## 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-D10_supernatant_DMSO_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D10_supernatant_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-D10_supernatant_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 02:27:51 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	2246	21973330	30326747	0	2156	8605394	0	0.391658	20114390

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	8612564	8612564
2.0	1.335404	3064275	3064275
3.0	1.4479	1068248	1068248
4.0	1.485632	352655	352655
5.0	1.498287	117547	117547
6.0	1.502532	46064	46064
7.0	1.503956	23229	23229
8.0	1.504433	14451	14451
9.0	1.504593	10443	10443
10.0	1.504647	7894	7894
11.0	1.504665	6406	6406
12.0	1.504671	5181	5181
13.0	1.504673	4265	4265
14.0	1.504674	3664	3664
15.0	1.504674	2993	2993
16.0	1.504674	2624	2624
17.0	1.504674	2202	2202
18.0	1.504674	1973	1973
19.0	1.504674	1682	1682
20.0	1.504674	1467	1467
21.0	1.504674	1256	1256
22.0	1.504674	1136	1136
23.0	1.504674	1076	1076
24.0	1.504674	967	967
25.0	1.504674	834	834
26.0	1.504674	797	797
27.0	1.504674	706	706
28.0	1.504674	642	642
29.0	1.504674	608	608
30.0	1.504674	521	521
31.0	1.504674	523	523
32.0	1.504674	491	491
33.0	1.504674	429	429
34.0	1.504674	377	377
35.0	1.504674	335	335
36.0	1.504674	324	324
37.0	1.504674	314	314
38.0	1.504674	286	286
39.0	1.504674	270	270
40.0	1.504674	249	249
41.0	1.504674	245	245
42.0	1.504674	229	229
43.0	1.504674	221	221
44.0	1.504674	208	208
45.0	1.504674	185	185
46.0	1.504674	185	185
47.0	1.504674	167	167
48.0	1.504674	141	141
49.0	1.504674	142	142
50.0	1.504674	129	129
51.0	1.504674	137	137
52.0	1.504674	120	120
53.0	1.504674	110	110
54.0	1.504674	119	119
55.0	1.504674	112	112
56.0	1.504674	120	120
57.0	1.504674	96	96
58.0	1.504674	114	114
59.0	1.504674	78	78
60.0	1.504674	79	79
61.0	1.504674	90	90
62.0	1.504674	92	92
63.0	1.504674	99	99
64.0	1.504674	86	86
65.0	1.504674	60	60
66.0	1.504674	65	65
67.0	1.504674	77	77
68.0	1.504674	55	55
69.0	1.504674	63	63
70.0	1.504674	64	64
71.0	1.504674	73	73
72.0	1.504674	54	54
73.0	1.504674	54	54
74.0	1.504674	58	58
75.0	1.504674	55	55
76.0	1.504674	56	56
77.0	1.504674	50	50
78.0	1.504674	41	41
79.0	1.504674	41	41
80.0	1.504674	36	36
81.0	1.504674	44	44
82.0	1.504674	26	26
83.0	1.504674	31	31
84.0	1.504674	36	36
85.0	1.504674	37	37
86.0	1.504674	33	33
87.0	1.504674	27	27
88.0	1.504674	39	39
89.0	1.504674	31	31
90.0	1.504674	32	32
91.0	1.504674	35	35
92.0	1.504674	24	24
93.0	1.504674	33	33
94.0	1.504674	36	36
95.0	1.504674	18	18
96.0	1.504674	19	19
97.0	1.504674	16	16
98.0	1.504674	19	19
99.0	1.504674	27	27
100.0	1.504674	21	21
101.0	0	27	27
102.0	0	26	26
103.0	0	17	17
104.0	0	11	11
105.0	0	19	19
106.0	0	14	14
107.0	0	18	18
108.0	0	20	20
109.0	0	20	20
110.0	0	19	19
111.0	0	25	25
112.0	0	13	13
113.0	0	18	18
114.0	0	19	19
115.0	0	16	16
116.0	0	9	9
117.0	0	11	11
118.0	0	17	17
119.0	0	11	11
120.0	0	13	13
121.0	0	20	20
122.0	0	10	10
123.0	0	20	20
124.0	0	10	10
125.0	0	7	7
126.0	0	20	20
127.0	0	8	8
128.0	0	11	11
129.0	0	13	13
130.0	0	13	13
131.0	0	13	13
132.0	0	13	13
133.0	0	14	14
134.0	0	7	7
135.0	0	17	17
136.0	0	10	10
137.0	0	10	10
138.0	0	5	5
139.0	0	11	11
140.0	0	7	7
141.0	0	6	6
142.0	0	10	10
143.0	0	10	10
144.0	0	9	9
145.0	0	6	6
146.0	0	8	8
147.0	0	13	13
148.0	0	4	4
149.0	0	12	12
150.0	0	10	10
151.0	0	9	9
152.0	0	7	7
153.0	0	5	5
154.0	0	9	9
155.0	0	9	9
156.0	0	7	7
157.0	0	9	9
158.0	0	9	9
159.0	0	9	9
160.0	0	6	6
161.0	0	4	4
162.0	0	6	6
163.0	0	1	1
164.0	0	8	8
165.0	0	2	2
166.0	0	2	2
167.0	0	4	4
169.0	0	3	3
170.0	0	4	4
171.0	0	4	4
172.0	0	7	7
173.0	0	5	5
174.0	0	2	2
175.0	0	3	3
176.0	0	4	4
177.0	0	6	6
178.0	0	3	3
179.0	0	7	7
180.0	0	4	4
181.0	0	2	2
182.0	0	5	5
183.0	0	5	5
184.0	0	5	5
185.0	0	4	4
186.0	0	1	1
187.0	0	4	4
188.0	0	5	5
189.0	0	5	5
190.0	0	3	3
191.0	0	3	3
192.0	0	5	5
193.0	0	4	4
194.0	0	4	4
195.0	0	2	2
196.0	0	2	2
197.0	0	5	5
198.0	0	1	1
199.0	0	5	5
200.0	0	3	3
201.0	0	5	5
202.0	0	2	2
203.0	0	3	3
204.0	0	7	7
205.0	0	2	2
206.0	0	5	5
207.0	0	2	2
208.0	0	3	3
209.0	0	2	2
210.0	0	2	2
211.0	0	5	5
212.0	0	2	2
213.0	0	1	1
214.0	0	3	3
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	1	1
219.0	0	5	5
221.0	0	3	3
222.0	0	1	1
223.0	0	4	4
224.0	0	2	2
226.0	0	4	4
227.0	0	1	1
228.0	0	2	2
229.0	0	5	5
230.0	0	2	2
231.0	0	2	2
232.0	0	2	2
233.0	0	3	3
234.0	0	2	2
235.0	0	1	1
236.0	0	2	2
237.0	0	2	2
239.0	0	2	2
240.0	0	2	2
241.0	0	2	2
242.0	0	6	6
243.0	0	1	1
245.0	0	1	1
246.0	0	1	1
248.0	0	4	4
249.0	0	1	1
250.0	0	2	2
251.0	0	3	3
252.0	0	2	2
254.0	0	3	3
255.0	0	1	1
256.0	0	2	2
257.0	0	1	1
258.0	0	1	1
259.0	0	2	2
261.0	0	2	2
263.0	0	1	1
264.0	0	4	4
266.0	0	1	1
267.0	0	1	1
272.0	0	1	1
275.0	0	1	1
278.0	0	2	2
279.0	0	3	3
280.0	0	2	2
282.0	0	3	3
283.0	0	2	2
287.0	0	4	4
288.0	0	1	1
291.0	0	1	1
293.0	0	1	1
294.0	0	2	2
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
299.0	0	1	1
300.0	0	2	2
301.0	0	1	1
304.0	0	1	1
306.0	0	1	1
312.0	0	1	1
314.0	0	1	1
315.0	0	1	1
318.0	0	1	1
320.0	0	1	1
321.0	0	1	1
324.0	0	2	2
325.0	0	1	1
326.0	0	1	1
327.0	0	1	1
329.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
339.0	0	1	1
340.0	0	1	1
342.0	0	1	1
344.0	0	2	2
349.0	0	1	1
354.0	0	1	1
356.0	0	1	1
358.0	0	4	4
359.0	0	3	3
362.0	0	1	1
363.0	0	1	1
375.0	0	1	1
383.0	0	1	1
389.0	0	1	1
391.0	0	2	2
392.0	0	1	1
393.0	0	1	1
399.0	0	1	1
400.0	0	2	2
401.0	0	1	1
408.0	0	2	2
409.0	0	1	1
416.0	0	1	1
421.0	0	1	1
428.0	0	1	1
430.0	0	1	1
435.0	0	1	1
436.0	0	2	2
438.0	0	1	1
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
458.0	0	2	2
460.0	0	1	1
468.0	0	1	1
485.0	0	1	1
499.0	0	1	1
509.0	0	1	1
517.0	0	1	1
528.0	0	1	1
532.0	0	1	1
538.0	0	1	1
540.0	0	1	1
548.0	0	1	1
557.0	0	1	1
578.0	0	1	1
607.0	0	1	1
631.0	0	1	1
635.0	0	1	1
637.0	0	1	1
643.0	0	1	1
644.0	0	1	1
651.0	0	1	1
663.0	0	1	1
669.0	0	1	1
674.0	0	1	1
688.0	0	1	1
745.0	0	1	1
759.0	0	1	1
769.0	0	1	1
788.0	0	1	1
790.0	0	1	1
813.0	0	1	1
827.0	0	1	1
833.0	0	1	1
836.0	0	1	1
849.0	0	1	1
861.0	0	1	1
878.0	0	1	1
902.0	0	1	1
964.0	0	1	1
1028.0	0	1	1
1038.0	0	1	1
1042.0	0	1	1
1048.0	0	1	1
1072.0	0	1	1
1087.0	0	1	1
1100.0	0	1	1
1111.0	0	1	1
1207.0	0	1	1
1227.0	0	1	1
1561.0	0	1	1