## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/hg38-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day19_adherent_DMSO_A65_S2.samtools-coordinate.metrics.txt    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 Aug 30 14:03:45 CEST 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	125	15825183	0	0	62	5300568	4293	0.334946	17993806

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000169	7077893	0	7079622
2.0	1.415238	2434775	4281	2434435
3.0	1.587492	726353	6	725657
4.0	1.658977	192449	0	192002
5.0	1.688643	50256	0	50082
6.0	1.700954	15492	0	15452
7.0	1.706063	6374	0	6357
8.0	1.708184	3620	0	3615
9.0	1.709064	2299	0	2294
10.0	1.709429	1696	0	1694
11.0	1.70958	1272	0	1271
12.0	1.709643	988	0	988
13.0	1.709669	782	0	781
14.0	1.70968	653	0	653
15.0	1.709685	572	0	572
16.0	1.709686	508	0	510
17.0	1.709687	443	0	441
18.0	1.709688	396	0	396
19.0	1.709688	354	0	354
20.0	1.709688	315	0	318
21.0	1.709688	264	0	261
22.0	1.709688	303	0	303
23.0	1.709688	233	0	233
24.0	1.709688	188	0	188
25.0	1.709688	200	0	199
26.0	1.709688	186	0	186
27.0	1.709688	146	0	147
28.0	1.709688	161	0	161
29.0	1.709688	146	0	146
30.0	1.709688	146	0	147
31.0	1.709688	119	0	117
32.0	1.709688	115	0	115
33.0	1.709688	104	0	106
34.0	1.709688	115	0	115
35.0	1.709688	111	0	110
36.0	1.709688	93	0	92
37.0	1.709688	102	0	102
38.0	1.709688	104	0	104
39.0	1.709688	91	0	91
40.0	1.709688	88	0	88
41.0	1.709688	61	0	61
42.0	1.709688	78	0	78
43.0	1.709688	77	0	77
44.0	1.709688	84	0	84
45.0	1.709688	75	0	76
46.0	1.709688	57	0	56
47.0	1.709688	57	0	58
48.0	1.709688	57	0	56
49.0	1.709688	55	0	55
50.0	1.709688	42	0	44
51.0	1.709688	49	0	48
52.0	1.709688	68	0	67
53.0	1.709688	56	0	56
54.0	1.709688	49	0	50
55.0	1.709688	34	0	34
56.0	1.709688	38	0	37
57.0	1.709688	45	0	45
58.0	1.709688	48	0	48
59.0	1.709688	36	0	36
60.0	1.709688	31	0	32
61.0	1.709688	27	0	26
62.0	1.709688	39	0	39
63.0	1.709688	19	0	21
64.0	1.709688	35	0	34
65.0	1.709688	30	0	29
66.0	1.709688	38	0	38
67.0	1.709688	32	0	32
68.0	1.709688	26	0	26
69.0	1.709688	23	0	23
70.0	1.709688	20	0	21
71.0	1.709688	17	0	16
72.0	1.709688	23	0	24
73.0	1.709688	35	0	35
74.0	1.709688	23	0	23
75.0	1.709688	23	0	22
76.0	1.709688	21	0	22
77.0	1.709688	18	0	17
78.0	1.709688	19	0	19
79.0	1.709688	21	0	21
80.0	1.709688	24	0	25
81.0	1.709688	22	0	21
82.0	1.709688	14	0	14
83.0	1.709688	17	0	19
84.0	1.709688	17	0	16
85.0	1.709688	12	0	11
86.0	1.709688	7	0	8
87.0	1.709688	13	0	12
88.0	1.709688	12	0	12
89.0	1.709688	14	0	14
90.0	1.709688	20	0	20
91.0	1.709688	14	0	14
92.0	1.709688	9	0	9
93.0	1.709688	10	0	10
94.0	1.709688	13	0	13
95.0	1.709688	13	0	13
96.0	1.709688	18	0	18
97.0	1.709688	16	0	16
98.0	1.709688	11	0	11
99.0	1.709688	15	0	16
100.0	1.709688	8	0	9
101.0	0	14	0	12
102.0	0	5	0	5
103.0	0	10	0	10
104.0	0	13	0	13
105.0	0	8	0	9
106.0	0	13	0	12
107.0	0	13	0	13
108.0	0	8	0	8
109.0	0	4	0	4
110.0	0	9	0	9
111.0	0	13	0	13
112.0	0	12	0	12
113.0	0	11	0	11
114.0	0	6	0	6
115.0	0	5	0	5
116.0	0	6	0	6
117.0	0	10	0	11
118.0	0	9	0	8
119.0	0	6	0	6
120.0	0	10	0	11
121.0	0	10	0	10
122.0	0	6	0	5
123.0	0	8	0	8
124.0	0	10	0	10
125.0	0	9	0	9
126.0	0	7	0	7
127.0	0	4	0	4
128.0	0	6	0	6
129.0	0	7	0	7
130.0	0	3	0	4
131.0	0	10	0	9
132.0	0	4	0	4
133.0	0	8	0	8
134.0	0	6	0	6
135.0	0	8	0	9
136.0	0	8	0	7
137.0	0	4	0	5
138.0	0	5	0	4
139.0	0	8	0	9
140.0	0	10	0	9
141.0	0	4	0	4
142.0	0	2	0	2
143.0	0	3	0	3
144.0	0	5	0	5
145.0	0	1	0	3
146.0	0	5	0	3
147.0	0	9	0	9
148.0	0	8	0	8
149.0	0	5	0	6
150.0	0	4	0	3
151.0	0	6	0	6
152.0	0	7	0	7
153.0	0	6	0	6
154.0	0	4	0	4
155.0	0	3	0	3
156.0	0	5	0	5
157.0	0	4	0	4
158.0	0	5	0	5
159.0	0	8	0	8
160.0	0	3	0	3
161.0	0	2	0	2
162.0	0	5	0	6
163.0	0	5	0	5
164.0	0	4	0	3
165.0	0	2	0	3
166.0	0	2	0	1
167.0	0	1	0	1
168.0	0	2	0	2
169.0	0	3	0	3
170.0	0	6	0	6
171.0	0	3	0	3
172.0	0	3	0	3
173.0	0	3	0	4
174.0	0	3	0	2
175.0	0	4	0	4
176.0	0	4	0	4
177.0	0	1	0	1
178.0	0	1	0	1
179.0	0	3	0	3
180.0	0	5	0	5
181.0	0	7	0	7
183.0	0	3	0	3
184.0	0	2	0	2
185.0	0	3	0	3
186.0	0	2	0	2
187.0	0	2	0	2
188.0	0	3	0	3
189.0	0	3	0	4
190.0	0	3	0	2
192.0	0	1	0	1
193.0	0	5	0	5
194.0	0	5	0	5
195.0	0	2	0	3
196.0	0	3	0	2
198.0	0	4	0	4
199.0	0	2	0	2
200.0	0	2	0	2
201.0	0	1	0	1
202.0	0	2	0	2
203.0	0	1	0	1
204.0	0	2	0	2
205.0	0	2	0	2
206.0	0	3	0	3
207.0	0	2	0	2
208.0	0	1	0	1
209.0	0	1	0	1
210.0	0	1	0	1
211.0	0	1	0	1
212.0	0	3	0	3
213.0	0	3	0	3
214.0	0	2	0	3
215.0	0	3	0	2
216.0	0	3	0	3
217.0	0	4	0	5
218.0	0	1	0	0
219.0	0	1	0	1
220.0	0	1	0	1
221.0	0	2	0	2
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	2	0	2
225.0	0	1	0	1
226.0	0	2	0	2
228.0	0	4	0	4
229.0	0	3	0	3
230.0	0	1	0	1
231.0	0	1	0	2
232.0	0	2	0	1
233.0	0	2	0	2
234.0	0	4	0	4
236.0	0	2	0	2
237.0	0	2	0	2
238.0	0	2	0	2
239.0	0	3	0	3
240.0	0	2	0	3
241.0	0	1	0	0
242.0	0	4	0	4
243.0	0	1	0	1
244.0	0	1	0	1
246.0	0	2	0	2
249.0	0	2	0	2
250.0	0	3	0	3
251.0	0	1	0	1
252.0	0	1	0	1
253.0	0	3	0	3
254.0	0	1	0	1
256.0	0	2	0	2
257.0	0	2	0	2
258.0	0	1	0	1
259.0	0	2	0	2
260.0	0	3	0	3
261.0	0	4	0	4
264.0	0	1	0	1
266.0	0	1	0	1
267.0	0	3	0	3
268.0	0	4	0	4
269.0	0	2	0	2
270.0	0	1	0	1
271.0	0	3	0	3
272.0	0	1	0	1
273.0	0	1	0	1
274.0	0	2	0	2
275.0	0	2	0	2
276.0	0	1	0	1
278.0	0	1	0	1
279.0	0	3	0	3
280.0	0	1	0	1
282.0	0	1	0	1
283.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	1	0	1
287.0	0	1	0	1
291.0	0	1	0	1
292.0	0	1	0	1
293.0	0	1	0	1
294.0	0	2	0	2
295.0	0	2	0	2
298.0	0	1	0	1
302.0	0	1	0	1
304.0	0	1	0	1
307.0	0	1	0	1
312.0	0	1	0	1
314.0	0	2	0	2
315.0	0	1	0	1
319.0	0	2	0	2
320.0	0	2	0	3
321.0	0	2	0	1
323.0	0	1	0	2
324.0	0	2	0	1
325.0	0	1	0	1
327.0	0	1	0	1
328.0	0	2	0	2
332.0	0	1	0	1
334.0	0	1	0	1
336.0	0	2	0	2
338.0	0	1	0	1
339.0	0	1	0	1
343.0	0	2	0	2
344.0	0	2	0	2
346.0	0	1	0	1
347.0	0	1	0	1
349.0	0	1	0	1
352.0	0	2	0	2
353.0	0	1	0	1
354.0	0	1	0	1
355.0	0	1	0	1
358.0	0	2	0	3
359.0	0	1	0	1
360.0	0	1	0	0
362.0	0	1	0	1
363.0	0	2	0	2
364.0	0	1	0	1
366.0	0	1	0	1
367.0	0	1	0	1
370.0	0	1	0	1
374.0	0	1	0	1
379.0	0	1	0	1
383.0	0	1	0	1
384.0	0	2	0	2
385.0	0	1	0	1
387.0	0	2	0	2
390.0	0	2	0	2
391.0	0	1	0	1
393.0	0	1	0	1
397.0	0	0	0	1
398.0	0	1	0	0
400.0	0	1	0	1
405.0	0	1	0	1
407.0	0	1	0	1
408.0	0	1	0	1
422.0	0	1	0	1
427.0	0	1	0	1
429.0	0	1	0	1
430.0	0	1	0	1
439.0	0	1	0	1
446.0	0	2	0	2
450.0	0	1	0	1
459.0	0	1	0	1
463.0	0	1	0	1
465.0	0	1	0	1
467.0	0	1	0	1
470.0	0	1	0	1
476.0	0	1	0	1
481.0	0	1	0	1
499.0	0	0	0	1
500.0	0	2	0	1
506.0	0	1	0	1
509.0	0	2	0	2
534.0	0	1	0	1
540.0	0	1	0	1
541.0	0	1	0	1
543.0	0	1	0	1
545.0	0	1	0	1
546.0	0	2	0	2
547.0	0	1	0	1
549.0	0	1	0	1
556.0	0	1	0	1
558.0	0	1	0	1
566.0	0	1	0	1
568.0	0	0	0	1
569.0	0	1	0	0
595.0	0	1	0	1
596.0	0	1	0	1
597.0	0	1	0	1
602.0	0	1	0	1
640.0	0	1	0	1
647.0	0	0	0	1
648.0	0	1	0	0
661.0	0	0	0	1
662.0	0	1	0	0
701.0	0	2	0	2
706.0	0	0	0	1
707.0	0	1	0	0
709.0	0	1	0	1
711.0	0	1	0	1
750.0	0	1	0	2
751.0	0	1	0	0
785.0	0	1	0	1
825.0	0	0	0	1
827.0	0	1	0	0
874.0	0	1	0	1
880.0	0	0	0	1
881.0	0	1	0	0
977.0	0	1	0	1
984.0	0	1	0	1
1003.0	0	0	0	1
1004.0	0	1	0	0
1008.0	0	1	0	1
1081.0	0	1	0	1
1109.0	0	1	0	1
1111.0	0	1	0	1
1131.0	0	0	0	1
1132.0	0	1	0	0
1193.0	0	0	0	1
1194.0	0	1	0	0
1278.0	0	1	0	1
1286.0	0	1	0	1
1298.0	0	0	0	1
1299.0	0	1	0	0
1321.0	0	0	0	1
1322.0	0	1	0	0
1492.0	0	0	0	1
1494.0	0	1	0	0
1640.0	0	1	0	1
1649.0	0	0	0	1
1651.0	0	1	0	0