1	1
141.0	0	2	2
142.0	0	6	6
143.0	0	3	3
144.0	0	3	3
145.0	0	1	1
146.0	0	3	3
147.0	0	2	2
149.0	0	4	4
150.0	0	4	4
151.0	0	2	2
153.0	0	2	2
155.0	0	1	1
156.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	2	2
160.0	0	2	2
161.0	0	3	3
162.0	0	1	1
163.0	0	4	4
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	3	3
168.0	0	2	2
169.0	0	2	2
172.0	0	1	1
173.0	0	2	2
175.0	0	3	3
176.0	0	1	1
178.0	0	1	1
181.0	0	2	2
183.0	0	2	2
184.0	0	2	2
191.0	0	1	1
192.0	0	2	2
193.0	0	3	3
194.0	0	2	2
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
200.0	0	1	1
201.0	0	2	2
209.0	0	1	1
215.0	0	2	2
216.0	0	1	1
219.0	0	2	2
221.0	0	2	2
222.0	0	1	1
230.0	0	1	1
231.0	0	1	1
234.0	0	1	1
236.0	0	1	1
241.0	0	1	1
251.0	0	2	2
256.0	0	1	1
274.0	0	1	1
276.0	0	1	1
279.0	0	1	1
280.0	0	1	1
282.0	0	1	1
284.0	0	1	1
290.0	0	1	1
291.0	0	1	1
292.0	0	1	1
294.0	0	1	1
297.0	0	1	1
299.0	0	1	1
309.0	0	1	1
320.0	0	1	1
321.0	0	1	1
354.0	0	1	1
365.0	0	1	1
368.0	0	2	2
370.0	0	1	1
373.0	0	1	1
394.0	0	1	1
425.0	0	1	1
450.0	0	1	1
464.0	0	1	1
469.0	0	1	1
474.0	0	1	1
526.0	0	1	1
534.0	0	1	1
559.0	0	1	1
562.0	0	1	1
575.0	0	1	1
590.0	0	1	1
917.0	0	1	1
1135.0	0	1	1
1273.0	0	1	1
7668.0	0	1	1