## 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-D12_supernatant_RU1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_RU1uM_2.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 03:03:08 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	1100	20247440	18736784	0	998	2819213	0	0.139259	65789421

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	16249669	16249669
2.0	1.735091	818560	818560
3.0	2.275449	155433	155433
4.0	2.672662	67181	67181
5.0	2.964649	36427	36427
6.0	3.179286	23079	23079
7.0	3.337064	15367	15367
8.0	3.453045	11028	11028
9.0	3.538301	8200	8200
10.0	3.600972	6140	6140
11.0	3.647041	4993	4993
12.0	3.680906	3903	3903
13.0	3.7058	3221	3221
14.0	3.724099	2712	2712
15.0	3.737551	2191	2191
16.0	3.747439	1845	1845
17.0	3.754708	1646	1646
18.0	3.760051	1442	1442
19.0	3.763979	1214	1214
20.0	3.766866	1079	1079
21.0	3.768988	928	928
22.0	3.770548	860	860
23.0	3.771695	790	790
24.0	3.772538	680	680
25.0	3.773158	637	637
26.0	3.773613	549	549
27.0	3.773948	500	500
28.0	3.774194	454	454
29.0	3.774375	391	391
30.0	3.774508	376	376
31.0	3.774606	324	324
32.0	3.774678	276	276
33.0	3.774731	311	311
34.0	3.77477	257	257
35.0	3.774798	281	281
36.0	3.774819	224	224
37.0	3.774835	203	203
38.0	3.774846	191	191
39.0	3.774854	165	165
40.0	3.77486	194	194
41.0	3.774865	168	168
42.0	3.774868	145	145
43.0	3.774871	133	133
44.0	3.774872	139	139
45.0	3.774874	146	146
46.0	3.774875	128	128
47.0	3.774875	132	132
48.0	3.774876	94	94
49.0	3.774876	92	92
50.0	3.774877	114	114
51.0	3.774877	85	85
52.0	3.774877	88	88
53.0	3.774877	90	90
54.0	3.774877	75	75
55.0	3.774877	69	69
56.0	3.774877	73	73
57.0	3.774877	71	71
58.0	3.774877	57	57
59.0	3.774877	54	54
60.0	3.774877	74	74
61.0	3.774877	62	62
62.0	3.774877	70	70
63.0	3.774877	55	55
64.0	3.774877	55	55
65.0	3.774877	43	43
66.0	3.774877	47	47
67.0	3.774877	43	43
68.0	3.774877	34	34
69.0	3.774877	36	36
70.0	3.774877	53	53
71.0	3.774877	42	42
72.0	3.774877	35	35
73.0	3.774877	41	41
74.0	3.774877	42	42
75.0	3.774877	30	30
76.0	3.774877	27	27
77.0	3.774877	44	44
78.0	3.774877	39	39
79.0	3.774877	27	27
80.0	3.774877	27	27
81.0	3.774877	34	34
82.0	3.774877	32	32
83.0	3.774877	30	30
84.0	3.774877	27	27
85.0	3.774877	35	35
86.0	3.774877	33	33
87.0	3.774877	25	25
88.0	3.774877	20	20
89.0	3.774877	20	20
90.0	3.774877	21	21
91.0	3.774877	16	16
92.0	3.774877	21	21
93.0	3.774877	24	24
94.0	3.774877	14	14
95.0	3.774877	24	24
96.0	3.774877	17	17
97.0	3.774877	20	20
98.0	3.774877	13	13
99.0	3.774877	16	16
100.0	3.774877	16	16
101.0	0	16	16
102.0	0	19	19
103.0	0	16	16
104.0	0	21	21
105.0	0	19	19
106.0	0	17	17
107.0	0	16	16
108.0	0	21	21
109.0	0	12	12
110.0	0	9	9
111.0	0	12	12
112.0	0	12	12
113.0	0	7	7
114.0	0	11	11
115.0	0	6	6
116.0	0	10	10
117.0	0	13	13
118.0	0	5	5
119.0	0	15	15
120.0	0	9	9
121.0	0	11	11
122.0	0	14	14
123.0	0	7	7
124.0	0	5	5
125.0	0	14	14
126.0	0	9	9
127.0	0	7	7
128.0	0	13	13
129.0	0	7	7
130.0	0	19	19
131.0	0	7	7
132.0	0	11	11
133.0	0	8	8
134.0	0	7	7
135.0	0	11	11
136.0	0	6	6
137.0	0	5	5
138.0	0	4	4
139.0	0	5	5
140.0	0	8	8
141.0	0	7	7
142.0	0	6	6
143.0	0	2	2
144.0	0	9	9
145.0	0	8	8
146.0	0	9	9
147.0	0	5	5
148.0	0	2	2
149.0	0	5	5
150.0	0	4	4
151.0	0	5	5
152.0	0	4	4
153.0	0	3	3
154.0	0	6	6
155.0	0	7	7
156.0	0	10	10
157.0	0	10	10
158.0	0	3	3
159.0	0	2	2
160.0	0	6	6
161.0	0	2	2
162.0	0	7	7
163.0	0	4	4
164.0	0	7	7
165.0	0	5	5
166.0	0	2	2
167.0	0	5	5
168.0	0	6	6
169.0	0	3	3
170.0	0	3	3
171.0	0	8	8
172.0	0	7	7
173.0	0	5	5
174.0	0	5	5
175.0	0	2	2
176.0	0	4	4
177.0	0	3	3
178.0	0	5	5
179.0	0	3	3
180.0	0	3	3
181.0	0	1	1
182.0	0	3	3
183.0	0	4	4
184.0	0	3	3
186.0	0	1	1
187.0	0	4	4
188.0	0	5	5
189.0	0	8	8
190.0	0	2	2
191.0	0	3	3
192.0	0	1	1
193.0	0	6	6
194.0	0	5	5
195.0	0	2	2
196.0	0	3	3
198.0	0	2	2
199.0	0	2	2
200.0	0	2	2
201.0	0	1	1
202.0	0	4	4
204.0	0	1	1
205.0	0	4	4
206.0	0	4	4
207.0	0	9	9
209.0	0	1	1
210.0	0	2	2
211.0	0	2	2
212.0	0	2	2
213.0	0	2	2
214.0	0	3	3
215.0	0	1	1
216.0	0	3	3
217.0	0	2	2
218.0	0	2	2
219.0	0	1	1
220.0	0	1	1
221.0	0	2	2
222.0	0	1	1
223.0	0	1	1
224.0	0	3	3
225.0	0	3	3
226.0	0	3	3
227.0	0	3	3
228.0	0	2	2
230.0	0	4	4
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	3	3
235.0	0	2	2
236.0	0	1	1
238.0	0	2	2
239.0	0	3	3
240.0	0	2	2
241.0	0	1	1
242.0	0	3	3
244.0	0	2	2
246.0	0	2	2
247.0	0	2	2
248.0	0	2	2
250.0	0	2	2
251.0	0	2	2
252.0	0	2	2
254.0	0	1	1
256.0	0	3	3
257.0	0	2	2
260.0	0	1	1
263.0	0	3	3
265.0	0	1	1
266.0	0	2	2
267.0	0	3	3
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	2	2
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
279.0	0	1	1
281.0	0	2	2
283.0	0	1	1
285.0	0	1	1
287.0	0	2	2
291.0	0	1	1
293.0	0	1	1
294.0	0	1	1
295.0	0	1	1
296.0	0	3	3
297.0	0	1	1
301.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
307.0	0	1	1
309.0	0	1	1
311.0	0	2	2
314.0	0	1	1
315.0	0	1	1
319.0	0	1	1
320.0	0	2	2
321.0	0	2	2
324.0	0	1	1
326.0	0	1	1
327.0	0	2	2
329.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
338.0	0	1	1
341.0	0	2	2
343.0	0	2	2
346.0	0	1	1
348.0	0	1	1
353.0	0	2	2
354.0	0	1	1
362.0	0	1	1
367.0	0	1	1
368.0	0	1	1
369.0	0	1	1
370.0	0	1	1
371.0	0	1	1
372.0	0	1	1
374.0	0	1	1
376.0	0	3	3
387.0	0	1	1
388.0	0	1	1
389.0	0	1	1
394.0	0	1	1
398.0	0	1	1
400.0	0	1	1
403.0	0	1	1
419.0	0	1	1
420.0	0	1	1
428.0	0	1	1
433.0	0	1	1
437.0	0	1	1
445.0	0	1	1
469.0	0	1	1
470.0	0	1	1
473.0	0	1	1
476.0	0	1	1
478.0	0	1	1
479.0	0	1	1
482.0	0	1	1
484.0	0	1	1
487.0	0	1	1
490.0	0	1	1
496.0	0	1	1
502.0	0	1	1
512.0	0	1	1
515.0	0	1	1
529.0	0	1	1
541.0	0	1	1
543.0	0	1	1
550.0	0	1	1
556.0	0	1	1
557.0	0	2	2
571.0	0	1	1
581.0	0	1	1
582.0	0	1	1
586.0	0	1	1
590.0	0	1	1
602.0	0	1	1
607.0	0	1	1
628.0	0	1	1
631.0	0	1	1
633.0	0	1	1
666.0	0	1	1
672.0	0	1	1
678.0	0	2	2
684.0	0	1	1
686.0	0	1	1
692.0	0	1	1
697.0	0	1	1
726.0	0	1	1
730.0	0	1	1
757.0	0	1	1
770.0	0	1	1
778.0	0	1	1
783.0	0	1	1
784.0	0	1	1
809.0	0	1	1
820.0	0	1	1
822.0	0	1	1
900.0	0	1	1
924.0	0	1	1
935.0	0	2	2
957.0	0	1	1
1005.0	0	1	1
1114.0	0	1	1
1150.0	0	1	1
1162.0	0	1	1
1174.0	0	1	1
1205.0	0	1	1
1605.0	0	1	1
2490.0	0	1	1