## 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-GSM919944.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919944.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919944.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 15:38:42 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	10243958	1374346	0	0	982861	0	0.095945	49912048

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8626384	8626384
2.0	1.814452	496273	496273
3.0	2.477783	81475	81475
4.0	3.018035	26027	26027
5.0	3.458043	11431	11431
6.0	3.816409	5969	5969
7.0	4.108281	3638	3638
8.0	4.345996	2298	2298
9.0	4.539604	1462	1462
10.0	4.697288	1165	1165
11.0	4.825714	835	835
12.0	4.930311	618	618
13.0	5.0155	534	534
14.0	5.084882	382	382
15.0	5.141391	313	313
16.0	5.187414	239	239
17.0	5.224898	227	227
18.0	5.255427	193	193
19.0	5.280291	189	189
20.0	5.300542	140	140
21.0	5.317035	105	105
22.0	5.330468	100	100
23.0	5.341409	85	85
24.0	5.350319	85	85
25.0	5.357577	79	79
26.0	5.363487	59	59
27.0	5.368301	55	55
28.0	5.372222	44	44
29.0	5.375415	51	51
30.0	5.378016	36	36
31.0	5.380134	38	38
32.0	5.381859	25	25
33.0	5.383264	34	34
34.0	5.384409	19	19
35.0	5.385341	28	28
36.0	5.3861	20	20
37.0	5.386718	23	23
38.0	5.387221	15	15
39.0	5.387631	20	20
40.0	5.387965	16	16
41.0	5.388237	13	13
42.0	5.388459	18	18
43.0	5.388639	13	13
44.0	5.388786	13	13
45.0	5.388906	15	15
46.0	5.389004	9	9
47.0	5.389083	7	7
48.0	5.389148	6	6
49.0	5.3892	6	6
50.0	5.389243	8	8
51.0	5.389278	7	7
52.0	5.389307	3	3
53.0	5.38933	8	8
54.0	5.389349	10	10
55.0	5.389364	4	4
56.0	5.389377	8	8
57.0	5.389387	9	9
58.0	5.389395	2	2
59.0	5.389402	2	2
60.0	5.389407	7	7
61.0	5.389412	7	7
62.0	5.389415	6	6
63.0	5.389418	4	4
64.0	5.389421	4	4
65.0	5.389423	6	6
66.0	5.389424	2	2
67.0	5.389426	5	5
68.0	5.389427	5	5
69.0	5.389428	6	6
70.0	5.389428	8	8
71.0	5.389429	6	6
72.0	5.389429	2	2
73.0	5.38943	3	3
74.0	5.38943	4	4
75.0	5.38943	2	2
76.0	5.389431	2	2
77.0	5.389431	4	4
78.0	5.389431	0	0
79.0	5.389431	3	3
80.0	5.389431	3	3
81.0	5.389431	4	4
82.0	5.389431	1	1
83.0	5.389431	2	2
84.0	5.389431	0	0
85.0	5.389431	2	2
86.0	5.389431	1	1
87.0	5.389431	1	1
88.0	5.389431	3	3
89.0	5.389431	2	2
90.0	5.389431	0	0
91.0	5.389431	2	2
92.0	5.389431	2	2
93.0	5.389431	2	2
94.0	5.389431	0	0
95.0	5.389431	1	1
96.0	5.389431	2	2
97.0	5.389431	3	3
98.0	5.389432	3	3
99.0	5.389432	2	2
100.0	5.389432	1	1
101.0	0	2	2
103.0	0	3	3
104.0	0	2	2
105.0	0	1	1
107.0	0	1	1
108.0	0	2	2
111.0	0	1	1
112.0	0	1	1
113.0	0	1	1
117.0	0	2	2
118.0	0	1	1
119.0	0	1	1
120.0	0	1	1
122.0	0	2	2
124.0	0	1	1
126.0	0	1	1
127.0	0	1	1
128.0	0	1	1
131.0	0	1	1
132.0	0	1	1
134.0	0	1	1
135.0	0	1	1
138.0	0	1	1
140.0	0	1	1
141.0	0	2	2
142.0	0	1	1
143.0	0	1	1
145.0	0	1	1
146.0	0	1	1
148.0	0	1	1
151.0	0	1	1
154.0	0	1	1
155.0	0	2	2
157.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	2	2
176.0	0	2	2
181.0	0	1	1
193.0	0	2	2
201.0	0	2	2
204.0	0	1	1
208.0	0	1	1
210.0	0	1	1
211.0	0	1	1
233.0	0	1	1
234.0	0	1	1
246.0	0	1	1
248.0	0	1	1
254.0	0	1	1
275.0	0	1	1
288.0	0	1	1
290.0	0	1	1
319.0	0	1	1
340.0	0	1	1
351.0	0	1	1
362.0	0	1	1
370.0	0	1	1
387.0	0	1	1
388.0	0	1	1
394.0	0	1	1
455.0	0	1	1
475.0	0	1	1
507.0	0	1	1
522.0	0	1	1
597.0	0	1	1
599.0	0	1	1
689.0	0	1	1
837.0	0	1	1
1385.0	0	1	1
2118.0	0	1	1