## 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-GSM919933.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919933.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919933.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 15:30:30 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	10585854	1878750	0	0	1657366	0	0.156564	30177456

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8161138	8161138
2.0	1.704134	493873	493873
3.0	2.199938	128052	128052
4.0	2.549051	54160	54160
5.0	2.794873	28401	28401
6.0	2.967965	16935	16935
7.0	3.089844	10993	10993
8.0	3.175664	7521	7521
9.0	3.236092	5351	5351
10.0	3.278642	3961	3961
11.0	3.308603	2859	2859
12.0	3.329699	2376	2376
13.0	3.344554	1844	1844
14.0	3.355014	1456	1456
15.0	3.362379	1282	1282
16.0	3.367565	1007	1007
17.0	3.371216	861	861
18.0	3.373787	710	710
19.0	3.375598	600	600
20.0	3.376873	500	500
21.0	3.37777	429	429
22.0	3.378402	367	367
23.0	3.378847	355	355
24.0	3.379161	296	296
25.0	3.379382	242	242
26.0	3.379537	211	211
27.0	3.379646	203	203
28.0	3.379723	172	172
29.0	3.379778	145	145
30.0	3.379816	151	151
31.0	3.379843	133	133
32.0	3.379862	111	111
33.0	3.379875	102	102
34.0	3.379884	110	110
35.0	3.379891	94	94
36.0	3.379896	102	102
37.0	3.379899	64	64
38.0	3.379901	61	61
39.0	3.379903	68	68
40.0	3.379904	81	81
41.0	3.379905	73	73
42.0	3.379905	57	57
43.0	3.379906	50	50
44.0	3.379906	51	51
45.0	3.379906	36	36
46.0	3.379906	41	41
47.0	3.379906	40	40
48.0	3.379906	32	32
49.0	3.379907	27	27
50.0	3.379907	32	32
51.0	3.379907	26	26
52.0	3.379907	23	23
53.0	3.379907	21	21
54.0	3.379907	16	16
55.0	3.379907	25	25
56.0	3.379907	9	9
57.0	3.379907	23	23
58.0	3.379907	13	13
59.0	3.379907	18	18
60.0	3.379907	15	15
61.0	3.379907	10	10
62.0	3.379907	16	16
63.0	3.379907	18	18
64.0	3.379907	14	14
65.0	3.379907	16	16
66.0	3.379907	11	11
67.0	3.379907	17	17
68.0	3.379907	15	15
69.0	3.379907	11	11
70.0	3.379907	10	10
71.0	3.379907	11	11
72.0	3.379907	7	7
73.0	3.379907	11	11
74.0	3.379907	7	7
75.0	3.379907	8	8
76.0	3.379907	9	9
77.0	3.379907	9	9
78.0	3.379907	7	7
79.0	3.379907	4	4
80.0	3.379907	1	1
81.0	3.379907	4	4
82.0	3.379907	4	4
83.0	3.379907	6	6
84.0	3.379907	11	11
85.0	3.379907	8	8
86.0	3.379907	10	10
87.0	3.379907	5	5
88.0	3.379907	5	5
89.0	3.379907	4	4
90.0	3.379907	8	8
91.0	3.379907	6	6
92.0	3.379907	4	4
93.0	3.379907	5	5
94.0	3.379907	5	5
95.0	3.379907	4	4
96.0	3.379907	3	3
97.0	3.379907	5	5
98.0	3.379907	1	1
99.0	3.379907	1	1
100.0	3.379907	1	1
101.0	0	4	4
102.0	0	2	2
103.0	0	1	1
104.0	0	5	5
105.0	0	5	5
106.0	0	1	1
107.0	0	4	4
108.0	0	5	5
109.0	0	3	3
110.0	0	1	1
111.0	0	5	5
112.0	0	1	1
113.0	0	1	1
114.0	0	4	4
115.0	0	5	5
117.0	0	3	3
118.0	0	2	2
119.0	0	2	2
120.0	0	2	2
124.0	0	5	5
126.0	0	6	6
127.0	0	5	5
129.0	0	2	2
130.0	0	3	3
131.0	0	1	1
132.0	0	2	2
133.0	0	2	2
134.0	0	1	1
135.0	0	1	1
137.0	0	2	2
138.0	0	1	1
139.0	0	5	5
140.0	0	1	1
141.0	0	1	1
144.0	0	2	2
145.0	0	2	2
147.0	0	4	4
148.0	0	2	2
149.0	0	2	2
152.0	0	1	1
153.0	0	2	2
157.0	0	1	1
158.0	0	1	1
160.0	0	1	1
161.0	0	2	2
163.0	0	1	1
164.0	0	2	2
167.0	0	2	2
174.0	0	1	1
175.0	0	1	1
177.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	1	1
189.0	0	2	2
191.0	0	1	1
192.0	0	1	1
193.0	0	1	1
199.0	0	1	1
200.0	0	1	1
202.0	0	2	2
204.0	0	2	2
208.0	0	1	1
209.0	0	1	1
211.0	0	3	3
213.0	0	2	2
225.0	0	1	1
227.0	0	1	1
229.0	0	1	1
237.0	0	1	1
242.0	0	1	1
255.0	0	1	1
256.0	0	1	1
265.0	0	1	1
276.0	0	1	1
285.0	0	1	1
294.0	0	1	1
297.0	0	1	1
319.0	0	1	1
327.0	0	1	1
335.0	0	1	1
363.0	0	1	1
366.0	0	1	1
382.0	0	1	1
410.0	0	1	1
414.0	0	1	1
423.0	0	1	1
486.0	0	1	1
575.0	0	1	1
605.0	0	1	1
712.0	0	1	1
716.0	0	1	1
1148.0	0	1	1