## 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_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uM_1.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_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 03:53:05 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	781	15220624	15236492	0	700	2339464	0	0.153723	44297523

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	11933645	11933645
2.0	1.709213	659509	659509
3.0	2.212195	125263	125263
4.0	2.568917	52868	52868
5.0	2.821908	29053	29053
6.0	3.001333	18049	18049
7.0	3.128583	12137	12137
8.0	3.218831	8783	8783
9.0	3.282835	6356	6356
10.0	3.328228	4879	4879
11.0	3.360422	3881	3881
12.0	3.383253	3174	3174
13.0	3.399446	2566	2566
14.0	3.41093	2071	2071
15.0	3.419075	1805	1805
16.0	3.424851	1520	1520
17.0	3.428948	1337	1337
18.0	3.431853	1145	1145
19.0	3.433913	951	951
20.0	3.435375	885	885
21.0	3.436411	728	728
22.0	3.437146	702	702
23.0	3.437668	618	618
24.0	3.438037	516	516
25.0	3.438299	492	492
26.0	3.438485	470	470
27.0	3.438617	465	465
28.0	3.438711	368	368
29.0	3.438777	348	348
30.0	3.438824	328	328
31.0	3.438858	279	279
32.0	3.438881	295	295
33.0	3.438898	242	242
34.0	3.43891	261	261
35.0	3.438918	200	200
36.0	3.438924	206	206
37.0	3.438929	206	206
38.0	3.438932	174	174
39.0	3.438934	157	157
40.0	3.438935	164	164
41.0	3.438936	170	170
42.0	3.438937	138	138
43.0	3.438938	125	125
44.0	3.438938	131	131
45.0	3.438938	112	112
46.0	3.438938	106	106
47.0	3.438939	115	115
48.0	3.438939	99	99
49.0	3.438939	87	87
50.0	3.438939	76	76
51.0	3.438939	106	106
52.0	3.438939	81	81
53.0	3.438939	74	74
54.0	3.438939	68	68
55.0	3.438939	75	75
56.0	3.438939	61	61
57.0	3.438939	59	59
58.0	3.438939	66	66
59.0	3.438939	52	52
60.0	3.438939	66	66
61.0	3.438939	52	52
62.0	3.438939	51	51
63.0	3.438939	51	51
64.0	3.438939	53	53
65.0	3.438939	49	49
66.0	3.438939	56	56
67.0	3.438939	40	40
68.0	3.438939	37	37
69.0	3.438939	36	36
70.0	3.438939	33	33
71.0	3.438939	29	29
72.0	3.438939	32	32
73.0	3.438939	31	31
74.0	3.438939	46	46
75.0	3.438939	27	27
76.0	3.438939	35	35
77.0	3.438939	32	32
78.0	3.438939	26	26
79.0	3.438939	20	20
80.0	3.438939	31	31
81.0	3.438939	22	22
82.0	3.438939	27	27
83.0	3.438939	35	35
84.0	3.438939	18	18
85.0	3.438939	31	31
86.0	3.438939	19	19
87.0	3.438939	31	31
88.0	3.438939	32	32
89.0	3.438939	19	19
90.0	3.438939	19	19
91.0	3.438939	20	20
92.0	3.438939	18	18
93.0	3.438939	28	28
94.0	3.438939	25	25
95.0	3.438939	18	18
96.0	3.438939	21	21
97.0	3.438939	16	16
98.0	3.438939	13	13
99.0	3.438939	23	23
100.0	3.438939	20	20
101.0	0	17	17
102.0	0	11	11
103.0	0	12	12
104.0	0	13	13
105.0	0	13	13
106.0	0	18	18
107.0	0	11	11
108.0	0	19	19
109.0	0	10	10
110.0	0	17	17
111.0	0	12	12
112.0	0	16	16
113.0	0	13	13
114.0	0	8	8
115.0	0	22	22
116.0	0	8	8
117.0	0	6	6
118.0	0	14	14
119.0	0	5	5
120.0	0	10	10
121.0	0	7	7
122.0	0	6	6
123.0	0	14	14
124.0	0	13	13
125.0	0	12	12
126.0	0	13	13
127.0	0	7	7
128.0	0	5	5
129.0	0	8	8
130.0	0	10	10
131.0	0	6	6
132.0	0	7	7
133.0	0	8	8
134.0	0	12	12
135.0	0	8	8
136.0	0	10	10
137.0	0	9	9
138.0	0	7	7
139.0	0	7	7
140.0	0	3	3
141.0	0	7	7
142.0	0	5	5
143.0	0	8	8
144.0	0	10	10
145.0	0	6	6
146.0	0	6	6
147.0	0	6	6
148.0	0	6	6
149.0	0	6	6
150.0	0	7	7
151.0	0	7	7
152.0	0	5	5
153.0	0	4	4
154.0	0	3	3
155.0	0	5	5
156.0	0	10	10
157.0	0	9	9
158.0	0	3	3
159.0	0	9	9
160.0	0	4	4
161.0	0	7	7
162.0	0	5	5
163.0	0	3	3
164.0	0	5	5
165.0	0	6	6
166.0	0	3	3
167.0	0	5	5
168.0	0	3	3
169.0	0	5	5
170.0	0	2	2
171.0	0	6	6
172.0	0	2	2
173.0	0	5	5
174.0	0	5	5
175.0	0	1	1
176.0	0	6	6
177.0	0	7	7
178.0	0	4	4
180.0	0	2	2
181.0	0	6	6
182.0	0	3	3
183.0	0	6	6
184.0	0	4	4
185.0	0	2	2
186.0	0	1	1
187.0	0	2	2
188.0	0	4	4
189.0	0	1	1
190.0	0	4	4
191.0	0	2	2
193.0	0	1	1
194.0	0	3	3
195.0	0	2	2
197.0	0	2	2
198.0	0	2	2
199.0	0	2	2
200.0	0	3	3
201.0	0	1	1
202.0	0	3	3
203.0	0	5	5
204.0	0	3	3
205.0	0	1	1
206.0	0	1	1
207.0	0	1	1
208.0	0	1	1
209.0	0	3	3
210.0	0	2	2
211.0	0	2	2
212.0	0	3	3
213.0	0	4	4
215.0	0	1	1
217.0	0	2	2
218.0	0	7	7
219.0	0	2	2
220.0	0	2	2
221.0	0	4	4
222.0	0	3	3
223.0	0	1	1
224.0	0	3	3
226.0	0	2	2
227.0	0	7	7
228.0	0	2	2
230.0	0	1	1
231.0	0	4	4
232.0	0	1	1
233.0	0	4	4
235.0	0	6	6
236.0	0	3	3
237.0	0	3	3
238.0	0	2	2
239.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	3	3
244.0	0	2	2
245.0	0	1	1
246.0	0	2	2
247.0	0	3	3
249.0	0	5	5
250.0	0	4	4
251.0	0	1	1
252.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	2	2
258.0	0	5	5
260.0	0	2	2
262.0	0	2	2
263.0	0	2	2
265.0	0	1	1
266.0	0	2	2
267.0	0	1	1
268.0	0	1	1
273.0	0	1	1
274.0	0	1	1
275.0	0	1	1
277.0	0	2	2
278.0	0	2	2
279.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	2	2
284.0	0	2	2
286.0	0	3	3
287.0	0	1	1
288.0	0	1	1
290.0	0	2	2
292.0	0	2	2
295.0	0	2	2
297.0	0	1	1
298.0	0	1	1
299.0	0	2	2
300.0	0	1	1
301.0	0	1	1
303.0	0	2	2
306.0	0	2	2
307.0	0	2	2
308.0	0	1	1
311.0	0	1	1
312.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	2	2
316.0	0	1	1
319.0	0	1	1
320.0	0	1	1
323.0	0	1	1
328.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
337.0	0	1	1
342.0	0	1	1
345.0	0	1	1
346.0	0	1	1
348.0	0	3	3
350.0	0	1	1
351.0	0	1	1
354.0	0	1	1
358.0	0	1	1
360.0	0	3	3
361.0	0	1	1
362.0	0	3	3
368.0	0	1	1
370.0	0	1	1
372.0	0	1	1
376.0	0	1	1
378.0	0	1	1
381.0	0	1	1
385.0	0	1	1
386.0	0	1	1
389.0	0	1	1
393.0	0	2	2
399.0	0	1	1
406.0	0	1	1
417.0	0	1	1
426.0	0	1	1
433.0	0	1	1
442.0	0	2	2
444.0	0	1	1
447.0	0	1	1
451.0	0	1	1
452.0	0	1	1
456.0	0	1	1
466.0	0	1	1
471.0	0	2	2
474.0	0	1	1
475.0	0	1	1
487.0	0	1	1
492.0	0	1	1
500.0	0	1	1
502.0	0	1	1
512.0	0	1	1
513.0	0	1	1
531.0	0	1	1
539.0	0	1	1
548.0	0	1	1
550.0	0	1	1
557.0	0	1	1
561.0	0	1	1
564.0	0	1	1
568.0	0	1	1
571.0	0	1	1
586.0	0	1	1
594.0	0	1	1
615.0	0	1	1
631.0	0	1	1
632.0	0	1	1
664.0	0	1	1
665.0	0	1	1
675.0	0	1	1
687.0	0	1	1
692.0	0	1	1
695.0	0	1	1
718.0	0	2	2
745.0	0	1	1
763.0	0	1	1
778.0	0	1	1
796.0	0	1	1
803.0	0	1	1
816.0	0	1	1
824.0	0	1	1
846.0	0	1	1
860.0	0	1	1
869.0	0	1	1
882.0	0	1	1
898.0	0	1	1
899.0	0	1	1
901.0	0	1	1
904.0	0	1	1
940.0	0	1	1
967.0	0	1	1
1022.0	0	1	1
1068.0	0	1	1
1086.0	0	1	1
1090.0	0	1	1
1207.0	0	1	1
1213.0	0	1	1
1243.0	0	1	1
1464.0	0	1	1
1484.0	0	1	1
1666.0	0	1	1
2645.0	0	1	1
2749.0	0	1	1