## 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_TA100nM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA100nM_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_TA100nM_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 03:36:16 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	1098	17867463	18453273	0	993	2737819	0	0.153252	52181235

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14012745	14012745
2.0	1.710056	785474	785474
3.0	2.214235	144653	144653
4.0	2.572231	60672	60672
5.0	2.826427	33065	33065
6.0	3.006921	20391	20391
7.0	3.135082	14072	14072
8.0	3.226083	9929	9929
9.0	3.290699	7441	7441
10.0	3.33658	5638	5638
11.0	3.369158	4455	4455
12.0	3.392291	3531	3531
13.0	3.408716	3012	3012
14.0	3.420379	2406	2406
15.0	3.42866	2070	2070
16.0	3.43454	1791	1791
17.0	3.438715	1530	1530
18.0	3.44168	1318	1318
19.0	3.443785	1157	1157
20.0	3.44528	1085	1085
21.0	3.446341	947	947
22.0	3.447095	774	774
23.0	3.44763	747	747
24.0	3.44801	658	658
25.0	3.448279	617	617
26.0	3.448471	566	566
27.0	3.448607	457	457
28.0	3.448704	444	444
29.0	3.448772	420	420
30.0	3.448821	389	389
31.0	3.448855	343	343
32.0	3.44888	327	327
33.0	3.448897	296	296
34.0	3.44891	228	228
35.0	3.448919	250	250
36.0	3.448925	229	229
37.0	3.448929	209	209
38.0	3.448932	218	218
39.0	3.448935	211	211
40.0	3.448936	187	187
41.0	3.448937	188	188
42.0	3.448938	153	153
43.0	3.448939	139	139
44.0	3.448939	110	110
45.0	3.448939	142	142
46.0	3.44894	106	106
47.0	3.44894	118	118
48.0	3.44894	113	113
49.0	3.44894	115	115
50.0	3.44894	100	100
51.0	3.44894	99	99
52.0	3.44894	80	80
53.0	3.44894	98	98
54.0	3.44894	76	76
55.0	3.44894	76	76
56.0	3.44894	82	82
57.0	3.44894	69	69
58.0	3.44894	81	81
59.0	3.44894	76	76
60.0	3.44894	80	80
61.0	3.44894	64	64
62.0	3.44894	53	53
63.0	3.44894	63	63
64.0	3.44894	61	61
65.0	3.44894	62	62
66.0	3.44894	46	46
67.0	3.44894	49	49
68.0	3.44894	33	33
69.0	3.44894	48	48
70.0	3.44894	47	47
71.0	3.44894	41	41
72.0	3.44894	41	41
73.0	3.44894	41	41
74.0	3.44894	42	42
75.0	3.44894	43	43
76.0	3.44894	40	40
77.0	3.44894	35	35
78.0	3.44894	37	37
79.0	3.44894	43	43
80.0	3.44894	39	39
81.0	3.44894	35	35
82.0	3.44894	27	27
83.0	3.44894	27	27
84.0	3.44894	30	30
85.0	3.44894	25	25
86.0	3.44894	41	41
87.0	3.44894	32	32
88.0	3.44894	29	29
89.0	3.44894	25	25
90.0	3.44894	26	26
91.0	3.44894	17	17
92.0	3.44894	20	20
93.0	3.44894	22	22
94.0	3.44894	23	23
95.0	3.44894	26	26
96.0	3.44894	26	26
97.0	3.44894	24	24
98.0	3.44894	22	22
99.0	3.44894	12	12
100.0	3.44894	16	16
101.0	0	12	12
102.0	0	14	14
103.0	0	23	23
104.0	0	19	19
105.0	0	15	15
106.0	0	14	14
107.0	0	14	14
108.0	0	19	19
109.0	0	12	12
110.0	0	8	8
111.0	0	12	12
112.0	0	12	12
113.0	0	13	13
114.0	0	16	16
115.0	0	10	10
116.0	0	18	18
117.0	0	14	14
118.0	0	15	15
119.0	0	14	14
120.0	0	15	15
121.0	0	9	9
122.0	0	16	16
123.0	0	12	12
124.0	0	15	15
125.0	0	8	8
126.0	0	14	14
127.0	0	11	11
128.0	0	14	14
129.0	0	15	15
130.0	0	9	9
131.0	0	10	10
132.0	0	7	7
133.0	0	8	8
134.0	0	8	8
135.0	0	9	9
136.0	0	7	7
137.0	0	2	2
138.0	0	9	9
139.0	0	9	9
140.0	0	8	8
141.0	0	6	6
142.0	0	6	6
143.0	0	8	8
144.0	0	11	11
145.0	0	6	6
146.0	0	7	7
147.0	0	10	10
148.0	0	7	7
149.0	0	7	7
150.0	0	9	9
151.0	0	7	7
152.0	0	6	6
153.0	0	6	6
154.0	0	9	9
155.0	0	7	7
156.0	0	6	6
157.0	0	7	7
158.0	0	8	8
159.0	0	5	5
160.0	0	3	3
161.0	0	7	7
162.0	0	11	11
163.0	0	4	4
164.0	0	4	4
165.0	0	2	2
166.0	0	7	7
167.0	0	5	5
168.0	0	10	10
169.0	0	4	4
170.0	0	7	7
171.0	0	7	7
172.0	0	4	4
173.0	0	2	2
174.0	0	4	4
175.0	0	6	6
176.0	0	7	7
177.0	0	5	5
178.0	0	2	2
179.0	0	4	4
180.0	0	7	7
181.0	0	7	7
182.0	0	7	7
183.0	0	3	3
184.0	0	5	5
185.0	0	1	1
186.0	0	1	1
187.0	0	1	1
188.0	0	3	3
189.0	0	5	5
190.0	0	6	6
191.0	0	7	7
192.0	0	7	7
193.0	0	2	2
194.0	0	5	5
195.0	0	2	2
196.0	0	4	4
198.0	0	2	2
199.0	0	4	4
200.0	0	7	7
201.0	0	4	4
202.0	0	2	2
203.0	0	3	3
204.0	0	3	3
205.0	0	5	5
206.0	0	3	3
207.0	0	1	1
208.0	0	5	5
209.0	0	2	2
210.0	0	4	4
212.0	0	3	3
214.0	0	5	5
215.0	0	2	2
216.0	0	2	2
217.0	0	1	1
218.0	0	3	3
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	3	3
223.0	0	1	1
224.0	0	6	6
227.0	0	3	3
228.0	0	3	3
230.0	0	2	2
231.0	0	4	4
232.0	0	1	1
233.0	0	1	1
234.0	0	2	2
235.0	0	1	1
237.0	0	3	3
239.0	0	1	1
240.0	0	2	2
241.0	0	1	1
242.0	0	4	4
243.0	0	3	3
244.0	0	2	2
245.0	0	2	2
246.0	0	3	3
247.0	0	3	3
249.0	0	2	2
250.0	0	1	1
251.0	0	1	1
252.0	0	3	3
253.0	0	1	1
254.0	0	1	1
256.0	0	1	1
257.0	0	1	1
260.0	0	2	2
261.0	0	1	1
263.0	0	2	2
264.0	0	5	5
266.0	0	1	1
267.0	0	2	2
268.0	0	3	3
269.0	0	2	2
273.0	0	1	1
274.0	0	1	1
275.0	0	1	1
276.0	0	2	2
277.0	0	3	3
278.0	0	3	3
279.0	0	1	1
281.0	0	4	4
283.0	0	1	1
284.0	0	2	2
285.0	0	4	4
286.0	0	1	1
289.0	0	1	1
290.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	3	3
295.0	0	1	1
297.0	0	1	1
299.0	0	2	2
301.0	0	1	1
303.0	0	1	1
304.0	0	2	2
308.0	0	1	1
309.0	0	2	2
310.0	0	3	3
311.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	3	3
317.0	0	1	1
318.0	0	2	2
320.0	0	1	1
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
324.0	0	1	1
327.0	0	3	3
328.0	0	2	2
329.0	0	1	1
330.0	0	3	3
331.0	0	2	2
332.0	0	1	1
336.0	0	1	1
337.0	0	1	1
342.0	0	2	2
343.0	0	1	1
344.0	0	1	1
345.0	0	1	1
346.0	0	2	2
350.0	0	1	1
351.0	0	2	2
352.0	0	1	1
355.0	0	2	2
357.0	0	1	1
358.0	0	2	2
360.0	0	1	1
361.0	0	3	3
362.0	0	1	1
363.0	0	2	2
364.0	0	1	1
366.0	0	2	2
370.0	0	1	1
373.0	0	1	1
379.0	0	1	1
387.0	0	2	2
388.0	0	2	2
390.0	0	1	1
391.0	0	2	2
392.0	0	1	1
393.0	0	1	1
395.0	0	1	1
400.0	0	1	1
403.0	0	1	1
404.0	0	2	2
408.0	0	1	1
410.0	0	1	1
412.0	0	1	1
413.0	0	1	1
417.0	0	2	2
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	1	1
423.0	0	1	1
424.0	0	1	1
428.0	0	1	1
434.0	0	1	1
436.0	0	1	1
451.0	0	1	1
453.0	0	1	1
460.0	0	1	1
476.0	0	1	1
477.0	0	1	1
485.0	0	1	1
491.0	0	1	1
492.0	0	2	2
493.0	0	1	1
504.0	0	1	1
510.0	0	1	1
512.0	0	1	1
527.0	0	1	1
529.0	0	1	1
536.0	0	2	2
537.0	0	1	1
538.0	0	1	1
541.0	0	2	2
542.0	0	1	1
552.0	0	1	1
556.0	0	1	1
560.0	0	1	1
570.0	0	1	1
579.0	0	1	1
580.0	0	1	1
582.0	0	1	1
583.0	0	1	1
598.0	0	1	1
603.0	0	1	1
626.0	0	1	1
629.0	0	1	1
632.0	0	1	1
634.0	0	1	1
636.0	0	2	2
642.0	0	1	1
666.0	0	1	1
672.0	0	1	1
697.0	0	1	1
701.0	0	1	1
710.0	0	1	1
724.0	0	1	1
734.0	0	1	1
737.0	0	1	1
739.0	0	1	1
744.0	0	2	2
746.0	0	1	1
751.0	0	1	1
809.0	0	1	1
834.0	0	1	1
864.0	0	1	1
866.0	0	1	1
924.0	0	1	1
935.0	0	1	1
955.0	0	1	1
977.0	0	1	1
1003.0	0	1	1
1097.0	0	1	1
1116.0	0	1	1
1169.0	0	1	1
1177.0	0	2	2
1186.0	0	1	1
1190.0	0	1	1
1200.0	0	1	1
1297.0	0	1	1
1382.0	0	1	1
1539.0	0	1	1
1601.0	0	1	1
1651.0	0	1	1
1754.0	0	1	1
2000.0	0	1	1
2513.0	0	1	1
3296.0	0	1	1