## 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_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA100nM_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_TA100nM_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 03:51:40 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	566	15560700	16687261	0	501	2377596	0	0.152808	45589222

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	12297082	12297082
2.0	1.710828	579889	579889
3.0	2.216106	127969	127969
4.0	2.575271	56705	56705
5.0	2.830576	31607	31607
6.0	3.012054	19958	19958
7.0	3.141054	13544	13544
8.0	3.232751	9472	9472
9.0	3.297931	7280	7280
10.0	3.344263	5505	5505
11.0	3.377198	4356	4356
12.0	3.400608	3508	3508
13.0	3.417249	2788	2788
14.0	3.429078	2348	2348
15.0	3.437486	2077	2077
16.0	3.443463	1686	1686
17.0	3.447712	1376	1376
18.0	3.450732	1250	1250
19.0	3.452879	1123	1123
20.0	3.454404	1047	1047
21.0	3.455489	887	887
22.0	3.45626	780	780
23.0	3.456808	712	712
24.0	3.457198	624	624
25.0	3.457475	583	583
26.0	3.457672	534	534
27.0	3.457811	470	470
28.0	3.457911	427	427
29.0	3.457982	404	404
30.0	3.458032	375	375
31.0	3.458068	300	300
32.0	3.458093	297	297
33.0	3.458111	270	270
34.0	3.458124	246	246
35.0	3.458133	259	259
36.0	3.458139	237	237
37.0	3.458144	234	234
38.0	3.458147	193	193
39.0	3.45815	173	173
40.0	3.458151	171	171
41.0	3.458152	169	169
42.0	3.458153	153	153
43.0	3.458154	156	156
44.0	3.458154	143	143
45.0	3.458155	136	136
46.0	3.458155	104	104
47.0	3.458155	120	120
48.0	3.458155	110	110
49.0	3.458155	95	95
50.0	3.458155	95	95
51.0	3.458155	102	102
52.0	3.458155	79	79
53.0	3.458155	82	82
54.0	3.458155	70	70
55.0	3.458155	65	65
56.0	3.458155	81	81
57.0	3.458155	63	63
58.0	3.458155	77	77
59.0	3.458155	63	63
60.0	3.458155	62	62
61.0	3.458155	62	62
62.0	3.458155	61	61
63.0	3.458155	43	43
64.0	3.458155	40	40
65.0	3.458155	54	54
66.0	3.458155	58	58
67.0	3.458155	50	50
68.0	3.458155	48	48
69.0	3.458155	48	48
70.0	3.458155	35	35
71.0	3.458155	40	40
72.0	3.458155	41	41
73.0	3.458155	39	39
74.0	3.458155	41	41
75.0	3.458155	44	44
76.0	3.458155	28	28
77.0	3.458155	28	28
78.0	3.458155	29	29
79.0	3.458155	33	33
80.0	3.458155	30	30
81.0	3.458155	29	29
82.0	3.458155	24	24
83.0	3.458155	35	35
84.0	3.458155	19	19
85.0	3.458155	28	28
86.0	3.458155	22	22
87.0	3.458155	33	33
88.0	3.458155	25	25
89.0	3.458155	24	24
90.0	3.458155	24	24
91.0	3.458155	28	28
92.0	3.458155	20	20
93.0	3.458155	26	26
94.0	3.458155	26	26
95.0	3.458155	23	23
96.0	3.458155	19	19
97.0	3.458155	16	16
98.0	3.458155	17	17
99.0	3.458155	23	23
100.0	3.458155	24	24
101.0	0	16	16
102.0	0	21	21
103.0	0	20	20
104.0	0	13	13
105.0	0	16	16
106.0	0	17	17
107.0	0	12	12
108.0	0	16	16
109.0	0	13	13
110.0	0	18	18
111.0	0	17	17
112.0	0	16	16
113.0	0	13	13
114.0	0	17	17
115.0	0	14	14
116.0	0	6	6
117.0	0	12	12
118.0	0	12	12
119.0	0	6	6
120.0	0	10	10
121.0	0	8	8
122.0	0	15	15
123.0	0	12	12
124.0	0	8	8
125.0	0	12	12
126.0	0	12	12
127.0	0	6	6
128.0	0	7	7
129.0	0	7	7
130.0	0	5	5
131.0	0	9	9
132.0	0	5	5
133.0	0	10	10
134.0	0	10	10
135.0	0	15	15
136.0	0	8	8
137.0	0	8	8
138.0	0	8	8
139.0	0	6	6
140.0	0	7	7
141.0	0	4	4
142.0	0	11	11
143.0	0	9	9
144.0	0	8	8
145.0	0	9	9
146.0	0	5	5
147.0	0	4	4
148.0	0	5	5
149.0	0	4	4
150.0	0	3	3
151.0	0	6	6
152.0	0	6	6
153.0	0	6	6
154.0	0	6	6
155.0	0	6	6
156.0	0	5	5
157.0	0	5	5
158.0	0	7	7
159.0	0	6	6
160.0	0	4	4
161.0	0	5	5
162.0	0	2	2
163.0	0	5	5
164.0	0	6	6
165.0	0	1	1
166.0	0	3	3
167.0	0	6	6
168.0	0	5	5
169.0	0	2	2
170.0	0	3	3
171.0	0	4	4
172.0	0	4	4
173.0	0	4	4
174.0	0	6	6
175.0	0	2	2
176.0	0	6	6
177.0	0	1	1
178.0	0	5	5
179.0	0	1	1
180.0	0	4	4
181.0	0	7	7
182.0	0	2	2
183.0	0	6	6
184.0	0	6	6
185.0	0	2	2
186.0	0	3	3
187.0	0	5	5
188.0	0	6	6
189.0	0	1	1
190.0	0	2	2
191.0	0	5	5
192.0	0	5	5
193.0	0	7	7
194.0	0	1	1
195.0	0	3	3
196.0	0	7	7
197.0	0	3	3
198.0	0	4	4
199.0	0	4	4
200.0	0	3	3
201.0	0	2	2
203.0	0	2	2
204.0	0	4	4
205.0	0	4	4
206.0	0	2	2
207.0	0	1	1
208.0	0	3	3
209.0	0	1	1
210.0	0	2	2
211.0	0	2	2
212.0	0	4	4
213.0	0	4	4
214.0	0	2	2
215.0	0	1	1
217.0	0	3	3
218.0	0	3	3
219.0	0	1	1
220.0	0	4	4
221.0	0	2	2
222.0	0	5	5
223.0	0	3	3
224.0	0	1	1
225.0	0	3	3
226.0	0	1	1
227.0	0	2	2
228.0	0	1	1
229.0	0	2	2
232.0	0	1	1
233.0	0	1	1
235.0	0	3	3
237.0	0	3	3
240.0	0	3	3
241.0	0	3	3
242.0	0	3	3
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
246.0	0	3	3
247.0	0	1	1
248.0	0	1	1
249.0	0	2	2
250.0	0	1	1
252.0	0	2	2
253.0	0	2	2
255.0	0	2	2
256.0	0	2	2
257.0	0	1	1
258.0	0	1	1
259.0	0	2	2
260.0	0	1	1
261.0	0	1	1
263.0	0	1	1
265.0	0	1	1
267.0	0	1	1
270.0	0	1	1
271.0	0	2	2
272.0	0	2	2
273.0	0	2	2
276.0	0	1	1
277.0	0	1	1
278.0	0	1	1
280.0	0	1	1
281.0	0	2	2
284.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	1	1
290.0	0	1	1
292.0	0	1	1
296.0	0	1	1
298.0	0	2	2
299.0	0	1	1
302.0	0	1	1
309.0	0	1	1
310.0	0	2	2
314.0	0	2	2
316.0	0	3	3
317.0	0	2	2
320.0	0	1	1
325.0	0	1	1
328.0	0	2	2
330.0	0	1	1
331.0	0	2	2
332.0	0	1	1
333.0	0	1	1
335.0	0	1	1
336.0	0	1	1
337.0	0	1	1
338.0	0	1	1
340.0	0	3	3
341.0	0	3	3
343.0	0	1	1
344.0	0	2	2
346.0	0	1	1
349.0	0	1	1
350.0	0	1	1
356.0	0	2	2
358.0	0	1	1
359.0	0	1	1
362.0	0	1	1
366.0	0	1	1
371.0	0	1	1
372.0	0	1	1
373.0	0	2	2
377.0	0	1	1
380.0	0	1	1
383.0	0	1	1
384.0	0	1	1
386.0	0	1	1
388.0	0	1	1
391.0	0	1	1
392.0	0	1	1
396.0	0	1	1
397.0	0	1	1
405.0	0	1	1
406.0	0	1	1
411.0	0	1	1
416.0	0	1	1
417.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	1	1
426.0	0	1	1
427.0	0	1	1
431.0	0	1	1
433.0	0	1	1
435.0	0	1	1
439.0	0	1	1
440.0	0	1	1
442.0	0	2	2
446.0	0	1	1
450.0	0	1	1
452.0	0	1	1
453.0	0	2	2
458.0	0	1	1
462.0	0	1	1
465.0	0	1	1
475.0	0	1	1
477.0	0	1	1
482.0	0	1	1
486.0	0	1	1
487.0	0	1	1
495.0	0	1	1
501.0	0	1	1
504.0	0	1	1
508.0	0	1	1
513.0	0	1	1
518.0	0	1	1
531.0	0	2	2
533.0	0	1	1
534.0	0	1	1
542.0	0	1	1
550.0	0	1	1
554.0	0	1	1
584.0	0	1	1
585.0	0	1	1
586.0	0	1	1
589.0	0	1	1
604.0	0	1	1
605.0	0	1	1
606.0	0	1	1
610.0	0	1	1
614.0	0	1	1
650.0	0	1	1
652.0	0	1	1
661.0	0	1	1
675.0	0	1	1
677.0	0	1	1
678.0	0	1	1
679.0	0	1	1
724.0	0	1	1
796.0	0	1	1
799.0	0	1	1
802.0	0	1	1
839.0	0	1	1
935.0	0	1	1
991.0	0	1	1
1391.0	0	1	1
2061.0	0	1	1