## 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-GSM1606214.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606214.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606214.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 14:29:46 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	28844362	4775318	0	0	3649037	0	0.126508	104169836

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23269363	23269363
2.0	1.758132	1343114	1343114
3.0	2.332897	291286	291286
4.0	2.768644	114432	114432
5.0	3.098998	57417	57417
6.0	3.349451	33372	33372
7.0	3.539327	21461	21461
8.0	3.683278	14322	14322
9.0	3.792411	10122	10122
10.0	3.875149	7429	7429
11.0	3.937876	5598	5598
12.0	3.98543	4397	4397
13.0	4.021483	3350	3350
14.0	4.048816	2684	2684
15.0	4.069538	2269	2269
16.0	4.085248	1789	1789
17.0	4.097158	1519	1519
18.0	4.106188	1280	1280
19.0	4.113033	1082	1082
20.0	4.118223	923	923
21.0	4.122158	831	831
22.0	4.125141	661	661
23.0	4.127402	653	653
24.0	4.129117	539	539
25.0	4.130416	429	429
26.0	4.131402	426	426
27.0	4.132149	354	354
28.0	4.132715	296	296
29.0	4.133145	295	295
30.0	4.13347	266	266
31.0	4.133717	239	239
32.0	4.133904	220	220
33.0	4.134046	171	171
34.0	4.134154	167	167
35.0	4.134235	173	173
36.0	4.134297	177	177
37.0	4.134344	137	137
38.0	4.134379	147	147
39.0	4.134406	118	118
40.0	4.134427	101	101
41.0	4.134442	95	95
42.0	4.134454	91	91
43.0	4.134463	101	101
44.0	4.13447	90	90
45.0	4.134475	65	65
46.0	4.134479	75	75
47.0	4.134481	51	51
48.0	4.134484	69	69
49.0	4.134485	58	58
50.0	4.134487	45	45
51.0	4.134488	51	51
52.0	4.134488	57	57
53.0	4.134489	36	36
54.0	4.134489	41	41
55.0	4.13449	38	38
56.0	4.13449	34	34
57.0	4.13449	28	28
58.0	4.13449	21	21
59.0	4.13449	28	28
60.0	4.13449	20	20
61.0	4.13449	32	32
62.0	4.134491	26	26
63.0	4.134491	21	21
64.0	4.134491	23	23
65.0	4.134491	19	19
66.0	4.134491	18	18
67.0	4.134491	19	19
68.0	4.134491	17	17
69.0	4.134491	13	13
70.0	4.134491	12	12
71.0	4.134491	12	12
72.0	4.134491	15	15
73.0	4.134491	11	11
74.0	4.134491	12	12
75.0	4.134491	12	12
76.0	4.134491	12	12
77.0	4.134491	14	14
78.0	4.134491	10	10
79.0	4.134491	7	7
80.0	4.134491	12	12
81.0	4.134491	17	17
82.0	4.134491	9	9
83.0	4.134491	14	14
84.0	4.134491	11	11
85.0	4.134491	9	9
86.0	4.134491	9	9
87.0	4.134491	4	4
88.0	4.134491	6	6
89.0	4.134491	7	7
90.0	4.134491	8	8
91.0	4.134491	3	3
92.0	4.134491	10	10
93.0	4.134491	6	6
94.0	4.134491	6	6
95.0	4.134491	7	7
96.0	4.134491	5	5
97.0	4.134491	1	1
98.0	4.134491	6	6
99.0	4.134491	1	1
100.0	4.134491	1	1
101.0	0	5	5
102.0	0	6	6
103.0	0	6	6
104.0	0	1	1
105.0	0	4	4
106.0	0	4	4
107.0	0	4	4
108.0	0	2	2
109.0	0	4	4
110.0	0	1	1
111.0	0	5	5
112.0	0	3	3
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
116.0	0	4	4
117.0	0	2	2
118.0	0	1	1
119.0	0	3	3
120.0	0	1	1
121.0	0	3	3
122.0	0	3	3
123.0	0	2	2
124.0	0	3	3
125.0	0	1	1
127.0	0	1	1
130.0	0	2	2
131.0	0	5	5
132.0	0	3	3
133.0	0	1	1
137.0	0	3	3
138.0	0	3	3
139.0	0	3	3
140.0	0	3	3
141.0	0	2	2
145.0	0	1	1
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
151.0	0	2	2
152.0	0	4	4
154.0	0	1	1
155.0	0	1	1
158.0	0	1	1
162.0	0	2	2
163.0	0	2	2
165.0	0	2	2
168.0	0	2	2
170.0	0	1	1
174.0	0	2	2
175.0	0	1	1
177.0	0	1	1
182.0	0	2	2
184.0	0	2	2
185.0	0	1	1
187.0	0	1	1
188.0	0	1	1
190.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	2	2
204.0	0	1	1
206.0	0	1	1
210.0	0	1	1
215.0	0	1	1
216.0	0	2	2
222.0	0	1	1
239.0	0	1	1
246.0	0	1	1
252.0	0	1	1
253.0	0	1	1
265.0	0	1	1
273.0	0	1	1
278.0	0	1	1
306.0	0	1	1
315.0	0	2	2
321.0	0	1	1
323.0	0	1	1
332.0	0	1	1
348.0	0	1	1
379.0	0	1	1
470.0	0	1	1
565.0	0	1	1
748.0	0	1	1
755.0	0	1	1
6816.0	0	1	1