## 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_RU1uMTA1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA1uM_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_RU1uMTA1uM_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 03:46:42 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	965	16649961	14873579	0	854	2306460	0	0.138548	54408120

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	13346781	13346781
2.0	1.736372	707865	707865
3.0	2.278616	127510	127510
4.0	2.677909	52839	52839
5.0	2.971937	29075	29075
6.0	3.188452	17978	17978
7.0	3.347887	12218	12218
8.0	3.46529	8617	8617
9.0	3.551743	6455	6455
10.0	3.615404	4833	4833
11.0	3.662283	3873	3873
12.0	3.696803	3128	3128
13.0	3.722222	2487	2487
14.0	3.74094	2133	2133
15.0	3.754724	1805	1805
16.0	3.764874	1519	1519
17.0	3.772348	1222	1222
18.0	3.777851	1101	1101
19.0	3.781904	940	940
20.0	3.784889	846	846
21.0	3.787086	773	773
22.0	3.788704	657	657
23.0	3.789896	580	580
24.0	3.790774	498	498
25.0	3.79142	509	509
26.0	3.791896	441	441
27.0	3.792246	364	364
28.0	3.792504	346	346
29.0	3.792694	324	324
30.0	3.792834	315	315
31.0	3.792937	278	278
32.0	3.793013	241	241
33.0	3.793069	250	250
34.0	3.79311	180	180
35.0	3.79314	184	184
36.0	3.793162	172	172
37.0	3.793179	187	187
38.0	3.793191	162	162
39.0	3.7932	144	144
40.0	3.793206	150	150
41.0	3.793211	123	123
42.0	3.793215	126	126
43.0	3.793217	122	122
44.0	3.793219	96	96
45.0	3.793221	102	102
46.0	3.793222	100	100
47.0	3.793222	89	89
48.0	3.793223	80	80
49.0	3.793223	88	88
50.0	3.793224	74	74
51.0	3.793224	87	87
52.0	3.793224	88	88
53.0	3.793224	61	61
54.0	3.793224	66	66
55.0	3.793224	72	72
56.0	3.793224	55	55
57.0	3.793224	49	49
58.0	3.793224	51	51
59.0	3.793224	59	59
60.0	3.793225	52	52
61.0	3.793225	51	51
62.0	3.793225	50	50
63.0	3.793225	46	46
64.0	3.793225	42	42
65.0	3.793225	37	37
66.0	3.793225	42	42
67.0	3.793225	35	35
68.0	3.793225	39	39
69.0	3.793225	40	40
70.0	3.793225	26	26
71.0	3.793225	28	28
72.0	3.793225	24	24
73.0	3.793225	31	31
74.0	3.793225	25	25
75.0	3.793225	30	30
76.0	3.793225	31	31
77.0	3.793225	30	30
78.0	3.793225	25	25
79.0	3.793225	34	34
80.0	3.793225	36	36
81.0	3.793225	29	29
82.0	3.793225	20	20
83.0	3.793225	22	22
84.0	3.793225	22	22
85.0	3.793225	34	34
86.0	3.793225	18	18
87.0	3.793225	21	21
88.0	3.793225	24	24
89.0	3.793225	19	19
90.0	3.793225	20	20
91.0	3.793225	15	15
92.0	3.793225	15	15
93.0	3.793225	18	18
94.0	3.793225	16	16
95.0	3.793225	19	19
96.0	3.793225	17	17
97.0	3.793225	15	15
98.0	3.793225	15	15
99.0	3.793225	16	16
100.0	3.793225	11	11
101.0	0	12	12
102.0	0	12	12
103.0	0	24	24
104.0	0	14	14
105.0	0	13	13
106.0	0	13	13
107.0	0	7	7
108.0	0	13	13
109.0	0	9	9
110.0	0	6	6
111.0	0	12	12
112.0	0	11	11
113.0	0	9	9
114.0	0	7	7
115.0	0	6	6
116.0	0	5	5
117.0	0	9	9
118.0	0	11	11
119.0	0	6	6
120.0	0	4	4
121.0	0	17	17
122.0	0	7	7
123.0	0	8	8
124.0	0	7	7
125.0	0	11	11
126.0	0	4	4
127.0	0	9	9
128.0	0	6	6
129.0	0	9	9
130.0	0	4	4
131.0	0	4	4
132.0	0	11	11
133.0	0	6	6
134.0	0	11	11
135.0	0	5	5
136.0	0	9	9
137.0	0	8	8
138.0	0	2	2
139.0	0	7	7
140.0	0	8	8
141.0	0	7	7
142.0	0	10	10
143.0	0	5	5
144.0	0	10	10
145.0	0	6	6
146.0	0	6	6
147.0	0	5	5
148.0	0	3	3
149.0	0	6	6
150.0	0	3	3
151.0	0	3	3
152.0	0	4	4
153.0	0	6	6
154.0	0	6	6
155.0	0	2	2
156.0	0	4	4
157.0	0	3	3
158.0	0	6	6
159.0	0	1	1
160.0	0	1	1
161.0	0	9	9
162.0	0	4	4
163.0	0	5	5
164.0	0	5	5
166.0	0	7	7
167.0	0	3	3
168.0	0	3	3
169.0	0	3	3
171.0	0	2	2
172.0	0	2	2
173.0	0	1	1
174.0	0	3	3
175.0	0	4	4
176.0	0	2	2
177.0	0	5	5
178.0	0	5	5
179.0	0	7	7
181.0	0	2	2
182.0	0	3	3
183.0	0	2	2
184.0	0	5	5
185.0	0	6	6
186.0	0	1	1
187.0	0	3	3
188.0	0	3	3
189.0	0	2	2
190.0	0	5	5
191.0	0	3	3
192.0	0	2	2
193.0	0	1	1
194.0	0	2	2
195.0	0	1	1
196.0	0	3	3
197.0	0	2	2
198.0	0	2	2
199.0	0	3	3
200.0	0	3	3
202.0	0	2	2
203.0	0	4	4
204.0	0	2	2
205.0	0	1	1
206.0	0	2	2
208.0	0	2	2
209.0	0	1	1
210.0	0	1	1
211.0	0	2	2
212.0	0	1	1
213.0	0	2	2
214.0	0	2	2
215.0	0	2	2
216.0	0	3	3
217.0	0	4	4
218.0	0	3	3
220.0	0	2	2
221.0	0	1	1
222.0	0	1	1
223.0	0	2	2
224.0	0	2	2
225.0	0	1	1
226.0	0	3	3
228.0	0	2	2
230.0	0	3	3
232.0	0	1	1
233.0	0	1	1
236.0	0	1	1
237.0	0	1	1
239.0	0	2	2
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	4	4
247.0	0	1	1
248.0	0	2	2
250.0	0	2	2
251.0	0	3	3
252.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	2	2
257.0	0	1	1
258.0	0	2	2
260.0	0	3	3
261.0	0	2	2
262.0	0	1	1
265.0	0	1	1
267.0	0	1	1
268.0	0	2	2
269.0	0	2	2
273.0	0	1	1
275.0	0	1	1
278.0	0	1	1
279.0	0	2	2
280.0	0	2	2
281.0	0	3	3
282.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	1	1
287.0	0	1	1
288.0	0	1	1
290.0	0	1	1
292.0	0	2	2
295.0	0	2	2
301.0	0	1	1
303.0	0	2	2
304.0	0	1	1
308.0	0	1	1
310.0	0	2	2
311.0	0	2	2
313.0	0	1	1
318.0	0	3	3
322.0	0	1	1
324.0	0	1	1
325.0	0	1	1
326.0	0	1	1
327.0	0	1	1
329.0	0	2	2
332.0	0	1	1
334.0	0	1	1
336.0	0	2	2
339.0	0	1	1
343.0	0	1	1
345.0	0	1	1
346.0	0	1	1
349.0	0	3	3
353.0	0	1	1
354.0	0	1	1
357.0	0	1	1
358.0	0	1	1
359.0	0	2	2
368.0	0	1	1
375.0	0	2	2
393.0	0	3	3
400.0	0	2	2
402.0	0	1	1
405.0	0	1	1
407.0	0	1	1
415.0	0	1	1
425.0	0	1	1
440.0	0	1	1
445.0	0	1	1
449.0	0	1	1
459.0	0	1	1
463.0	0	1	1
467.0	0	1	1
473.0	0	1	1
484.0	0	1	1
489.0	0	1	1
495.0	0	1	1
504.0	0	1	1
505.0	0	1	1
506.0	0	1	1
507.0	0	2	2
511.0	0	1	1
517.0	0	1	1
525.0	0	2	2
550.0	0	1	1
551.0	0	2	2
574.0	0	1	1
621.0	0	1	1
631.0	0	1	1
640.0	0	1	1
659.0	0	2	2
663.0	0	1	1
666.0	0	1	1
676.0	0	1	1
679.0	0	1	1
684.0	0	1	1
692.0	0	1	1
705.0	0	1	1
714.0	0	1	1
721.0	0	1	1
734.0	0	1	1
741.0	0	1	1
744.0	0	1	1
818.0	0	1	1
854.0	0	1	1
883.0	0	1	1
901.0	0	1	1
983.0	0	1	1
991.0	0	1	1
1084.0	0	1	1
1145.0	0	1	1
1396.0	0	1	1
1719.0	0	1	1
2758.0	0	1	1