## 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_DMSO_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_adherent_DMSO_2.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_DMSO_2.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 03:26:50 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	394	7872598	10620967	0	345	1368579	0	0.173858	19934901

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6022803	6022803
2.0	1.673737	329670	329670
3.0	2.127659	62428	62428
4.0	2.433483	26966	26966
5.0	2.639527	15125	15125
6.0	2.778348	9671	9671
7.0	2.871876	6510	6510
8.0	2.934889	4798	4798
9.0	2.977344	3607	3607
10.0	3.005947	2727	2727
11.0	3.025218	2237	2237
12.0	3.038201	1701	1701
13.0	3.046949	1520	1520
14.0	3.052843	1286	1286
15.0	3.056813	1054	1054
16.0	3.059488	894	894
17.0	3.061291	788	788
18.0	3.062505	792	792
19.0	3.063323	650	650
20.0	3.063874	566	566
21.0	3.064246	504	504
22.0	3.064496	451	451
23.0	3.064665	394	394
24.0	3.064778	369	369
25.0	3.064855	348	348
26.0	3.064906	323	323
27.0	3.064941	286	286
28.0	3.064964	260	260
29.0	3.06498	250	250
30.0	3.064991	261	261
31.0	3.064998	205	205
32.0	3.065003	203	203
33.0	3.065006	173	173
34.0	3.065008	148	148
35.0	3.06501	167	167
36.0	3.065011	142	142
37.0	3.065011	141	141
38.0	3.065012	130	130
39.0	3.065012	145	145
40.0	3.065012	110	110
41.0	3.065012	102	102
42.0	3.065013	114	114
43.0	3.065013	93	93
44.0	3.065013	94	94
45.0	3.065013	84	84
46.0	3.065013	82	82
47.0	3.065013	73	73
48.0	3.065013	75	75
49.0	3.065013	69	69
50.0	3.065013	69	69
51.0	3.065013	70	70
52.0	3.065013	60	60
53.0	3.065013	50	50
54.0	3.065013	50	50
55.0	3.065013	52	52
56.0	3.065013	57	57
57.0	3.065013	46	46
58.0	3.065013	47	47
59.0	3.065013	38	38
60.0	3.065013	53	53
61.0	3.065013	49	49
62.0	3.065013	54	54
63.0	3.065013	35	35
64.0	3.065013	38	38
65.0	3.065013	32	32
66.0	3.065013	31	31
67.0	3.065013	42	42
68.0	3.065013	37	37
69.0	3.065013	30	30
70.0	3.065013	35	35
71.0	3.065013	25	25
72.0	3.065013	30	30
73.0	3.065013	27	27
74.0	3.065013	19	19
75.0	3.065013	21	21
76.0	3.065013	27	27
77.0	3.065013	24	24
78.0	3.065013	17	17
79.0	3.065013	16	16
80.0	3.065013	22	22
81.0	3.065013	20	20
82.0	3.065013	24	24
83.0	3.065013	21	21
84.0	3.065013	23	23
85.0	3.065013	15	15
86.0	3.065013	22	22
87.0	3.065013	21	21
88.0	3.065013	14	14
89.0	3.065013	14	14
90.0	3.065013	17	17
91.0	3.065013	13	13
92.0	3.065013	18	18
93.0	3.065013	17	17
94.0	3.065013	16	16
95.0	3.065013	10	10
96.0	3.065013	15	15
97.0	3.065013	10	10
98.0	3.065013	11	11
99.0	3.065013	19	19
100.0	3.065013	19	19
101.0	0	14	14
102.0	0	9	9
103.0	0	21	21
104.0	0	8	8
105.0	0	16	16
106.0	0	17	17
107.0	0	16	16
108.0	0	12	12
109.0	0	7	7
110.0	0	13	13
111.0	0	14	14
112.0	0	11	11
113.0	0	8	8
114.0	0	8	8
115.0	0	5	5
116.0	0	6	6
117.0	0	12	12
118.0	0	4	4
119.0	0	8	8
120.0	0	7	7
121.0	0	17	17
122.0	0	11	11
123.0	0	6	6
124.0	0	13	13
125.0	0	4	4
126.0	0	9	9
127.0	0	6	6
128.0	0	7	7
129.0	0	9	9
130.0	0	10	10
131.0	0	12	12
132.0	0	8	8
133.0	0	8	8
134.0	0	8	8
135.0	0	9	9
136.0	0	6	6
137.0	0	6	6
138.0	0	2	2
139.0	0	7	7
140.0	0	5	5
141.0	0	4	4
142.0	0	7	7
143.0	0	3	3
144.0	0	9	9
145.0	0	5	5
146.0	0	6	6
147.0	0	3	3
148.0	0	8	8
149.0	0	5	5
150.0	0	7	7
151.0	0	8	8
152.0	0	7	7
153.0	0	8	8
154.0	0	3	3
155.0	0	5	5
156.0	0	6	6
157.0	0	11	11
158.0	0	9	9
159.0	0	7	7
160.0	0	8	8
161.0	0	5	5
162.0	0	3	3
163.0	0	5	5
164.0	0	3	3
165.0	0	5	5
166.0	0	5	5
167.0	0	8	8
168.0	0	4	4
169.0	0	2	2
170.0	0	10	10
171.0	0	6	6
172.0	0	5	5
173.0	0	3	3
174.0	0	2	2
175.0	0	1	1
176.0	0	4	4
177.0	0	7	7
178.0	0	4	4
179.0	0	4	4
180.0	0	1	1
181.0	0	3	3
182.0	0	1	1
183.0	0	3	3
184.0	0	3	3
185.0	0	3	3
186.0	0	1	1
187.0	0	3	3
188.0	0	4	4
189.0	0	2	2
190.0	0	3	3
191.0	0	4	4
192.0	0	6	6
193.0	0	3	3
194.0	0	9	9
195.0	0	6	6
196.0	0	2	2
197.0	0	2	2
198.0	0	6	6
199.0	0	2	2
200.0	0	1	1
201.0	0	1	1
202.0	0	1	1
203.0	0	1	1
204.0	0	6	6
205.0	0	2	2
206.0	0	4	4
207.0	0	2	2
208.0	0	2	2
209.0	0	1	1
210.0	0	3	3
211.0	0	3	3
212.0	0	4	4
213.0	0	4	4
214.0	0	2	2
215.0	0	1	1
217.0	0	2	2
219.0	0	3	3
220.0	0	1	1
221.0	0	2	2
223.0	0	2	2
224.0	0	1	1
225.0	0	1	1
226.0	0	2	2
227.0	0	1	1
228.0	0	1	1
229.0	0	2	2
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	4	4
234.0	0	1	1
235.0	0	1	1
236.0	0	4	4
237.0	0	1	1
238.0	0	1	1
240.0	0	6	6
242.0	0	2	2
243.0	0	4	4
244.0	0	2	2
246.0	0	2	2
249.0	0	3	3
251.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	1	1
257.0	0	1	1
258.0	0	1	1
261.0	0	2	2
262.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	2	2
267.0	0	3	3
269.0	0	1	1
270.0	0	2	2
273.0	0	1	1
274.0	0	2	2
275.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
280.0	0	1	1
281.0	0	1	1
282.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	2	2
288.0	0	3	3
289.0	0	1	1
290.0	0	2	2
291.0	0	1	1
292.0	0	1	1
296.0	0	1	1
298.0	0	1	1
302.0	0	2	2
303.0	0	1	1
304.0	0	1	1
306.0	0	1	1
307.0	0	1	1
309.0	0	2	2
312.0	0	2	2
316.0	0	1	1
319.0	0	2	2
320.0	0	1	1
322.0	0	2	2
326.0	0	2	2
328.0	0	1	1
330.0	0	2	2
333.0	0	2	2
335.0	0	1	1
336.0	0	1	1
340.0	0	1	1
342.0	0	1	1
344.0	0	2	2
349.0	0	1	1
355.0	0	1	1
361.0	0	1	1
364.0	0	1	1
372.0	0	1	1
373.0	0	1	1
374.0	0	1	1
382.0	0	1	1
385.0	0	1	1
391.0	0	1	1
400.0	0	2	2
406.0	0	1	1
407.0	0	1	1
411.0	0	1	1
413.0	0	1	1
428.0	0	1	1
432.0	0	2	2
442.0	0	1	1
454.0	0	2	2
455.0	0	1	1
456.0	0	1	1
459.0	0	1	1
466.0	0	1	1
470.0	0	1	1
491.0	0	1	1
493.0	0	1	1
503.0	0	1	1
512.0	0	1	1
530.0	0	1	1
534.0	0	1	1
551.0	0	1	1
553.0	0	1	1
557.0	0	1	1
570.0	0	1	1
597.0	0	1	1
618.0	0	1	1
624.0	0	1	1
648.0	0	1	1
668.0	0	1	1
693.0	0	1	1
713.0	0	1	1
735.0	0	1	1
756.0	0	1	1
757.0	0	1	1
769.0	0	1	1
786.0	0	1	1
788.0	0	1	1
814.0	0	1	1
936.0	0	1	1
952.0	0	1	1
1006.0	0	1	1
1011.0	0	1	1
1047.0	0	1	1
1130.0	0	1	1
1150.0	0	1	1
1177.0	0	1	1
1196.0	0	1	1
1254.0	0	1	1
1292.0	0	1	1
1758.0	0	1	1