## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_supernatant_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_supernatant_TA_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D19_supernatant_TA_1.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 06 02:53:22 CEST 2023

## 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	470	20888210	21312618	0	364	3799333	0	0.181896	50223093

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14810451	14810451
2.0	1.659741	1824103	1824103
3.0	2.094998	275604	275604
4.0	2.382156	69548	69548
5.0	2.571605	30518	30518
6.0	2.696592	17966	17966
7.0	2.779052	11977	11977
8.0	2.833453	8518	8518
9.0	2.869344	6227	6227
10.0	2.893023	4844	4844
11.0	2.908645	3776	3776
12.0	2.918951	2994	2994
13.0	2.925751	2466	2466
14.0	2.930237	1949	1949
15.0	2.933196	1753	1753
16.0	2.935149	1530	1530
17.0	2.936437	1254	1254
18.0	2.937287	1113	1113
19.0	2.937848	989	989
20.0	2.938217	874	874
21.0	2.938461	730	730
22.0	2.938622	692	692
23.0	2.938729	592	592
24.0	2.938799	544	544
25.0	2.938845	448	448
26.0	2.938876	479	479
27.0	2.938896	356	356
28.0	2.938909	355	355
29.0	2.938918	339	339
30.0	2.938923	289	289
31.0	2.938927	281	281
32.0	2.93893	277	277
33.0	2.938931	248	248
34.0	2.938933	207	207
35.0	2.938933	188	188
36.0	2.938934	170	170
37.0	2.938934	175	175
38.0	2.938934	132	132
39.0	2.938934	149	149
40.0	2.938934	129	129
41.0	2.938935	133	133
42.0	2.938935	109	109
43.0	2.938935	93	93
44.0	2.938935	116	116
45.0	2.938935	93	93
46.0	2.938935	100	100
47.0	2.938935	87	87
48.0	2.938935	95	95
49.0	2.938935	90	90
50.0	2.938935	70	70
51.0	2.938935	82	82
52.0	2.938935	65	65
53.0	2.938935	71	71
54.0	2.938935	80	80
55.0	2.938935	53	53
56.0	2.938935	67	67
57.0	2.938935	58	58
58.0	2.938935	50	50
59.0	2.938935	63	63
60.0	2.938935	35	35
61.0	2.938935	57	57
62.0	2.938935	53	53
63.0	2.938935	37	37
64.0	2.938935	48	48
65.0	2.938935	47	47
66.0	2.938935	53	53
67.0	2.938935	53	53
68.0	2.938935	31	31
69.0	2.938935	28	28
70.0	2.938935	36	36
71.0	2.938935	28	28
72.0	2.938935	37	37
73.0	2.938935	34	34
74.0	2.938935	30	30
75.0	2.938935	26	26
76.0	2.938935	28	28
77.0	2.938935	27	27
78.0	2.938935	33	33
79.0	2.938935	31	31
80.0	2.938935	24	24
81.0	2.938935	27	27
82.0	2.938935	23	23
83.0	2.938935	25	25
84.0	2.938935	29	29
85.0	2.938935	35	35
86.0	2.938935	14	14
87.0	2.938935	20	20
88.0	2.938935	23	23
89.0	2.938935	23	23
90.0	2.938935	15	15
91.0	2.938935	13	13
92.0	2.938935	14	14
93.0	2.938935	19	19
94.0	2.938935	19	19
95.0	2.938935	14	14
96.0	2.938935	13	13
97.0	2.938935	14	14
98.0	2.938935	15	15
99.0	2.938935	19	19
100.0	2.938935	19	19
101.0	0	12	12
102.0	0	16	16
103.0	0	15	15
104.0	0	9	9
105.0	0	13	13
106.0	0	16	16
107.0	0	9	9
108.0	0	17	17
109.0	0	8	8
110.0	0	10	10
111.0	0	14	14
112.0	0	12	12
113.0	0	9	9
114.0	0	6	6
115.0	0	9	9
116.0	0	7	7
117.0	0	13	13
118.0	0	6	6
119.0	0	7	7
120.0	0	6	6
121.0	0	10	10
122.0	0	11	11
123.0	0	12	12
124.0	0	7	7
125.0	0	8	8
126.0	0	8	8
127.0	0	13	13
128.0	0	8	8
129.0	0	10	10
130.0	0	5	5
131.0	0	7	7
132.0	0	7	7
133.0	0	7	7
134.0	0	3	3
135.0	0	4	4
136.0	0	5	5
137.0	0	7	7
138.0	0	8	8
139.0	0	9	9
140.0	0	5	5
141.0	0	6	6
142.0	0	5	5
143.0	0	8	8
144.0	0	5	5
145.0	0	3	3
146.0	0	8	8
147.0	0	8	8
148.0	0	5	5
149.0	0	4	4
150.0	0	3	3
151.0	0	7	7
152.0	0	6	6
153.0	0	3	3
154.0	0	8	8
155.0	0	8	8
156.0	0	5	5
157.0	0	5	5
158.0	0	3	3
159.0	0	4	4
160.0	0	5	5
161.0	0	6	6
162.0	0	8	8
163.0	0	4	4
164.0	0	9	9
165.0	0	4	4
166.0	0	3	3
167.0	0	2	2
168.0	0	3	3
169.0	0	5	5
170.0	0	6	6
171.0	0	5	5
172.0	0	1	1
173.0	0	5	5
174.0	0	1	1
175.0	0	3	3
176.0	0	2	2
177.0	0	3	3
178.0	0	5	5
179.0	0	2	2
180.0	0	4	4
182.0	0	5	5
183.0	0	4	4
184.0	0	1	1
185.0	0	2	2
186.0	0	5	5
187.0	0	2	2
188.0	0	3	3
189.0	0	3	3
190.0	0	4	4
191.0	0	5	5
193.0	0	3	3
194.0	0	1	1
195.0	0	6	6
196.0	0	5	5
197.0	0	2	2
198.0	0	2	2
199.0	0	3	3
200.0	0	5	5
201.0	0	6	6
202.0	0	5	5
203.0	0	5	5
204.0	0	1	1
205.0	0	3	3
206.0	0	4	4
207.0	0	3	3
208.0	0	6	6
209.0	0	2	2
210.0	0	1	1
211.0	0	4	4
212.0	0	1	1
213.0	0	2	2
215.0	0	4	4
216.0	0	3	3
217.0	0	1	1
218.0	0	5	5
219.0	0	7	7
220.0	0	3	3
221.0	0	3	3
222.0	0	3	3
223.0	0	2	2
224.0	0	1	1
226.0	0	2	2
227.0	0	2	2
228.0	0	2	2
229.0	0	2	2
230.0	0	2	2
232.0	0	3	3
233.0	0	5	5
234.0	0	1	1
235.0	0	3	3
238.0	0	1	1
239.0	0	2	2
241.0	0	3	3
242.0	0	1	1
243.0	0	3	3
244.0	0	1	1
245.0	0	1	1
246.0	0	2	2
247.0	0	2	2
248.0	0	2	2
250.0	0	1	1
251.0	0	1	1
252.0	0	4	4
257.0	0	1	1
258.0	0	1	1
260.0	0	1	1
261.0	0	3	3
262.0	0	1	1
263.0	0	4	4
264.0	0	1	1
269.0	0	1	1
271.0	0	1	1
274.0	0	1	1
275.0	0	2	2
276.0	0	2	2
277.0	0	1	1
278.0	0	1	1
280.0	0	1	1
283.0	0	1	1
284.0	0	3	3
285.0	0	1	1
286.0	0	1	1
289.0	0	1	1
290.0	0	1	1
293.0	0	2	2
294.0	0	2	2
295.0	0	1	1
297.0	0	1	1
300.0	0	2	2
301.0	0	1	1
303.0	0	1	1
304.0	0	2	2
305.0	0	1	1
306.0	0	1	1
309.0	0	1	1
310.0	0	1	1
313.0	0	3	3
314.0	0	2	2
317.0	0	2	2
318.0	0	1	1
319.0	0	1	1
320.0	0	1	1
323.0	0	1	1
326.0	0	1	1
330.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	3	3
339.0	0	2	2
341.0	0	1	1
342.0	0	1	1
343.0	0	1	1
348.0	0	1	1
350.0	0	1	1
351.0	0	2	2
352.0	0	2	2
354.0	0	1	1
355.0	0	1	1
356.0	0	1	1
365.0	0	1	1
369.0	0	1	1
374.0	0	1	1
376.0	0	1	1
379.0	0	2	2
393.0	0	1	1
394.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
404.0	0	1	1
406.0	0	1	1
412.0	0	1	1
413.0	0	1	1
419.0	0	1	1
421.0	0	1	1
423.0	0	1	1
443.0	0	1	1
444.0	0	1	1
446.0	0	1	1
452.0	0	1	1
470.0	0	1	1
477.0	0	1	1
478.0	0	1	1
485.0	0	1	1
498.0	0	2	2
500.0	0	1	1
508.0	0	1	1
511.0	0	3	3
517.0	0	1	1
526.0	0	1	1
537.0	0	1	1
538.0	0	1	1
548.0	0	1	1
564.0	0	1	1
589.0	0	1	1
591.0	0	1	1
603.0	0	1	1
611.0	0	1	1
615.0	0	1	1
619.0	0	1	1
630.0	0	1	1
640.0	0	1	1
687.0	0	1	1
688.0	0	1	1
689.0	0	1	1
697.0	0	1	1
731.0	0	1	1
732.0	0	1	1
747.0	0	1	1
750.0	0	1	1
756.0	0	2	2
767.0	0	1	1
769.0	0	1	1
793.0	0	1	1
843.0	0	1	1
889.0	0	1	1
894.0	0	1	1
950.0	0	1	1
965.0	0	1	1
977.0	0	1	1
982.0	0	1	1
1007.0	0	1	1
1039.0	0	1	1
1041.0	0	1	1
1055.0	0	1	1
1115.0	0	1	1
1171.0	0	1	1
1182.0	0	1	1
1213.0	0	1	1
1237.0	0	1	1
1308.0	0	1	1
1437.0	0	1	1
1505.0	0	1	1
1586.0	0	1	1