## 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-GSM919945.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919945.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919945.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 15:48:02 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	9415633	1613926	0	0	1090912	0	0.115862	37429829

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7680120	7680120
2.0	1.777591	482309	482309
3.0	2.382239	89132	89132
4.0	2.852409	30887	30887
5.0	3.218008	14603	14603
6.0	3.502295	8066	8066
7.0	3.723354	4928	4928
8.0	3.895247	3313	3313
9.0	4.02891	2294	2294
10.0	4.132846	1705	1705
11.0	4.213665	1282	1282
12.0	4.276509	947	947
13.0	4.325376	716	716
14.0	4.363374	566	566
15.0	4.392922	436	436
16.0	4.415898	403	403
17.0	4.433763	337	337
18.0	4.447656	269	269
19.0	4.458458	217	217
20.0	4.466858	201	201
21.0	4.47339	196	196
22.0	4.478469	158	158
23.0	4.482418	113	113
24.0	4.485489	138	138
25.0	4.487877	125	125
26.0	4.489734	102	102
27.0	4.491178	72	72
28.0	4.492301	83	83
29.0	4.493174	61	61
30.0	4.493853	55	55
31.0	4.494381	49	49
32.0	4.494791	45	45
33.0	4.49511	55	55
34.0	4.495358	49	49
35.0	4.495551	45	45
36.0	4.495702	33	33
37.0	4.495818	22	22
38.0	4.495909	26	26
39.0	4.49598	22	22
40.0	4.496034	23	23
41.0	4.496077	30	30
42.0	4.49611	18	18
43.0	4.496136	28	28
44.0	4.496156	16	16
45.0	4.496172	21	21
46.0	4.496184	11	11
47.0	4.496193	13	13
48.0	4.496201	23	23
49.0	4.496206	13	13
50.0	4.496211	16	16
51.0	4.496214	10	10
52.0	4.496217	9	9
53.0	4.496219	20	20
54.0	4.496221	12	12
55.0	4.496222	13	13
56.0	4.496223	5	5
57.0	4.496224	13	13
58.0	4.496224	9	9
59.0	4.496225	5	5
60.0	4.496225	9	9
61.0	4.496225	9	9
62.0	4.496225	6	6
63.0	4.496226	5	5
64.0	4.496226	8	8
65.0	4.496226	5	5
66.0	4.496226	9	9
67.0	4.496226	5	5
68.0	4.496226	1	1
69.0	4.496226	3	3
70.0	4.496226	5	5
71.0	4.496226	6	6
72.0	4.496226	5	5
73.0	4.496226	4	4
74.0	4.496226	5	5
75.0	4.496226	1	1
76.0	4.496226	3	3
77.0	4.496226	3	3
78.0	4.496226	2	2
79.0	4.496226	4	4
80.0	4.496226	3	3
81.0	4.496226	4	4
82.0	4.496226	3	3
83.0	4.496226	3	3
84.0	4.496226	2	2
85.0	4.496226	2	2
86.0	4.496226	1	1
87.0	4.496226	3	3
88.0	4.496226	2	2
89.0	4.496226	3	3
90.0	4.496226	1	1
91.0	4.496226	2	2
92.0	4.496226	2	2
93.0	4.496226	1	1
94.0	4.496226	1	1
95.0	4.496226	0	0
96.0	4.496226	2	2
97.0	4.496226	0	0
98.0	4.496226	2	2
99.0	4.496226	2	2
100.0	4.496226	1	1
101.0	0	2	2
102.0	0	2	2
103.0	0	2	2
104.0	0	1	1
105.0	0	1	1
107.0	0	2	2
110.0	0	3	3
111.0	0	2	2
112.0	0	2	2
116.0	0	1	1
119.0	0	1	1
121.0	0	4	4
123.0	0	2	2
124.0	0	1	1
125.0	0	2	2
127.0	0	2	2
129.0	0	1	1
131.0	0	3	3
134.0	0	1	1
138.0	0	2	2
139.0	0	1	1
142.0	0	2	2
144.0	0	1	1
145.0	0	1	1
146.0	0	1	1
148.0	0	1	1
149.0	0	3	3
150.0	0	1	1
151.0	0	1	1
157.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	1	1
164.0	0	1	1
165.0	0	1	1
167.0	0	1	1
175.0	0	1	1
176.0	0	1	1
177.0	0	1	1
181.0	0	1	1
182.0	0	1	1
183.0	0	1	1
200.0	0	1	1
205.0	0	1	1
216.0	0	1	1
217.0	0	3	3
225.0	0	1	1
232.0	0	1	1
235.0	0	2	2
239.0	0	1	1
245.0	0	1	1
253.0	0	1	1
254.0	0	1	1
266.0	0	1	1
276.0	0	1	1
297.0	0	1	1
325.0	0	1	1
334.0	0	1	1
358.0	0	1	1
371.0	0	1	1
399.0	0	1	1
438.0	0	1	1
439.0	0	2	2
462.0	0	1	1
477.0	0	1	1
484.0	0	1	1
524.0	0	1	1
664.0	0	1	1
763.0	0	1	1
1235.0	0	1	1
1780.0	0	1	1