## 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_adherent_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_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-D12_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 03:07:59 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	526	20362445	12359195	0	426	3450051	0	0.16944	53091585

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	14667030	14667030
2.0	1.681449	1789544	1789544
3.0	2.145821	285304	285304
4.0	2.462267	73312	73312
5.0	2.677909	30917	30917
6.0	2.824857	17595	17595
7.0	2.924995	11047	11047
8.0	2.993234	7529	7529
9.0	3.039736	5496	5496
10.0	3.071424	4083	4083
11.0	3.093018	3207	3207
12.0	3.107733	2395	2395
13.0	3.11776	1954	1954
14.0	3.124594	1553	1553
15.0	3.12925	1307	1307
16.0	3.132424	1077	1077
17.0	3.134586	841	841
18.0	3.136059	750	750
19.0	3.137064	663	663
20.0	3.137748	566	566
21.0	3.138214	509	509
22.0	3.138532	456	456
23.0	3.138748	403	403
24.0	3.138896	366	366
25.0	3.138997	305	305
26.0	3.139065	251	251
27.0	3.139112	236	236
28.0	3.139144	238	238
29.0	3.139165	199	199
30.0	3.13918	174	174
31.0	3.13919	185	185
32.0	3.139197	148	148
33.0	3.139202	131	131
34.0	3.139205	127	127
35.0	3.139207	125	125
36.0	3.139209	108	108
37.0	3.13921	117	117
38.0	3.13921	96	96
39.0	3.139211	102	102
40.0	3.139211	61	61
41.0	3.139211	71	71
42.0	3.139211	65	65
43.0	3.139211	63	63
44.0	3.139212	69	69
45.0	3.139212	52	52
46.0	3.139212	65	65
47.0	3.139212	61	61
48.0	3.139212	47	47
49.0	3.139212	56	56
50.0	3.139212	45	45
51.0	3.139212	41	41
52.0	3.139212	48	48
53.0	3.139212	27	27
54.0	3.139212	41	41
55.0	3.139212	31	31
56.0	3.139212	37	37
57.0	3.139212	45	45
58.0	3.139212	28	28
59.0	3.139212	34	34
60.0	3.139212	28	28
61.0	3.139212	33	33
62.0	3.139212	33	33
63.0	3.139212	28	28
64.0	3.139212	15	15
65.0	3.139212	27	27
66.0	3.139212	22	22
67.0	3.139212	24	24
68.0	3.139212	19	19
69.0	3.139212	24	24
70.0	3.139212	14	14
71.0	3.139212	27	27
72.0	3.139212	16	16
73.0	3.139212	16	16
74.0	3.139212	15	15
75.0	3.139212	11	11
76.0	3.139212	13	13
77.0	3.139212	17	17
78.0	3.139212	12	12
79.0	3.139212	12	12
80.0	3.139212	15	15
81.0	3.139212	9	9
82.0	3.139212	11	11
83.0	3.139212	9	9
84.0	3.139212	11	11
85.0	3.139212	10	10
86.0	3.139212	16	16
87.0	3.139212	15	15
88.0	3.139212	10	10
89.0	3.139212	11	11
90.0	3.139212	10	10
91.0	3.139212	7	7
92.0	3.139212	11	11
93.0	3.139212	10	10
94.0	3.139212	4	4
95.0	3.139212	9	9
96.0	3.139212	5	5
97.0	3.139212	8	8
98.0	3.139212	8	8
99.0	3.139212	7	7
100.0	3.139212	10	10
101.0	0	7	7
102.0	0	4	4
103.0	0	8	8
104.0	0	7	7
105.0	0	8	8
106.0	0	4	4
107.0	0	6	6
108.0	0	3	3
109.0	0	5	5
110.0	0	2	2
111.0	0	2	2
112.0	0	2	2
113.0	0	5	5
114.0	0	5	5
115.0	0	3	3
116.0	0	4	4
117.0	0	7	7
118.0	0	4	4
119.0	0	5	5
120.0	0	2	2
121.0	0	3	3
122.0	0	2	2
123.0	0	3	3
124.0	0	6	6
126.0	0	4	4
127.0	0	4	4
128.0	0	4	4
129.0	0	5	5
130.0	0	2	2
131.0	0	9	9
132.0	0	3	3
133.0	0	7	7
134.0	0	4	4
135.0	0	3	3
136.0	0	3	3
137.0	0	3	3
138.0	0	3	3
139.0	0	4	4
141.0	0	4	4
142.0	0	3	3
143.0	0	2	2
144.0	0	2	2
145.0	0	3	3
146.0	0	1	1
148.0	0	2	2
149.0	0	2	2
150.0	0	1	1
151.0	0	3	3
152.0	0	1	1
154.0	0	1	1
155.0	0	1	1
156.0	0	2	2
157.0	0	2	2
159.0	0	1	1
160.0	0	1	1
161.0	0	1	1
162.0	0	2	2
163.0	0	1	1
164.0	0	1	1
167.0	0	3	3
169.0	0	1	1
170.0	0	1	1
171.0	0	3	3
172.0	0	2	2
173.0	0	1	1
174.0	0	1	1
175.0	0	1	1
177.0	0	1	1
179.0	0	1	1
181.0	0	1	1
183.0	0	2	2
184.0	0	1	1
185.0	0	2	2
186.0	0	2	2
187.0	0	1	1
188.0	0	1	1
189.0	0	2	2
190.0	0	1	1
191.0	0	2	2
193.0	0	2	2
194.0	0	1	1
196.0	0	1	1
197.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	2	2
202.0	0	1	1
203.0	0	2	2
206.0	0	1	1
207.0	0	3	3
209.0	0	1	1
211.0	0	1	1
212.0	0	2	2
213.0	0	1	1
217.0	0	1	1
220.0	0	1	1
223.0	0	1	1
224.0	0	2	2
225.0	0	1	1
226.0	0	1	1
229.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
236.0	0	1	1
237.0	0	1	1
239.0	0	1	1
240.0	0	3	3
242.0	0	2	2
243.0	0	1	1
244.0	0	1	1
245.0	0	1	1
247.0	0	1	1
249.0	0	1	1
252.0	0	2	2
254.0	0	1	1
255.0	0	2	2
258.0	0	3	3
265.0	0	1	1
267.0	0	1	1
269.0	0	1	1
271.0	0	3	3
272.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
279.0	0	1	1
281.0	0	2	2
290.0	0	1	1
293.0	0	1	1
295.0	0	1	1
296.0	0	1	1
301.0	0	1	1
313.0	0	1	1
315.0	0	1	1
317.0	0	1	1
339.0	0	1	1
347.0	0	1	1
349.0	0	2	2
356.0	0	1	1
361.0	0	1	1
362.0	0	1	1
378.0	0	1	1
387.0	0	1	1
393.0	0	1	1
397.0	0	1	1
400.0	0	1	1
408.0	0	1	1
417.0	0	1	1
454.0	0	1	1
464.0	0	1	1
467.0	0	2	2
470.0	0	1	1
484.0	0	1	1
492.0	0	1	1
494.0	0	1	1
500.0	0	1	1
527.0	0	1	1
538.0	0	1	1
560.0	0	1	1
564.0	0	1	1
565.0	0	1	1
586.0	0	1	1
624.0	0	1	1
638.0	0	1	1
644.0	0	1	1
651.0	0	1	1
675.0	0	2	2
696.0	0	1	1
724.0	0	1	1
751.0	0	1	1
823.0	0	1	1
893.0	0	1	1