## 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-D18_adherent_DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_adherent_DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D18_adherent_DMSO_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 03:57:06 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	137	10686202	3996828	0	105	8933460	0	0.83598	1756749

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	0.999999	263259	263259
2.0	1.002281	185708	185708
3.0	1.002286	164190	164190
4.0	1.002286	150552	150552
5.0	1.002286	142632	142632
6.0	1.002286	133990	133990
7.0	1.002286	126071	126071
8.0	1.002286	116248	116248
9.0	1.002286	103779	103779
10.0	1.002286	88963	88963
11.0	1.002286	73900	73900
12.0	1.002286	58821	58821
13.0	1.002286	45096	45096
14.0	1.002286	32392	32392
15.0	1.002286	22577	22577
16.0	1.002286	15210	15210
17.0	1.002286	9877	9877
18.0	1.002286	6230	6230
19.0	1.002286	3951	3951
20.0	1.002286	2353	2353
21.0	1.002286	1449	1449
22.0	1.002286	956	956
23.0	1.002286	644	644
24.0	1.002286	441	441
25.0	1.002286	324	324
26.0	1.002286	253	253
27.0	1.002286	230	230
28.0	1.002286	180	180
29.0	1.002286	171	171
30.0	1.002286	152	152
31.0	1.002286	146	146
32.0	1.002286	134	134
33.0	1.002286	81	81
34.0	1.002286	88	88
35.0	1.002286	68	68
36.0	1.002286	73	73
37.0	1.002286	70	70
38.0	1.002286	54	54
39.0	1.002286	59	59
40.0	1.002286	52	52
41.0	1.002286	48	48
42.0	1.002286	45	45
43.0	1.002286	39	39
44.0	1.002286	39	39
45.0	1.002286	36	36
46.0	1.002286	28	28
47.0	1.002286	31	31
48.0	1.002286	29	29
49.0	1.002286	46	46
50.0	1.002286	28	28
51.0	1.002286	24	24
52.0	1.002286	30	30
53.0	1.002286	27	27
54.0	1.002286	29	29
55.0	1.002286	25	25
56.0	1.002286	18	18
57.0	1.002286	19	19
58.0	1.002286	20	20
59.0	1.002286	16	16
60.0	1.002286	18	18
61.0	1.002286	16	16
62.0	1.002286	20	20
63.0	1.002286	18	18
64.0	1.002286	24	24
65.0	1.002286	18	18
66.0	1.002286	14	14
67.0	1.002286	14	14
68.0	1.002286	12	12
69.0	1.002286	15	15
70.0	1.002286	18	18
71.0	1.002286	8	8
72.0	1.002286	12	12
73.0	1.002286	10	10
74.0	1.002286	9	9
75.0	1.002286	12	12
76.0	1.002286	10	10
77.0	1.002286	12	12
78.0	1.002286	5	5
79.0	1.002286	7	7
80.0	1.002286	6	6
81.0	1.002286	7	7
82.0	1.002286	10	10
83.0	1.002286	14	14
84.0	1.002286	10	10
85.0	1.002286	14	14
86.0	1.002286	6	6
87.0	1.002286	4	4
88.0	1.002286	6	6
89.0	1.002286	7	7
90.0	1.002286	6	6
91.0	1.002286	10	10
92.0	1.002286	3	3
93.0	1.002286	6	6
94.0	1.002286	8	8
95.0	1.002286	4	4
96.0	1.002286	2	2
97.0	1.002286	3	3
98.0	1.002286	12	12
99.0	1.002286	10	10
100.0	1.002286	6	6
101.0	0	4	4
102.0	0	10	10
103.0	0	6	6
104.0	0	4	4
105.0	0	9	9
106.0	0	5	5
107.0	0	6	6
108.0	0	9	9
109.0	0	2	2
110.0	0	7	7
111.0	0	6	6
112.0	0	7	7
113.0	0	5	5
114.0	0	4	4
115.0	0	2	2
116.0	0	6	6
117.0	0	3	3
118.0	0	7	7
119.0	0	4	4
120.0	0	7	7
121.0	0	1	1
122.0	0	6	6
123.0	0	2	2
124.0	0	4	4
125.0	0	1	1
126.0	0	4	4
127.0	0	3	3
128.0	0	4	4
129.0	0	4	4
130.0	0	5	5
132.0	0	2	2
133.0	0	3	3
134.0	0	3	3
135.0	0	2	2
136.0	0	3	3
137.0	0	3	3
139.0	0	5	5
140.0	0	1	1
142.0	0	2	2
143.0	0	4	4
144.0	0	2	2
145.0	0	3	3
146.0	0	2	2
147.0	0	5	5
148.0	0	1	1
149.0	0	2	2
150.0	0	1	1
151.0	0	2	2
152.0	0	3	3
153.0	0	2	2
155.0	0	1	1
157.0	0	2	2
158.0	0	2	2
159.0	0	2	2
160.0	0	1	1
162.0	0	3	3
163.0	0	1	1
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
167.0	0	2	2
168.0	0	2	2
169.0	0	2	2
171.0	0	3	3
174.0	0	1	1
175.0	0	1	1
176.0	0	2	2
177.0	0	1	1
178.0	0	3	3
179.0	0	1	1
181.0	0	4	4
182.0	0	2	2
184.0	0	2	2
185.0	0	3	3
186.0	0	2	2
188.0	0	2	2
193.0	0	2	2
195.0	0	3	3
197.0	0	2	2
198.0	0	1	1
200.0	0	2	2
201.0	0	2	2
206.0	0	1	1
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	2	2
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
216.0	0	1	1
221.0	0	1	1
222.0	0	1	1
223.0	0	1	1
225.0	0	2	2
227.0	0	1	1
228.0	0	2	2
230.0	0	2	2
237.0	0	1	1
250.0	0	1	1
262.0	0	1	1
264.0	0	1	1
265.0	0	1	1
271.0	0	1	1
272.0	0	1	1
277.0	0	1	1
292.0	0	1	1
295.0	0	1	1
307.0	0	1	1
316.0	0	1	1
352.0	0	1	1
368.0	0	1	1
382.0	0	1	1
392.0	0	1	1
399.0	0	1	1
525.0	0	1	1
526.0	0	1	1
533.0	0	1	1
544.0	0	1	1
549.0	0	1	1
559.0	0	1	1
652.0	0	1	1
670.0	0	1	1
737.0	0	2	2
776.0	0	1	1
789.0	0	1	1
807.0	0	1	1
878.0	0	1	1
942.0	0	1	1
1092.0	0	1	1
1293.0	0	1	1
1351.0	0	1	1
1462.0	0	1	1