## 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-GSM1606229.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606229.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606229.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 15:07:58 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	22889193	3061306	0	0	3564630	0	0.155734	65641867

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17599158	17599158
2.0	1.705606	1136505	1136505
3.0	2.203486	277680	277680
4.0	2.554793	116539	116539
5.0	2.802678	60780	60780
6.0	2.977587	36422	36422
7.0	3.101003	23241	23241
8.0	3.188087	16198	16198
9.0	3.249534	11531	11531
10.0	3.292891	8620	8620
11.0	3.323484	6373	6373
12.0	3.345071	4939	4939
13.0	3.360302	4015	4015
14.0	3.37105	3194	3194
15.0	3.378634	2629	2629
16.0	3.383985	2108	2108
17.0	3.38776	1716	1716
18.0	3.390424	1466	1466
19.0	3.392304	1250	1250
20.0	3.393631	1062	1062
21.0	3.394567	941	941
22.0	3.395227	824	824
23.0	3.395693	670	670
24.0	3.396022	646	646
25.0	3.396254	547	547
26.0	3.396418	432	432
27.0	3.396533	395	395
28.0	3.396615	389	389
29.0	3.396672	310	310
30.0	3.396713	303	303
31.0	3.396741	286	286
32.0	3.396761	248	248
33.0	3.396776	228	228
34.0	3.396786	219	219
35.0	3.396793	175	175
36.0	3.396798	187	187
37.0	3.396801	149	149
38.0	3.396804	155	155
39.0	3.396806	123	123
40.0	3.396807	127	127
41.0	3.396808	102	102
42.0	3.396808	105	105
43.0	3.396809	97	97
44.0	3.396809	73	73
45.0	3.396809	66	66
46.0	3.39681	75	75
47.0	3.39681	59	59
48.0	3.39681	53	53
49.0	3.39681	76	76
50.0	3.39681	45	45
51.0	3.39681	58	58
52.0	3.39681	57	57
53.0	3.39681	45	45
54.0	3.39681	43	43
55.0	3.39681	35	35
56.0	3.39681	47	47
57.0	3.39681	41	41
58.0	3.39681	32	32
59.0	3.39681	35	35
60.0	3.39681	24	24
61.0	3.39681	27	27
62.0	3.39681	21	21
63.0	3.39681	27	27
64.0	3.39681	19	19
65.0	3.39681	16	16
66.0	3.39681	23	23
67.0	3.39681	26	26
68.0	3.39681	21	21
69.0	3.39681	13	13
70.0	3.39681	20	20
71.0	3.39681	11	11
72.0	3.39681	10	10
73.0	3.39681	14	14
74.0	3.39681	12	12
75.0	3.39681	15	15
76.0	3.39681	17	17
77.0	3.39681	13	13
78.0	3.39681	15	15
79.0	3.39681	12	12
80.0	3.39681	6	6
81.0	3.39681	11	11
82.0	3.39681	8	8
83.0	3.39681	5	5
84.0	3.39681	10	10
85.0	3.39681	9	9
86.0	3.39681	9	9
87.0	3.39681	6	6
88.0	3.39681	7	7
89.0	3.39681	5	5
90.0	3.39681	16	16
91.0	3.39681	4	4
92.0	3.39681	5	5
93.0	3.39681	3	3
94.0	3.39681	4	4
95.0	3.39681	7	7
96.0	3.39681	8	8
97.0	3.39681	4	4
98.0	3.39681	5	5
99.0	3.39681	7	7
100.0	3.39681	6	6
101.0	0	4	4
102.0	0	3	3
103.0	0	2	2
104.0	0	2	2
105.0	0	1	1
106.0	0	4	4
107.0	0	3	3
108.0	0	6	6
109.0	0	1	1
110.0	0	5	5
111.0	0	3	3
112.0	0	3	3
113.0	0	5	5
114.0	0	3	3
115.0	0	1	1
116.0	0	4	4
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
120.0	0	1	1
122.0	0	1	1
125.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	2	2
129.0	0	3	3
130.0	0	1	1
131.0	0	1	1
132.0	0	1	1
134.0	0	1	1
135.0	0	2	2
137.0	0	4	4
139.0	0	1	1
140.0	0	2	2
141.0	0	3	3
143.0	0	4	4
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	3	3
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
163.0	0	1	1
164.0	0	4	4
165.0	0	1	1
166.0	0	1	1
167.0	0	1	1
170.0	0	2	2
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
177.0	0	1	1
180.0	0	1	1
184.0	0	1	1
188.0	0	1	1
190.0	0	1	1
192.0	0	1	1
193.0	0	1	1
195.0	0	1	1
198.0	0	1	1
201.0	0	1	1
203.0	0	1	1
211.0	0	2	2
212.0	0	1	1
221.0	0	1	1
240.0	0	1	1
245.0	0	1	1
256.0	0	1	1
260.0	0	1	1
268.0	0	1	1
283.0	0	1	1
318.0	0	1	1
319.0	0	1	1
339.0	0	1	1
402.0	0	1	1
1265.0	0	1	1