## 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-D1_adherent_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D1_adherent_TA_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D1_adherent_TA_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 02:21:13 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	1079	23192150	29564874	0	925	4032470	0	0.173888	58714813

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	16947628	16947628
2.0	1.673682	1739453	1739453
3.0	2.12753	250092	250092
4.0	2.43328	77469	77469
5.0	2.639257	39273	39273
6.0	2.778021	23920	23920
7.0	2.871504	16180	16180
8.0	2.934481	11429	11429
9.0	2.976908	8652	8652
10.0	3.005491	6486	6486
11.0	3.024746	5063	5063
12.0	3.037718	4170	4170
13.0	3.046457	3423	3423
14.0	3.052344	2785	2785
15.0	3.05631	2385	2385
16.0	3.058982	1968	1968
17.0	3.060782	1734	1734
18.0	3.061995	1416	1416
19.0	3.062812	1293	1293
20.0	3.063362	1200	1200
21.0	3.063733	977	977
22.0	3.063983	929	929
23.0	3.064151	834	834
24.0	3.064265	732	732
25.0	3.064341	630	630
26.0	3.064392	576	576
27.0	3.064427	546	546
28.0	3.06445	495	495
29.0	3.064466	419	419
30.0	3.064477	424	424
31.0	3.064484	380	380
32.0	3.064489	359	359
33.0	3.064492	314	314
34.0	3.064494	267	267
35.0	3.064496	278	278
36.0	3.064497	250	250
37.0	3.064497	229	229
38.0	3.064498	215	215
39.0	3.064498	217	217
40.0	3.064498	202	202
41.0	3.064498	193	193
42.0	3.064498	183	183
43.0	3.064498	156	156
44.0	3.064499	141	141
45.0	3.064499	145	145
46.0	3.064499	122	122
47.0	3.064499	129	129
48.0	3.064499	128	128
49.0	3.064499	106	106
50.0	3.064499	88	88
51.0	3.064499	90	90
52.0	3.064499	98	98
53.0	3.064499	86	86
54.0	3.064499	89	89
55.0	3.064499	90	90
56.0	3.064499	73	73
57.0	3.064499	76	76
58.0	3.064499	75	75
59.0	3.064499	62	62
60.0	3.064499	65	65
61.0	3.064499	51	51
62.0	3.064499	53	53
63.0	3.064499	41	41
64.0	3.064499	55	55
65.0	3.064499	61	61
66.0	3.064499	35	35
67.0	3.064499	41	41
68.0	3.064499	42	42
69.0	3.064499	35	35
70.0	3.064499	37	37
71.0	3.064499	38	38
72.0	3.064499	32	32
73.0	3.064499	27	27
74.0	3.064499	33	33
75.0	3.064499	33	33
76.0	3.064499	42	42
77.0	3.064499	38	38
78.0	3.064499	32	32
79.0	3.064499	30	30
80.0	3.064499	34	34
81.0	3.064499	22	22
82.0	3.064499	24	24
83.0	3.064499	27	27
84.0	3.064499	24	24
85.0	3.064499	25	25
86.0	3.064499	15	15
87.0	3.064499	15	15
88.0	3.064499	28	28
89.0	3.064499	16	16
90.0	3.064499	20	20
91.0	3.064499	20	20
92.0	3.064499	15	15
93.0	3.064499	27	27
94.0	3.064499	14	14
95.0	3.064499	20	20
96.0	3.064499	30	30
97.0	3.064499	20	20
98.0	3.064499	19	19
99.0	3.064499	12	12
100.0	3.064499	24	24
101.0	0	13	13
102.0	0	24	24
103.0	0	22	22
104.0	0	18	18
105.0	0	16	16
106.0	0	18	18
107.0	0	15	15
108.0	0	14	14
109.0	0	13	13
110.0	0	15	15
111.0	0	12	12
112.0	0	9	9
113.0	0	18	18
114.0	0	11	11
115.0	0	10	10
116.0	0	8	8
117.0	0	10	10
118.0	0	3	3
119.0	0	7	7
120.0	0	11	11
121.0	0	8	8
122.0	0	14	14
123.0	0	13	13
124.0	0	10	10
125.0	0	10	10
126.0	0	9	9
127.0	0	10	10
128.0	0	5	5
129.0	0	13	13
130.0	0	8	8
131.0	0	7	7
132.0	0	12	12
133.0	0	5	5
134.0	0	5	5
135.0	0	9	9
136.0	0	9	9
137.0	0	6	6
138.0	0	7	7
139.0	0	6	6
140.0	0	7	7
141.0	0	4	4
142.0	0	6	6
143.0	0	2	2
144.0	0	4	4
145.0	0	8	8
146.0	0	10	10
147.0	0	3	3
148.0	0	11	11
149.0	0	8	8
150.0	0	6	6
151.0	0	3	3
152.0	0	10	10
153.0	0	5	5
154.0	0	3	3
155.0	0	2	2
156.0	0	3	3
157.0	0	7	7
158.0	0	1	1
159.0	0	4	4
160.0	0	4	4
161.0	0	6	6
162.0	0	5	5
163.0	0	2	2
164.0	0	5	5
165.0	0	7	7
166.0	0	7	7
167.0	0	2	2
168.0	0	3	3
169.0	0	4	4
170.0	0	5	5
171.0	0	5	5
172.0	0	3	3
173.0	0	4	4
174.0	0	2	2
175.0	0	4	4
176.0	0	6	6
177.0	0	6	6
178.0	0	1	1
179.0	0	7	7
181.0	0	7	7
183.0	0	4	4
184.0	0	2	2
185.0	0	2	2
186.0	0	7	7
187.0	0	3	3
188.0	0	3	3
189.0	0	5	5
190.0	0	4	4
191.0	0	2	2
192.0	0	4	4
193.0	0	6	6
194.0	0	5	5
195.0	0	5	5
196.0	0	1	1
197.0	0	3	3
198.0	0	3	3
199.0	0	2	2
200.0	0	3	3
201.0	0	2	2
202.0	0	4	4
203.0	0	2	2
204.0	0	4	4
205.0	0	2	2
206.0	0	3	3
208.0	0	3	3
209.0	0	1	1
210.0	0	4	4
211.0	0	4	4
212.0	0	3	3
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
217.0	0	2	2
219.0	0	1	1
220.0	0	1	1
223.0	0	2	2
224.0	0	2	2
225.0	0	4	4
226.0	0	3	3
227.0	0	1	1
228.0	0	1	1
229.0	0	2	2
230.0	0	1	1
231.0	0	3	3
233.0	0	4	4
234.0	0	1	1
235.0	0	2	2
236.0	0	1	1
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
240.0	0	1	1
241.0	0	2	2
242.0	0	1	1
243.0	0	1	1
244.0	0	1	1
245.0	0	5	5
246.0	0	4	4
247.0	0	1	1
248.0	0	1	1
249.0	0	3	3
250.0	0	3	3
251.0	0	4	4
252.0	0	2	2
254.0	0	4	4
255.0	0	5	5
256.0	0	3	3
258.0	0	2	2
259.0	0	2	2
261.0	0	2	2
262.0	0	3	3
263.0	0	2	2
264.0	0	3	3
265.0	0	3	3
267.0	0	1	1
269.0	0	1	1
270.0	0	2	2
271.0	0	3	3
272.0	0	1	1
273.0	0	1	1
275.0	0	1	1
277.0	0	1	1
278.0	0	1	1
279.0	0	2	2
280.0	0	2	2
281.0	0	1	1
283.0	0	1	1
284.0	0	2	2
285.0	0	3	3
286.0	0	1	1
287.0	0	1	1
291.0	0	1	1
292.0	0	2	2
293.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
306.0	0	1	1
307.0	0	1	1
308.0	0	1	1
309.0	0	1	1
315.0	0	1	1
319.0	0	1	1
320.0	0	1	1
324.0	0	1	1
327.0	0	2	2
332.0	0	1	1
338.0	0	2	2
340.0	0	2	2
349.0	0	1	1
351.0	0	1	1
355.0	0	1	1
362.0	0	2	2
365.0	0	1	1
366.0	0	1	1
369.0	0	1	1
372.0	0	1	1
374.0	0	1	1
376.0	0	1	1
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
382.0	0	1	1
384.0	0	1	1
386.0	0	1	1
388.0	0	1	1
389.0	0	1	1
393.0	0	2	2
399.0	0	3	3
401.0	0	1	1
404.0	0	1	1
405.0	0	1	1
408.0	0	2	2
409.0	0	1	1
411.0	0	2	2
413.0	0	1	1
420.0	0	1	1
421.0	0	1	1
426.0	0	1	1
430.0	0	1	1
432.0	0	1	1
435.0	0	1	1
437.0	0	1	1
438.0	0	1	1
439.0	0	1	1
441.0	0	1	1
443.0	0	1	1
448.0	0	1	1
461.0	0	1	1
464.0	0	2	2
469.0	0	2	2
471.0	0	1	1
483.0	0	2	2
491.0	0	1	1
502.0	0	1	1
503.0	0	1	1
504.0	0	2	2
521.0	0	1	1
534.0	0	3	3
538.0	0	1	1
542.0	0	2	2
547.0	0	1	1
553.0	0	1	1
558.0	0	1	1
576.0	0	1	1
577.0	0	1	1
588.0	0	2	2
589.0	0	1	1
604.0	0	1	1
610.0	0	1	1
616.0	0	1	1
633.0	0	1	1
634.0	0	1	1
653.0	0	1	1
659.0	0	1	1
663.0	0	1	1
664.0	0	1	1
676.0	0	1	1
682.0	0	1	1
688.0	0	1	1
690.0	0	1	1
694.0	0	1	1
710.0	0	1	1
714.0	0	1	1
724.0	0	1	1
726.0	0	1	1
754.0	0	1	1
796.0	0	1	1
802.0	0	1	1
804.0	0	1	1
818.0	0	1	1
853.0	0	1	1
854.0	0	1	1
874.0	0	1	1
938.0	0	1	1
984.0	0	1	1
991.0	0	2	2
1003.0	0	1	1
1004.0	0	1	1
1008.0	0	1	1
1045.0	0	1	1
1116.0	0	1	1
1247.0	0	1	1
1777.0	0	1	1