## 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-GSM1606207.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606207.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606207.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: Mon Nov 01 20:52:31 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	35473307	6468722	0	0	4624317	0	0.13036	123957603

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28400228	28400228
2.0	1.751133	1700417	1700417
3.0	2.315333	374715	374715
4.0	2.739122	147085	147085
5.0	3.057445	74050	74050
6.0	3.296547	42752	42752
7.0	3.476144	27393	27393
8.0	3.611046	18288	18288
9.0	3.712375	12916	12916
10.0	3.788486	9371	9371
11.0	3.845656	7210	7210
12.0	3.888598	5535	5535
13.0	3.920853	4381	4381
14.0	3.945081	3516	3516
15.0	3.96328	2801	2801
16.0	3.976949	2397	2397
17.0	3.987217	1931	1931
18.0	3.994929	1614	1614
19.0	4.000722	1305	1305
20.0	4.005073	1199	1199
21.0	4.008342	998	998
22.0	4.010797	850	850
23.0	4.012641	779	779
24.0	4.014026	697	697
25.0	4.015066	588	588
26.0	4.015848	525	525
27.0	4.016435	443	443
28.0	4.016875	379	379
29.0	4.017207	371	371
30.0	4.017455	352	352
31.0	4.017642	280	280
32.0	4.017783	295	295
33.0	4.017888	242	242
34.0	4.017967	213	213
35.0	4.018027	202	202
36.0	4.018071	185	185
37.0	4.018105	169	169
38.0	4.01813	127	127
39.0	4.018149	140	140
40.0	4.018163	117	117
41.0	4.018174	116	116
42.0	4.018182	102	102
43.0	4.018188	85	85
44.0	4.018193	87	87
45.0	4.018196	78	78
46.0	4.018198	82	82
47.0	4.0182	78	78
48.0	4.018202	75	75
49.0	4.018203	59	59
50.0	4.018204	43	43
51.0	4.018204	59	59
52.0	4.018205	52	52
53.0	4.018205	55	55
54.0	4.018205	58	58
55.0	4.018206	39	39
56.0	4.018206	51	51
57.0	4.018206	34	34
58.0	4.018206	43	43
59.0	4.018206	35	35
60.0	4.018206	36	36
61.0	4.018206	35	35
62.0	4.018206	28	28
63.0	4.018206	22	22
64.0	4.018206	29	29
65.0	4.018206	18	18
66.0	4.018206	26	26
67.0	4.018206	16	16
68.0	4.018206	20	20
69.0	4.018206	17	17
70.0	4.018206	20	20
71.0	4.018206	17	17
72.0	4.018206	10	10
73.0	4.018206	14	14
74.0	4.018206	7	7
75.0	4.018206	16	16
76.0	4.018206	13	13
77.0	4.018206	19	19
78.0	4.018206	13	13
79.0	4.018206	17	17
80.0	4.018206	15	15
81.0	4.018206	12	12
82.0	4.018206	13	13
83.0	4.018206	4	4
84.0	4.018206	11	11
85.0	4.018206	7	7
86.0	4.018206	15	15
87.0	4.018206	3	3
88.0	4.018206	9	9
89.0	4.018206	8	8
90.0	4.018206	8	8
91.0	4.018206	10	10
92.0	4.018206	8	8
93.0	4.018206	2	2
94.0	4.018206	4	4
95.0	4.018206	9	9
96.0	4.018206	5	5
97.0	4.018206	4	4
98.0	4.018206	4	4
99.0	4.018206	8	8
100.0	4.018206	3	3
101.0	0	4	4
102.0	0	6	6
103.0	0	3	3
104.0	0	3	3
105.0	0	2	2
106.0	0	6	6
107.0	0	5	5
108.0	0	9	9
109.0	0	3	3
110.0	0	1	1
111.0	0	3	3
112.0	0	2	2
113.0	0	1	1
114.0	0	1	1
115.0	0	6	6
116.0	0	5	5
117.0	0	5	5
118.0	0	4	4
119.0	0	1	1
120.0	0	4	4
122.0	0	2	2
123.0	0	2	2
124.0	0	3	3
125.0	0	3	3
128.0	0	1	1
129.0	0	3	3
131.0	0	1	1
132.0	0	1	1
134.0	0	2	2
136.0	0	1	1
139.0	0	2	2
142.0	0	1	1
143.0	0	2	2
144.0	0	4	4
145.0	0	1	1
147.0	0	1	1
149.0	0	4	4
151.0	0	2	2
152.0	0	2	2
154.0	0	1	1
155.0	0	4	4
159.0	0	1	1
161.0	0	1	1
162.0	0	1	1
163.0	0	2	2
165.0	0	1	1
167.0	0	1	1
168.0	0	1	1
169.0	0	1	1
177.0	0	1	1
179.0	0	1	1
182.0	0	1	1
183.0	0	1	1
186.0	0	1	1
197.0	0	1	1
200.0	0	1	1
206.0	0	1	1
209.0	0	1	1
215.0	0	1	1
217.0	0	1	1
218.0	0	1	1
225.0	0	1	1
228.0	0	1	1
235.0	0	1	1
253.0	0	1	1
261.0	0	1	1
285.0	0	1	1
303.0	0	1	1
345.0	0	1	1
583.0	0	1	1
6261.0	0	1	1