## 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_TA_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA_3.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_TA_3.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 03:02:12 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	181	6773407	6314768	0	144	793940	0	0.117223	26588364

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	5620703	5620703
2.0	1.77511	257963	257963
3.0	2.375905	45246	45246
4.0	2.841587	18750	18750
5.0	3.202541	10289	10289
6.0	3.48232	6174	6174
7.0	3.69918	3999	3999
8.0	3.86727	2896	2896
9.0	3.997558	2080	2080
10.0	4.098546	1623	1623
11.0	4.176822	1274	1274
12.0	4.237495	1014	1014
13.0	4.284523	846	846
14.0	4.320975	665	665
15.0	4.34923	606	606
16.0	4.37113	501	501
17.0	4.388105	423	423
18.0	4.401262	367	367
19.0	4.411461	322	322
20.0	4.419366	286	286
21.0	4.425493	212	212
22.0	4.430242	206	206
23.0	4.433923	185	185
24.0	4.436777	152	152
25.0	4.438988	162	162
26.0	4.440703	121	121
27.0	4.442031	137	137
28.0	4.443061	101	101
29.0	4.44386	105	105
30.0	4.444478	88	88
31.0	4.444958	86	86
32.0	4.44533	78	78
33.0	4.445618	76	76
34.0	4.445841	86	86
35.0	4.446014	80	80
36.0	4.446149	59	59
37.0	4.446253	59	59
38.0	4.446333	50	50
39.0	4.446396	64	64
40.0	4.446444	53	53
41.0	4.446482	53	53
42.0	4.446511	60	60
43.0	4.446533	53	53
44.0	4.446551	38	38
45.0	4.446564	35	35
46.0	4.446575	37	37
47.0	4.446583	29	29
48.0	4.446589	34	34
49.0	4.446594	21	21
50.0	4.446598	32	32
51.0	4.446601	28	28
52.0	4.446603	34	34
53.0	4.446605	23	23
54.0	4.446606	34	34
55.0	4.446607	23	23
56.0	4.446608	22	22
57.0	4.446609	17	17
58.0	4.446609	17	17
59.0	4.44661	17	17
60.0	4.44661	26	26
61.0	4.44661	23	23
62.0	4.44661	14	14
63.0	4.446611	30	30
64.0	4.446611	18	18
65.0	4.446611	14	14
66.0	4.446611	11	11
67.0	4.446611	16	16
68.0	4.446611	16	16
69.0	4.446611	19	19
70.0	4.446611	13	13
71.0	4.446611	16	16
72.0	4.446611	23	23
73.0	4.446611	10	10
74.0	4.446611	9	9
75.0	4.446611	14	14
76.0	4.446611	9	9
77.0	4.446611	11	11
78.0	4.446611	9	9
79.0	4.446611	5	5
80.0	4.446611	6	6
81.0	4.446611	14	14
82.0	4.446611	12	12
83.0	4.446611	7	7
84.0	4.446611	3	3
85.0	4.446611	9	9
86.0	4.446611	7	7
87.0	4.446611	8	8
88.0	4.446611	7	7
89.0	4.446611	1	1
90.0	4.446611	5	5
91.0	4.446611	2	2
92.0	4.446611	6	6
93.0	4.446611	6	6
94.0	4.446611	9	9
95.0	4.446611	6	6
96.0	4.446611	3	3
97.0	4.446611	4	4
98.0	4.446611	10	10
99.0	4.446611	3	3
100.0	4.446611	6	6
101.0	0	5	5
102.0	0	7	7
103.0	0	3	3
104.0	0	2	2
105.0	0	2	2
106.0	0	2	2
107.0	0	5	5
108.0	0	2	2
109.0	0	5	5
110.0	0	4	4
111.0	0	5	5
112.0	0	1	1
113.0	0	3	3
114.0	0	7	7
115.0	0	2	2
117.0	0	2	2
118.0	0	3	3
119.0	0	4	4
120.0	0	3	3
121.0	0	4	4
122.0	0	1	1
123.0	0	6	6
124.0	0	4	4
125.0	0	1	1
126.0	0	2	2
127.0	0	3	3
128.0	0	1	1
129.0	0	3	3
130.0	0	3	3
131.0	0	3	3
132.0	0	1	1
134.0	0	2	2
135.0	0	5	5
136.0	0	1	1
137.0	0	5	5
138.0	0	2	2
139.0	0	2	2
140.0	0	2	2
142.0	0	2	2
143.0	0	2	2
144.0	0	3	3
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	1	1
150.0	0	5	5
152.0	0	1	1
153.0	0	2	2
154.0	0	2	2
155.0	0	5	5
157.0	0	1	1
158.0	0	2	2
159.0	0	1	1
162.0	0	2	2
163.0	0	1	1
164.0	0	2	2
165.0	0	2	2
167.0	0	1	1
170.0	0	4	4
171.0	0	2	2
173.0	0	2	2
174.0	0	1	1
176.0	0	3	3
178.0	0	2	2
180.0	0	1	1
181.0	0	2	2
184.0	0	1	1
185.0	0	1	1
189.0	0	1	1
195.0	0	1	1
196.0	0	2	2
197.0	0	1	1
199.0	0	2	2
202.0	0	1	1
204.0	0	1	1
205.0	0	2	2
206.0	0	1	1
208.0	0	1	1
213.0	0	2	2
222.0	0	1	1
228.0	0	2	2
237.0	0	1	1
245.0	0	2	2
256.0	0	3	3
258.0	0	1	1
259.0	0	2	2
260.0	0	1	1
267.0	0	1	1
272.0	0	1	1
276.0	0	1	1
278.0	0	1	1
280.0	0	1	1
287.0	0	1	1
292.0	0	1	1
296.0	0	2	2
298.0	0	1	1
304.0	0	1	1
312.0	0	2	2
314.0	0	1	1
330.0	0	1	1
346.0	0	1	1
347.0	0	1	1
356.0	0	2	2
360.0	0	1	1
420.0	0	1	1
437.0	0	1	1
455.0	0	1	1
467.0	0	1	1
548.0	0	1	1
716.0	0	1	1
744.0	0	1	1