## 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_Day12_adherent_DMSO_A61_S9.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day12_adherent_DMSO_A61_S9.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day12_adherent_DMSO_A61_S9.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 14:04:32 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	254	27622315	0	0	151	3857412	8649	0.13965	89623774

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000267	21159746	0	21166234
2.0	1.73523	2158859	8637	2153924
3.0	2.275256	282449	6	281190
4.0	2.672048	70298	0	70085
5.0	2.963598	30463	0	30422
6.0	3.177819	16488	0	16471
7.0	3.335221	10345	0	10337
8.0	3.450875	6919	0	6917
9.0	3.535854	4846	0	4846
10.0	3.598293	3437	0	3431
11.0	3.644171	2615	0	2615
12.0	3.677881	2057	0	2056
13.0	3.70265	1564	0	1562
14.0	3.720849	1327	0	1331
15.0	3.734222	1001	0	997
16.0	3.744047	881	0	877
17.0	3.751266	725	0	729
18.0	3.756571	662	0	658
19.0	3.760469	543	0	543
20.0	3.763333	458	0	458
21.0	3.765437	444	0	446
22.0	3.766983	380	0	379
23.0	3.768119	354	0	354
24.0	3.768954	287	0	288
25.0	3.769567	269	0	267
26.0	3.770018	265	0	266
27.0	3.770349	223	0	224
28.0	3.770592	186	0	185
29.0	3.770771	194	0	195
30.0	3.770902	159	0	157
31.0	3.770999	179	0	179
32.0	3.77107	133	0	134
33.0	3.771122	153	0	152
34.0	3.77116	105	0	106
35.0	3.771188	122	0	121
36.0	3.771209	111	0	113
37.0	3.771224	108	0	106
38.0	3.771235	108	0	108
39.0	3.771243	78	0	78
40.0	3.771249	97	0	99
41.0	3.771254	70	0	70
42.0	3.771257	85	0	83
43.0	3.77126	79	0	81
44.0	3.771261	67	0	66
45.0	3.771263	68	0	67
46.0	3.771264	62	0	62
47.0	3.771264	59	0	59
48.0	3.771265	47	0	51
49.0	3.771265	52	0	48
50.0	3.771265	51	0	51
51.0	3.771266	50	0	51
52.0	3.771266	52	0	51
53.0	3.771266	43	0	45
54.0	3.771266	42	0	40
55.0	3.771266	39	0	39
56.0	3.771266	41	0	42
57.0	3.771266	40	0	39
58.0	3.771266	39	0	41
59.0	3.771266	33	0	32
60.0	3.771266	41	0	40
61.0	3.771266	48	0	49
62.0	3.771266	39	0	38
63.0	3.771266	30	0	30
64.0	3.771266	23	0	23
65.0	3.771266	24	0	24
66.0	3.771266	20	0	20
67.0	3.771266	26	0	27
68.0	3.771266	17	0	16
69.0	3.771266	22	0	23
70.0	3.771266	31	0	30
71.0	3.771266	16	0	16
72.0	3.771266	32	0	32
73.0	3.771266	22	0	23
74.0	3.771266	24	0	23
75.0	3.771266	25	0	25
76.0	3.771266	17	0	17
77.0	3.771266	20	0	20
78.0	3.771266	22	0	22
79.0	3.771266	22	0	22
80.0	3.771266	19	0	19
81.0	3.771266	12	0	12
82.0	3.771266	19	0	19
83.0	3.771266	19	0	19
84.0	3.771266	15	0	16
85.0	3.771266	15	0	16
86.0	3.771266	19	0	17
87.0	3.771266	13	0	13
88.0	3.771266	11	0	12
89.0	3.771266	12	0	11
90.0	3.771266	10	0	10
91.0	3.771266	20	0	21
92.0	3.771266	12	0	12
93.0	3.771266	17	0	16
94.0	3.771266	13	0	13
95.0	3.771266	10	0	10
96.0	3.771266	12	0	12
97.0	3.771266	11	0	11
98.0	3.771266	14	0	14
99.0	3.771266	8	0	8
100.0	3.771266	7	0	7
101.0	0	10	0	11
102.0	0	16	0	15
103.0	0	7	0	7
104.0	0	7	0	7
105.0	0	5	0	6
106.0	0	11	0	11
107.0	0	6	0	5
108.0	0	14	0	14
109.0	0	5	0	5
110.0	0	11	0	11
111.0	0	8	0	8
112.0	0	7	0	7
113.0	0	12	0	12
114.0	0	7	0	7
115.0	0	5	0	5
116.0	0	3	0	3
117.0	0	9	0	9
118.0	0	6	0	7
119.0	0	7	0	6
120.0	0	7	0	7
121.0	0	3	0	3
122.0	0	8	0	8
123.0	0	8	0	8
124.0	0	6	0	6
125.0	0	6	0	6
126.0	0	4	0	4
127.0	0	6	0	6
128.0	0	3	0	3
129.0	0	8	0	8
130.0	0	5	0	5
131.0	0	7	0	7
132.0	0	2	0	2
133.0	0	1	0	1
134.0	0	5	0	5
135.0	0	4	0	4
136.0	0	8	0	8
137.0	0	8	0	8
138.0	0	6	0	6
139.0	0	7	0	7
140.0	0	4	0	5
141.0	0	2	0	1
142.0	0	3	0	3
143.0	0	8	0	8
144.0	0	7	0	7
145.0	0	3	0	3
146.0	0	2	0	2
147.0	0	4	0	4
148.0	0	3	0	3
149.0	0	6	0	6
150.0	0	4	0	4
151.0	0	3	0	3
152.0	0	3	0	3
153.0	0	3	0	3
154.0	0	7	0	7
155.0	0	3	0	3
156.0	0	2	0	2
157.0	0	2	0	2
158.0	0	7	0	7
159.0	0	2	0	2
160.0	0	4	0	4
161.0	0	1	0	1
162.0	0	9	0	9
163.0	0	4	0	5
164.0	0	4	0	4
165.0	0	7	0	6
166.0	0	5	0	5
167.0	0	6	0	6
168.0	0	4	0	4
169.0	0	5	0	5
170.0	0	2	0	2
171.0	0	3	0	3
172.0	0	2	0	2
174.0	0	3	0	3
175.0	0	3	0	3
176.0	0	2	0	2
177.0	0	2	0	2
179.0	0	1	0	2
180.0	0	4	0	4
181.0	0	5	0	4
182.0	0	2	0	2
183.0	0	4	0	4
184.0	0	4	0	4
185.0	0	7	0	8
186.0	0	2	0	1
188.0	0	1	0	1
189.0	0	5	0	5
190.0	0	1	0	1
191.0	0	2	0	2
192.0	0	2	0	2
193.0	0	1	0	1
194.0	0	2	0	2
195.0	0	1	0	1
196.0	0	1	0	1
197.0	0	1	0	2
198.0	0	1	0	0
199.0	0	2	0	3
200.0	0	4	0	3
201.0	0	5	0	5
202.0	0	1	0	2
203.0	0	3	0	2
204.0	0	3	0	4
205.0	0	2	0	1
206.0	0	2	0	2
207.0	0	2	0	3
208.0	0	2	0	2
209.0	0	3	0	2
211.0	0	4	0	4
212.0	0	2	0	2
215.0	0	2	0	3
216.0	0	1	0	0
217.0	0	2	0	2
218.0	0	1	0	1
219.0	0	1	0	1
220.0	0	3	0	4
221.0	0	3	0	2
222.0	0	3	0	3
223.0	0	2	0	2
225.0	0	2	0	2
226.0	0	2	0	3
227.0	0	1	0	0
228.0	0	3	0	3
229.0	0	1	0	2
230.0	0	3	0	2
231.0	0	1	0	2
232.0	0	1	0	0
234.0	0	2	0	2
235.0	0	1	0	1
236.0	0	1	0	1
237.0	0	1	0	1
238.0	0	1	0	1
239.0	0	1	0	1
240.0	0	2	0	2
241.0	0	1	0	1
242.0	0	1	0	1
243.0	0	1	0	1
244.0	0	2	0	2
245.0	0	1	0	1
247.0	0	1	0	1
248.0	0	3	0	3
249.0	0	1	0	1
251.0	0	3	0	3
252.0	0	2	0	2
253.0	0	1	0	1
255.0	0	0	0	1
256.0	0	1	0	0
258.0	0	1	0	1
259.0	0	2	0	2
260.0	0	1	0	1
261.0	0	1	0	1
262.0	0	2	0	2
263.0	0	1	0	1
264.0	0	1	0	1
266.0	0	1	0	1
267.0	0	2	0	2
269.0	0	0	0	1
270.0	0	1	0	0
273.0	0	1	0	1
274.0	0	1	0	2
275.0	0	1	0	0
277.0	0	1	0	1
278.0	0	1	0	1
280.0	0	1	0	1
282.0	0	2	0	2
284.0	0	1	0	1
285.0	0	1	0	1
287.0	0	1	0	1
288.0	0	1	0	1
291.0	0	2	0	2
294.0	0	2	0	2
296.0	0	3	0	3
299.0	0	1	0	1
302.0	0	2	0	2
303.0	0	0	0	1
304.0	0	1	0	0
305.0	0	1	0	1
307.0	0	2	0	2
311.0	0	1	0	1
312.0	0	2	0	2
313.0	0	2	0	2
315.0	0	2	0	2
316.0	0	1	0	1
317.0	0	2	0	2
320.0	0	1	0	1
322.0	0	2	0	2
324.0	0	1	0	1
325.0	0	1	0	1
327.0	0	1	0	2
328.0	0	1	0	0
329.0	0	0	0	1
330.0	0	1	0	0
336.0	0	1	0	1
337.0	0	2	0	2
338.0	0	2	0	3
339.0	0	4	0	3
342.0	0	1	0	1
343.0	0	1	0	1
347.0	0	1	0	1
349.0	0	1	0	1
351.0	0	1	0	1
352.0	0	1	0	1
356.0	0	1	0	1
357.0	0	2	0	2
359.0	0	1	0	1
361.0	0	1	0	1
362.0	0	1	0	1
364.0	0	2	0	2
365.0	0	2	0	2
366.0	0	1	0	1
373.0	0	1	0	1
382.0	0	1	0	1
383.0	0	1	0	1
386.0	0	0	0	1
387.0	0	1	0	0
390.0	0	1	0	1
391.0	0	1	0	1
393.0	0	1	0	1
397.0	0	1	0	2
398.0	0	1	0	0
399.0	0	0	0	1
400.0	0	1	0	0
403.0	0	0	0	1
404.0	0	1	0	0
410.0	0	1	0	2
411.0	0	1	0	0
413.0	0	1	0	1
414.0	0	2	0	2
416.0	0	1	0	1
420.0	0	1	0	2
421.0	0	3	0	2
425.0	0	1	0	1
431.0	0	1	0	1
441.0	0	1	0	1
445.0	0	1	0	1
446.0	0	1	0	1
448.0	0	1	0	1
450.0	0	1	0	1
452.0	0	1	0	1
453.0	0	1	0	1
454.0	0	1	0	1
473.0	0	1	0	1
475.0	0	1	0	1
478.0	0	1	0	1
479.0	0	1	0	1
483.0	0	0	0	1
484.0	0	1	0	1
485.0	0	1	0	0
488.0	0	1	0	1
489.0	0	0	0	1
490.0	0	2	0	1
492.0	0	1	0	1
497.0	0	1	0	1
502.0	0	1	0	1
507.0	0	1	0	1
521.0	0	0	0	1
522.0	0	1	0	0
524.0	0	1	0	1
525.0	0	0	0	1
526.0	0	1	0	0
532.0	0	1	0	1
552.0	0	1	0	1
560.0	0	0	0	1
561.0	0	1	0	0
571.0	0	1	0	1
573.0	0	1	0	1
588.0	0	1	0	1
596.0	0	1	0	1
601.0	0	1	0	1
604.0	0	1	0	1
606.0	0	1	0	1
607.0	0	1	0	1
609.0	0	2	0	2
618.0	0	1	0	1
620.0	0	1	0	1
626.0	0	1	0	1
632.0	0	1	0	1
642.0	0	1	0	1
643.0	0	1	0	1
656.0	0	1	0	1
699.0	0	1	0	1
702.0	0	1	0	1
727.0	0	1	0	1
732.0	0	1	0	1
794.0	0	0	0	1
795.0	0	2	0	1
823.0	0	1	0	1
851.0	0	0	0	1
852.0	0	1	0	0
870.0	0	1	0	1
903.0	0	1	0	1
914.0	0	0	0	1
915.0	0	1	0	0
956.0	0	1	0	1
963.0	0	1	0	1
987.0	0	1	0	1
1015.0	0	0	0	1
1016.0	0	1	0	0
1032.0	0	1	0	1
1061.0	0	1	0	1
1079.0	0	1	0	1
1248.0	0	1	0	1
1325.0	0	1	0	1
1395.0	0	1	0	1
1401.0	0	1	0	1
1478.0	0	0	0	1
1479.0	0	1	0	0
1607.0	0	1	0	1
1977.0	0	1	0	1
2088.0	0	1	0	1