## 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-GSM1606333.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM1606333.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM1606333.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 14:18:37 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	25058111	3103702	0	0	2972734	0	0.118634	97082143

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20205002	20205002
2.0	1.772508	1419701	1419701
3.0	2.369277	261517	261517
4.0	2.830287	89813	89813
5.0	3.18642	40925	40925
6.0	3.461536	21858	21858
7.0	3.674066	13133	13133
8.0	3.838246	8530	8530
9.0	3.965077	5705	5705
10.0	4.063055	4113	4113
11.0	4.138744	2916	2916
12.0	4.197214	2280	2280
13.0	4.242383	1705	1705
14.0	4.277276	1336	1336
15.0	4.304232	1042	1042
16.0	4.325055	838	838
17.0	4.341141	700	700
18.0	4.353568	587	587
19.0	4.363167	443	443
20.0	4.370583	417	417
21.0	4.376312	348	348
22.0	4.380738	257	257
23.0	4.384156	237	237
24.0	4.386797	205	205
25.0	4.388838	176	176
26.0	4.390414	153	153
27.0	4.391631	130	130
28.0	4.392572	148	148
29.0	4.393298	97	97
30.0	4.39386	94	94
31.0	4.394293	77	77
32.0	4.394628	72	72
33.0	4.394887	61	61
34.0	4.395087	48	48
35.0	4.395241	53	53
36.0	4.395361	50	50
37.0	4.395453	37	37
38.0	4.395524	39	39
39.0	4.395579	34	34
40.0	4.395621	36	36
41.0	4.395654	31	31
42.0	4.39568	25	25
43.0	4.395699	15	15
44.0	4.395714	24	24
45.0	4.395726	26	26
46.0	4.395735	17	17
47.0	4.395742	25	25
48.0	4.395747	17	17
49.0	4.395752	19	19
50.0	4.395755	9	9
51.0	4.395757	14	14
52.0	4.395759	12	12
53.0	4.395761	6	6
54.0	4.395762	9	9
55.0	4.395763	11	11
56.0	4.395763	7	7
57.0	4.395764	13	13
58.0	4.395764	9	9
59.0	4.395765	11	11
60.0	4.395765	10	10
61.0	4.395765	5	5
62.0	4.395765	9	9
63.0	4.395765	4	4
64.0	4.395765	4	4
65.0	4.395765	2	2
66.0	4.395766	4	4
67.0	4.395766	6	6
68.0	4.395766	7	7
69.0	4.395766	2	2
70.0	4.395766	4	4
71.0	4.395766	2	2
72.0	4.395766	6	6
73.0	4.395766	6	6
74.0	4.395766	3	3
75.0	4.395766	7	7
76.0	4.395766	3	3
77.0	4.395766	1	1
78.0	4.395766	1	1
79.0	4.395766	3	3
80.0	4.395766	1	1
81.0	4.395766	0	0
82.0	4.395766	4	4
83.0	4.395766	1	1
84.0	4.395766	3	3
85.0	4.395766	2	2
86.0	4.395766	1	1
87.0	4.395766	4	4
88.0	4.395766	1	1
89.0	4.395766	2	2
90.0	4.395766	1	1
91.0	4.395766	2	2
92.0	4.395766	1	1
93.0	4.395766	1	1
94.0	4.395766	1	1
95.0	4.395766	1	1
96.0	4.395766	0	0
97.0	4.395766	0	0
98.0	4.395766	2	2
99.0	4.395766	2	2
100.0	4.395766	1	1
101.0	0	1	1
102.0	0	1	1
110.0	0	1	1
111.0	0	1	1
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
116.0	0	3	3
117.0	0	1	1
120.0	0	1	1
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
132.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
148.0	0	1	1
150.0	0	1	1
167.0	0	1	1
179.0	0	1	1
200.0	0	2	2
225.0	0	1	1
237.0	0	1	1
275.0	0	1	1
277.0	0	1	1
287.0	0	1	1
303.0	0	1	1
325.0	0	1	1
356.0	0	2	2
367.0	0	1	1
371.0	0	1	1
442.0	0	1	1
461.0	0	1	1
472.0	0	1	1
528.0	0	1	1
553.0	0	1	1
785.0	0	1	1
17055.0	0	1	1