## 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-GSM919948.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919948.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919948.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 15:56:18 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	8674258	1706900	0	0	1462374	0	0.168588	22745328

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6498292	6498292
2.0	1.682929	481754	481754
3.0	2.149321	111482	111482
4.0	2.467834	45548	45548
5.0	2.685355	23331	23331
6.0	2.833907	13778	13778
7.0	2.935357	8883	8883
8.0	3.004641	5980	5980
9.0	3.051956	4385	4385
10.0	3.084269	3256	3256
11.0	3.106337	2443	2443
12.0	3.121408	1986	1986
13.0	3.1317	1436	1436
14.0	3.138729	1254	1254
15.0	3.143529	1010	1010
16.0	3.146807	815	815
17.0	3.149046	695	695
18.0	3.150575	606	606
19.0	3.151619	484	484
20.0	3.152332	421	421
21.0	3.152819	393	393
22.0	3.153151	343	343
23.0	3.153379	323	323
24.0	3.153534	242	242
25.0	3.15364	216	216
26.0	3.153712	183	183
27.0	3.153761	164	164
28.0	3.153795	183	183
29.0	3.153818	140	140
30.0	3.153834	118	118
31.0	3.153845	103	103
32.0	3.153852	123	123
33.0	3.153857	89	89
34.0	3.15386	101	101
35.0	3.153863	67	67
36.0	3.153864	77	77
37.0	3.153865	75	75
38.0	3.153866	60	60
39.0	3.153867	59	59
40.0	3.153867	45	45
41.0	3.153867	46	46
42.0	3.153867	42	42
43.0	3.153867	36	36
44.0	3.153868	43	43
45.0	3.153868	31	31
46.0	3.153868	34	34
47.0	3.153868	27	27
48.0	3.153868	16	16
49.0	3.153868	32	32
50.0	3.153868	37	37
51.0	3.153868	21	21
52.0	3.153868	24	24
53.0	3.153868	21	21
54.0	3.153868	22	22
55.0	3.153868	15	15
56.0	3.153868	15	15
57.0	3.153868	11	11
58.0	3.153868	15	15
59.0	3.153868	16	16
60.0	3.153868	14	14
61.0	3.153868	14	14
62.0	3.153868	16	16
63.0	3.153868	16	16
64.0	3.153868	12	12
65.0	3.153868	12	12
66.0	3.153868	12	12
67.0	3.153868	9	9
68.0	3.153868	14	14
69.0	3.153868	10	10
70.0	3.153868	6	6
71.0	3.153868	8	8
72.0	3.153868	5	5
73.0	3.153868	11	11
74.0	3.153868	11	11
75.0	3.153868	5	5
76.0	3.153868	8	8
77.0	3.153868	7	7
78.0	3.153868	6	6
79.0	3.153868	9	9
80.0	3.153868	7	7
81.0	3.153868	7	7
82.0	3.153868	3	3
83.0	3.153868	9	9
84.0	3.153868	9	9
85.0	3.153868	6	6
86.0	3.153868	4	4
87.0	3.153868	8	8
88.0	3.153868	3	3
89.0	3.153868	2	2
90.0	3.153868	8	8
91.0	3.153868	1	1
92.0	3.153868	7	7
93.0	3.153868	2	2
94.0	3.153868	7	7
95.0	3.153868	2	2
96.0	3.153868	1	1
97.0	3.153868	2	2
98.0	3.153868	3	3
99.0	3.153868	1	1
100.0	3.153868	7	7
101.0	0	1	1
102.0	0	3	3
103.0	0	1	1
104.0	0	5	5
105.0	0	2	2
106.0	0	2	2
107.0	0	1	1
109.0	0	2	2
110.0	0	3	3
111.0	0	1	1
112.0	0	1	1
113.0	0	1	1
114.0	0	1	1
115.0	0	3	3
116.0	0	1	1
118.0	0	2	2
119.0	0	3	3
120.0	0	1	1
122.0	0	2	2
123.0	0	1	1
125.0	0	3	3
126.0	0	2	2
127.0	0	1	1
128.0	0	2	2
130.0	0	1	1
131.0	0	1	1
133.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
141.0	0	2	2
144.0	0	2	2
146.0	0	2	2
147.0	0	3	3
148.0	0	2	2
150.0	0	1	1
152.0	0	1	1
153.0	0	1	1
154.0	0	1	1
158.0	0	3	3
163.0	0	2	2
164.0	0	1	1
165.0	0	1	1
167.0	0	3	3
168.0	0	2	2
170.0	0	1	1
174.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	1	1
180.0	0	1	1
183.0	0	1	1
185.0	0	1	1
186.0	0	1	1
188.0	0	1	1
190.0	0	2	2
192.0	0	1	1
193.0	0	1	1
197.0	0	2	2
207.0	0	1	1
208.0	0	1	1
214.0	0	1	1
215.0	0	2	2
221.0	0	2	2
232.0	0	1	1
239.0	0	1	1
245.0	0	1	1
249.0	0	1	1
258.0	0	1	1
278.0	0	1	1
282.0	0	1	1
307.0	0	1	1
359.0	0	1	1
372.0	0	1	1
376.0	0	1	1
388.0	0	1	1
401.0	0	1	1
402.0	0	1	1
414.0	0	1	1
422.0	0	1	1
437.0	0	2	2
502.0	0	1	1
522.0	0	1	1
584.0	0	1	1
609.0	0	1	1
708.0	0	1	1
831.0	0	1	1
1062.0	0	1	1
1635.0	0	1	1