## 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-GSM919950.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/star/Xenopus_tropicalis_v9.1-GSM919950.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/xt_rna/results/qc/markdup/Xenopus_tropicalis_v9.1-GSM919950.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 15:56:44 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	8151565	1641832	0	0	1591063	0	0.195185	18065457

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	5839057	5839057
2.0	1.636848	480744	480744
3.0	2.042424	111972	111972
4.0	2.300714	46252	46252
5.0	2.465206	24419	24419
6.0	2.569962	14547	14547
7.0	2.636676	9714	9714
8.0	2.679162	6729	6729
9.0	2.70622	4789	4789
10.0	2.723452	3610	3610
11.0	2.734425	2812	2812
12.0	2.741414	2175	2175
13.0	2.745865	1682	1682
14.0	2.748699	1493	1493
15.0	2.750504	1190	1190
16.0	2.751654	1049	1049
17.0	2.752386	882	882
18.0	2.752852	708	708
19.0	2.753149	657	657
20.0	2.753338	558	558
21.0	2.753459	474	474
22.0	2.753535	391	391
23.0	2.753584	357	357
24.0	2.753615	327	327
25.0	2.753635	291	291
26.0	2.753648	241	241
27.0	2.753656	220	220
28.0	2.753661	198	198
29.0	2.753664	218	218
30.0	2.753666	183	183
31.0	2.753668	172	172
32.0	2.753668	148	148
33.0	2.753669	116	116
34.0	2.753669	108	108
35.0	2.75367	106	106
36.0	2.75367	111	111
37.0	2.75367	88	88
38.0	2.75367	86	86
39.0	2.75367	87	87
40.0	2.75367	84	84
41.0	2.75367	74	74
42.0	2.75367	62	62
43.0	2.75367	53	53
44.0	2.75367	49	49
45.0	2.75367	49	49
46.0	2.75367	44	44
47.0	2.75367	50	50
48.0	2.75367	50	50
49.0	2.75367	41	41
50.0	2.75367	38	38
51.0	2.75367	41	41
52.0	2.75367	26	26
53.0	2.75367	37	37
54.0	2.75367	39	39
55.0	2.75367	29	29
56.0	2.75367	25	25
57.0	2.75367	24	24
58.0	2.75367	22	22
59.0	2.75367	16	16
60.0	2.75367	22	22
61.0	2.75367	21	21
62.0	2.75367	28	28
63.0	2.75367	16	16
64.0	2.75367	14	14
65.0	2.75367	20	20
66.0	2.75367	18	18
67.0	2.75367	11	11
68.0	2.75367	20	20
69.0	2.75367	14	14
70.0	2.75367	15	15
71.0	2.75367	9	9
72.0	2.75367	17	17
73.0	2.75367	11	11
74.0	2.75367	12	12
75.0	2.75367	8	8
76.0	2.75367	11	11
77.0	2.75367	8	8
78.0	2.75367	11	11
79.0	2.75367	15	15
80.0	2.75367	13	13
81.0	2.75367	8	8
82.0	2.75367	5	5
83.0	2.75367	6	6
84.0	2.75367	8	8
85.0	2.75367	4	4
86.0	2.75367	13	13
87.0	2.75367	5	5
88.0	2.75367	6	6
89.0	2.75367	3	3
90.0	2.75367	6	6
91.0	2.75367	3	3
92.0	2.75367	6	6
93.0	2.75367	7	7
94.0	2.75367	10	10
95.0	2.75367	8	8
96.0	2.75367	6	6
97.0	2.75367	5	5
98.0	2.75367	6	6
99.0	2.75367	3	3
100.0	2.75367	6	6
101.0	0	3	3
102.0	0	10	10
103.0	0	2	2
104.0	0	7	7
105.0	0	5	5
106.0	0	2	2
107.0	0	2	2
108.0	0	2	2
109.0	0	1	1
111.0	0	4	4
112.0	0	4	4
113.0	0	7	7
114.0	0	2	2
115.0	0	6	6
116.0	0	2	2
117.0	0	2	2
118.0	0	5	5
119.0	0	3	3
120.0	0	3	3
121.0	0	2	2
122.0	0	2	2
123.0	0	1	1
124.0	0	3	3
125.0	0	5	5
126.0	0	1	1
127.0	0	2	2
130.0	0	4	4
131.0	0	3	3
132.0	0	3	3
133.0	0	3	3
134.0	0	2	2
136.0	0	3	3
137.0	0	3	3
138.0	0	2	2
139.0	0	2	2
140.0	0	2	2
141.0	0	3	3
142.0	0	1	1
143.0	0	1	1
144.0	0	3	3
145.0	0	1	1
146.0	0	3	3
147.0	0	1	1
148.0	0	1	1
149.0	0	2	2
150.0	0	1	1
151.0	0	1	1
155.0	0	3	3
156.0	0	1	1
157.0	0	1	1
158.0	0	3	3
159.0	0	1	1
160.0	0	3	3
161.0	0	3	3
162.0	0	5	5
164.0	0	1	1
165.0	0	1	1
168.0	0	2	2
169.0	0	1	1
170.0	0	3	3
172.0	0	1	1
173.0	0	1	1
174.0	0	1	1
176.0	0	1	1
177.0	0	1	1
178.0	0	3	3
179.0	0	1	1
181.0	0	1	1
183.0	0	1	1
184.0	0	1	1
188.0	0	1	1
190.0	0	1	1
191.0	0	2	2
193.0	0	1	1
197.0	0	3	3
198.0	0	1	1
203.0	0	2	2
206.0	0	2	2
208.0	0	2	2
211.0	0	1	1
216.0	0	3	3
217.0	0	1	1
219.0	0	1	1
221.0	0	1	1
222.0	0	1	1
226.0	0	1	1
228.0	0	1	1
231.0	0	3	3
234.0	0	1	1
235.0	0	1	1
239.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
252.0	0	1	1
253.0	0	1	1
256.0	0	1	1
264.0	0	1	1
279.0	0	1	1
281.0	0	1	1
283.0	0	2	2
299.0	0	1	1
308.0	0	1	1
310.0	0	1	1
322.0	0	1	1
330.0	0	1	1
331.0	0	1	1
346.0	0	1	1
347.0	0	1	1
358.0	0	1	1
370.0	0	2	2
375.0	0	1	1
394.0	0	1	1
403.0	0	1	1
410.0	0	1	1
417.0	0	1	1
465.0	0	1	1
487.0	0	1	1
560.0	0	1	1
577.0	0	1	1
597.0	0	1	1
604.0	0	1	1
606.0	0	1	1
612.0	0	1	1
626.0	0	1	1
655.0	0	1	1
681.0	0	1	1
705.0	0	1	1
727.0	0	1	1
817.0	0	1	1
969.0	0	1	1
1131.0	0	1	1
1154.0	0	1	1
1544.0	0	1	1
2648.0	0	1	1