## 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-GSM919946.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919946.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919946.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 15:44:45 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	9581146	1759110	0	0	1398820	0	0.145997	29534645

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7446050	7446050
2.0	1.722958	517325	517325
3.0	2.245627	111450	111450
4.0	2.623495	42584	42584
5.0	2.896678	21092	21092
6.0	3.094177	12121	12121
7.0	3.236961	7716	7716
8.0	3.340188	5189	5189
9.0	3.414817	3587	3587
10.0	3.468771	2666	2666
11.0	3.507777	2036	2036
12.0	3.535977	1559	1559
13.0	3.556364	1263	1263
14.0	3.571103	1022	1022
15.0	3.581759	871	871
16.0	3.589463	723	723
17.0	3.595032	586	586
18.0	3.599059	477	477
19.0	3.60197	433	433
20.0	3.604074	347	347
21.0	3.605596	287	287
22.0	3.606695	246	246
23.0	3.607491	222	222
24.0	3.608066	201	201
25.0	3.608481	151	151
26.0	3.608782	154	154
27.0	3.608999	122	122
28.0	3.609156	118	118
29.0	3.60927	113	113
30.0	3.609352	106	106
31.0	3.609411	90	90
32.0	3.609454	80	80
33.0	3.609485	71	71
34.0	3.609507	78	78
35.0	3.609524	51	51
36.0	3.609535	59	59
37.0	3.609544	45	45
38.0	3.60955	69	69
39.0	3.609554	47	47
40.0	3.609558	46	46
41.0	3.60956	41	41
42.0	3.609562	46	46
43.0	3.609563	53	53
44.0	3.609564	34	34
45.0	3.609564	27	27
46.0	3.609565	31	31
47.0	3.609565	26	26
48.0	3.609565	27	27
49.0	3.609565	24	24
50.0	3.609566	28	28
51.0	3.609566	22	22
52.0	3.609566	17	17
53.0	3.609566	26	26
54.0	3.609566	18	18
55.0	3.609566	17	17
56.0	3.609566	16	16
57.0	3.609566	13	13
58.0	3.609566	15	15
59.0	3.609566	17	17
60.0	3.609566	9	9
61.0	3.609566	16	16
62.0	3.609566	13	13
63.0	3.609566	15	15
64.0	3.609566	15	15
65.0	3.609566	7	7
66.0	3.609566	9	9
67.0	3.609566	11	11
68.0	3.609566	7	7
69.0	3.609566	7	7
70.0	3.609566	5	5
71.0	3.609566	8	8
72.0	3.609566	2	2
73.0	3.609566	4	4
74.0	3.609566	5	5
75.0	3.609566	11	11
76.0	3.609566	5	5
77.0	3.609566	5	5
78.0	3.609566	7	7
79.0	3.609566	6	6
80.0	3.609566	7	7
81.0	3.609566	8	8
82.0	3.609566	6	6
83.0	3.609566	8	8
84.0	3.609566	3	3
85.0	3.609566	3	3
86.0	3.609566	4	4
87.0	3.609566	7	7
88.0	3.609566	3	3
89.0	3.609566	4	4
90.0	3.609566	4	4
91.0	3.609566	3	3
92.0	3.609566	3	3
93.0	3.609566	2	2
94.0	3.609566	0	0
95.0	3.609566	3	3
96.0	3.609566	1	1
97.0	3.609566	3	3
98.0	3.609566	3	3
99.0	3.609566	5	5
100.0	3.609566	1	1
101.0	0	4	4
103.0	0	1	1
104.0	0	3	3
105.0	0	3	3
106.0	0	3	3
107.0	0	1	1
108.0	0	1	1
109.0	0	4	4
110.0	0	1	1
111.0	0	1	1
113.0	0	3	3
114.0	0	1	1
115.0	0	2	2
117.0	0	2	2
118.0	0	3	3
119.0	0	2	2
120.0	0	2	2
121.0	0	1	1
122.0	0	5	5
123.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
127.0	0	1	1
128.0	0	4	4
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
132.0	0	1	1
134.0	0	4	4
135.0	0	1	1
136.0	0	1	1
138.0	0	3	3
142.0	0	2	2
145.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	1	1
152.0	0	1	1
156.0	0	1	1
157.0	0	1	1
162.0	0	2	2
166.0	0	1	1
171.0	0	1	1
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	1	1
184.0	0	1	1
187.0	0	1	1
190.0	0	1	1
192.0	0	1	1
196.0	0	1	1
199.0	0	2	2
205.0	0	1	1
209.0	0	1	1
210.0	0	1	1
218.0	0	1	1
219.0	0	2	2
220.0	0	1	1
221.0	0	1	1
223.0	0	1	1
232.0	0	1	1
244.0	0	1	1
256.0	0	1	1
290.0	0	1	1
299.0	0	2	2
308.0	0	1	1
310.0	0	1	1
311.0	0	1	1
315.0	0	1	1
328.0	0	1	1
341.0	0	1	1
342.0	0	1	1
353.0	0	1	1
365.0	0	1	1
368.0	0	1	1
372.0	0	1	1
382.0	0	1	1
413.0	0	1	1
417.0	0	1	1
456.0	0	1	1
469.0	0	1	1
478.0	0	1	1
486.0	0	1	1
566.0	0	1	1
638.0	0	1	1
1145.0	0	1	1
1598.0	0	1	1