## 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-GSM919925.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919925.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919925.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 15:40:35 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	10038666	1675676	0	0	1877373	0	0.187014	23376886

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7121410	7121410
2.0	1.650882	758380	758380
3.0	2.074529	147794	147794
4.0	2.350274	52852	52852
5.0	2.529751	25965	25965
6.0	2.646569	15053	15053
7.0	2.722604	9481	9481
8.0	2.772094	6511	6511
9.0	2.804306	4616	4616
10.0	2.825272	3339	3339
11.0	2.838919	2488	2488
12.0	2.847801	1973	1973
13.0	2.853582	1636	1636
14.0	2.857345	1247	1247
15.0	2.859794	1077	1077
16.0	2.861388	895	895
17.0	2.862426	721	721
18.0	2.863101	612	612
19.0	2.863541	529	529
20.0	2.863827	453	453
21.0	2.864013	360	360
22.0	2.864135	341	341
23.0	2.864213	319	319
24.0	2.864265	268	268
25.0	2.864298	230	230
26.0	2.86432	220	220
27.0	2.864334	174	174
28.0	2.864343	177	177
29.0	2.864349	142	142
30.0	2.864353	133	133
31.0	2.864356	136	136
32.0	2.864358	107	107
33.0	2.864359	113	113
34.0	2.864359	87	87
35.0	2.86436	88	88
36.0	2.86436	96	96
37.0	2.86436	70	70
38.0	2.86436	67	67
39.0	2.86436	55	55
40.0	2.86436	53	53
41.0	2.864361	53	53
42.0	2.864361	56	56
43.0	2.864361	35	35
44.0	2.864361	44	44
45.0	2.864361	33	33
46.0	2.864361	34	34
47.0	2.864361	23	23
48.0	2.864361	32	32
49.0	2.864361	26	26
50.0	2.864361	25	25
51.0	2.864361	25	25
52.0	2.864361	25	25
53.0	2.864361	21	21
54.0	2.864361	20	20
55.0	2.864361	14	14
56.0	2.864361	25	25
57.0	2.864361	19	19
58.0	2.864361	19	19
59.0	2.864361	13	13
60.0	2.864361	16	16
61.0	2.864361	13	13
62.0	2.864361	19	19
63.0	2.864361	15	15
64.0	2.864361	22	22
65.0	2.864361	11	11
66.0	2.864361	14	14
67.0	2.864361	15	15
68.0	2.864361	9	9
69.0	2.864361	14	14
70.0	2.864361	16	16
71.0	2.864361	11	11
72.0	2.864361	11	11
73.0	2.864361	13	13
74.0	2.864361	9	9
75.0	2.864361	7	7
76.0	2.864361	10	10
77.0	2.864361	6	6
78.0	2.864361	7	7
79.0	2.864361	5	5
80.0	2.864361	12	12
81.0	2.864361	4	4
82.0	2.864361	9	9
83.0	2.864361	3	3
84.0	2.864361	1	1
85.0	2.864361	3	3
86.0	2.864361	5	5
87.0	2.864361	1	1
88.0	2.864361	4	4
89.0	2.864361	5	5
90.0	2.864361	10	10
91.0	2.864361	6	6
92.0	2.864361	4	4
93.0	2.864361	6	6
94.0	2.864361	2	2
95.0	2.864361	3	3
96.0	2.864361	3	3
97.0	2.864361	3	3
98.0	2.864361	3	3
99.0	2.864361	2	2
100.0	2.864361	3	3
101.0	0	1	1
102.0	0	2	2
103.0	0	2	2
104.0	0	1	1
105.0	0	3	3
106.0	0	4	4
107.0	0	2	2
108.0	0	2	2
110.0	0	1	1
111.0	0	1	1
112.0	0	2	2
113.0	0	1	1
114.0	0	2	2
115.0	0	2	2
116.0	0	1	1
117.0	0	3	3
118.0	0	2	2
119.0	0	2	2
121.0	0	2	2
122.0	0	2	2
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	3	3
131.0	0	1	1
132.0	0	2	2
133.0	0	1	1
134.0	0	3	3
136.0	0	1	1
138.0	0	2	2
140.0	0	1	1
144.0	0	3	3
146.0	0	2	2
147.0	0	2	2
148.0	0	2	2
149.0	0	1	1
150.0	0	1	1
151.0	0	2	2
154.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
167.0	0	3	3
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
180.0	0	1	1
182.0	0	1	1
183.0	0	2	2
184.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
191.0	0	2	2
193.0	0	1	1
194.0	0	1	1
198.0	0	1	1
201.0	0	2	2
202.0	0	1	1
207.0	0	1	1
208.0	0	1	1
212.0	0	1	1
217.0	0	1	1
219.0	0	1	1
220.0	0	1	1
222.0	0	1	1
227.0	0	1	1
232.0	0	1	1
236.0	0	1	1
237.0	0	1	1
240.0	0	1	1
244.0	0	1	1
250.0	0	2	2
252.0	0	1	1
255.0	0	1	1
265.0	0	1	1
282.0	0	1	1
292.0	0	1	1
295.0	0	1	1
317.0	0	1	1
320.0	0	1	1
345.0	0	1	1
355.0	0	1	1
374.0	0	1	1
383.0	0	1	1
399.0	0	1	1
403.0	0	1	1
408.0	0	1	1
447.0	0	1	1
489.0	0	1	1
510.0	0	1	1
651.0	0	1	1
663.0	0	1	1
668.0	0	1	1
985.0	0	1	1
1005.0	0	1	1
1370.0	0	1	1