## 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-GSM1606193.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606193.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606193.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 13:37:28 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	33842629	5392248	0	0	5076598	0	0.150006	101216225

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	25979541	25979541
2.0	1.715796	1966232	1966232
3.0	2.228161	421841	421841
4.0	2.594909	161235	161235
5.0	2.857426	79374	79374
6.0	3.045335	45490	45490
7.0	3.179839	28335	28335
8.0	3.276117	19181	19181
9.0	3.345032	13199	13199
10.0	3.394362	9614	9614
11.0	3.429671	7284	7284
12.0	3.454946	5671	5671
13.0	3.473037	4422	4422
14.0	3.485987	3525	3525
15.0	3.495256	2814	2814
16.0	3.501891	2395	2395
17.0	3.506641	1915	1915
18.0	3.51004	1560	1560
19.0	3.512474	1378	1378
20.0	3.514215	1176	1176
21.0	3.515462	994	994
22.0	3.516355	821	821
23.0	3.516993	772	772
24.0	3.517451	658	658
25.0	3.517778	601	601
26.0	3.518012	529	529
27.0	3.51818	479	479
28.0	3.5183	410	410
29.0	3.518386	392	392
30.0	3.518447	334	334
31.0	3.518491	274	274
32.0	3.518523	259	259
33.0	3.518546	274	274
34.0	3.518562	209	209
35.0	3.518573	189	189
36.0	3.518582	172	172
37.0	3.518587	167	167
38.0	3.518592	137	137
39.0	3.518595	143	143
40.0	3.518597	142	142
41.0	3.518598	135	135
42.0	3.5186	103	103
43.0	3.5186	100	100
44.0	3.518601	96	96
45.0	3.518601	84	84
46.0	3.518602	84	84
47.0	3.518602	73	73
48.0	3.518602	54	54
49.0	3.518602	63	63
50.0	3.518602	72	72
51.0	3.518602	58	58
52.0	3.518602	55	55
53.0	3.518602	57	57
54.0	3.518602	47	47
55.0	3.518602	32	32
56.0	3.518602	42	42
57.0	3.518602	25	25
58.0	3.518602	29	29
59.0	3.518602	30	30
60.0	3.518602	39	39
61.0	3.518602	26	26
62.0	3.518602	23	23
63.0	3.518602	17	17
64.0	3.518602	20	20
65.0	3.518602	22	22
66.0	3.518602	24	24
67.0	3.518602	14	14
68.0	3.518602	19	19
69.0	3.518602	15	15
70.0	3.518602	16	16
71.0	3.518602	23	23
72.0	3.518602	14	14
73.0	3.518602	14	14
74.0	3.518602	16	16
75.0	3.518602	13	13
76.0	3.518602	12	12
77.0	3.518602	11	11
78.0	3.518602	11	11
79.0	3.518602	10	10
80.0	3.518602	11	11
81.0	3.518602	16	16
82.0	3.518602	13	13
83.0	3.518602	9	9
84.0	3.518602	8	8
85.0	3.518602	8	8
86.0	3.518602	4	4
87.0	3.518602	9	9
88.0	3.518602	5	5
89.0	3.518602	6	6
90.0	3.518602	7	7
91.0	3.518602	5	5
92.0	3.518602	7	7
93.0	3.518602	10	10
94.0	3.518602	5	5
95.0	3.518602	1	1
96.0	3.518602	3	3
97.0	3.518602	6	6
98.0	3.518602	1	1
99.0	3.518602	5	5
100.0	3.518602	5	5
101.0	0	2	2
102.0	0	5	5
103.0	0	5	5
104.0	0	4	4
105.0	0	2	2
106.0	0	3	3
107.0	0	4	4
108.0	0	3	3
109.0	0	3	3
110.0	0	2	2
111.0	0	4	4
112.0	0	6	6
113.0	0	4	4
114.0	0	2	2
115.0	0	2	2
116.0	0	4	4
117.0	0	7	7
118.0	0	2	2
120.0	0	6	6
121.0	0	1	1
122.0	0	2	2
123.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	2	2
127.0	0	1	1
128.0	0	2	2
129.0	0	1	1
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
133.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
141.0	0	1	1
142.0	0	1	1
143.0	0	2	2
144.0	0	4	4
145.0	0	1	1
146.0	0	1	1
147.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
153.0	0	3	3
154.0	0	1	1
158.0	0	1	1
164.0	0	1	1
166.0	0	1	1
167.0	0	1	1
168.0	0	5	5
172.0	0	1	1
175.0	0	1	1
177.0	0	1	1
178.0	0	1	1
180.0	0	1	1
183.0	0	1	1
184.0	0	1	1
197.0	0	1	1
200.0	0	1	1
214.0	0	1	1
229.0	0	1	1
240.0	0	1	1
246.0	0	1	1
259.0	0	1	1
265.0	0	1	1
278.0	0	1	1
282.0	0	1	1
286.0	0	1	1
289.0	0	1	1
293.0	0	1	1
301.0	0	2	2
311.0	0	1	1
329.0	0	1	1
331.0	0	1	1
366.0	0	1	1
370.0	0	1	1
377.0	0	1	1
400.0	0	1	1
597.0	0	1	1
3198.0	0	1	1