## 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-D19_adherent_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D19_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-D19_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 03:33:47 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	357	18026540	10852271	0	292	7072056	0	0.392318	16460186

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6796006	6796006
2.0	1.334486	2693436	2693436
3.0	1.446367	961452	961452
4.0	1.483789	312512	312512
5.0	1.496307	99603	99603
6.0	1.500494	34867	34867
7.0	1.501894	15295	15295
8.0	1.502363	8513	8513
9.0	1.502519	5583	5583
10.0	1.502572	4004	4004
11.0	1.502589	3106	3106
12.0	1.502595	2311	2311
13.0	1.502597	1941	1941
14.0	1.502598	1549	1549
15.0	1.502598	1265	1265
16.0	1.502598	1021	1021
17.0	1.502598	925	925
18.0	1.502598	825	825
19.0	1.502598	733	733
20.0	1.502598	641	641
21.0	1.502598	560	560
22.0	1.502598	463	463
23.0	1.502598	464	464
24.0	1.502598	363	363
25.0	1.502598	365	365
26.0	1.502598	326	326
27.0	1.502598	303	303
28.0	1.502598	277	277
29.0	1.502598	263	263
30.0	1.502598	238	238
31.0	1.502598	210	210
32.0	1.502598	199	199
33.0	1.502598	193	193
34.0	1.502598	183	183
35.0	1.502598	154	154
36.0	1.502598	161	161
37.0	1.502598	128	128
38.0	1.502598	141	141
39.0	1.502598	144	144
40.0	1.502598	134	134
41.0	1.502598	115	115
42.0	1.502598	120	120
43.0	1.502598	99	99
44.0	1.502598	96	96
45.0	1.502598	90	90
46.0	1.502598	87	87
47.0	1.502598	84	84
48.0	1.502598	78	78
49.0	1.502598	65	65
50.0	1.502598	71	71
51.0	1.502598	69	69
52.0	1.502598	60	60
53.0	1.502598	61	61
54.0	1.502598	52	52
55.0	1.502598	49	49
56.0	1.502598	40	40
57.0	1.502598	74	74
58.0	1.502598	51	51
59.0	1.502598	60	60
60.0	1.502598	59	59
61.0	1.502598	41	41
62.0	1.502598	46	46
63.0	1.502598	47	47
64.0	1.502598	48	48
65.0	1.502598	40	40
66.0	1.502598	45	45
67.0	1.502598	33	33
68.0	1.502598	32	32
69.0	1.502598	34	34
70.0	1.502598	37	37
71.0	1.502598	30	30
72.0	1.502598	33	33
73.0	1.502598	33	33
74.0	1.502598	33	33
75.0	1.502598	29	29
76.0	1.502598	22	22
77.0	1.502598	28	28
78.0	1.502598	34	34
79.0	1.502598	28	28
80.0	1.502598	24	24
81.0	1.502598	22	22
82.0	1.502598	24	24
83.0	1.502598	23	23
84.0	1.502598	27	27
85.0	1.502598	24	24
86.0	1.502598	23	23
87.0	1.502598	21	21
88.0	1.502598	19	19
89.0	1.502598	18	18
90.0	1.502598	14	14
91.0	1.502598	20	20
92.0	1.502598	20	20
93.0	1.502598	17	17
94.0	1.502598	13	13
95.0	1.502598	22	22
96.0	1.502598	25	25
97.0	1.502598	11	11
98.0	1.502598	11	11
99.0	1.502598	24	24
100.0	1.502598	22	22
101.0	0	10	10
102.0	0	13	13
103.0	0	9	9
104.0	0	14	14
105.0	0	15	15
106.0	0	16	16
107.0	0	12	12
108.0	0	12	12
109.0	0	15	15
110.0	0	9	9
111.0	0	5	5
112.0	0	16	16
113.0	0	10	10
114.0	0	11	11
115.0	0	17	17
116.0	0	13	13
117.0	0	14	14
118.0	0	9	9
119.0	0	5	5
120.0	0	9	9
121.0	0	7	7
122.0	0	7	7
123.0	0	11	11
124.0	0	6	6
125.0	0	10	10
126.0	0	4	4
127.0	0	7	7
128.0	0	9	9
129.0	0	5	5
130.0	0	13	13
131.0	0	9	9
132.0	0	7	7
133.0	0	4	4
134.0	0	3	3
135.0	0	2	2
136.0	0	8	8
137.0	0	10	10
138.0	0	6	6
139.0	0	5	5
140.0	0	4	4
141.0	0	7	7
142.0	0	5	5
143.0	0	10	10
144.0	0	8	8
145.0	0	4	4
146.0	0	10	10
147.0	0	6	6
148.0	0	10	10
149.0	0	10	10
150.0	0	2	2
151.0	0	9	9
152.0	0	2	2
153.0	0	7	7
154.0	0	2	2
155.0	0	8	8
156.0	0	10	10
157.0	0	11	11
158.0	0	7	7
159.0	0	4	4
160.0	0	6	6
161.0	0	6	6
162.0	0	3	3
163.0	0	2	2
164.0	0	6	6
165.0	0	2	2
166.0	0	8	8
167.0	0	6	6
168.0	0	3	3
169.0	0	8	8
170.0	0	9	9
171.0	0	7	7
172.0	0	7	7
173.0	0	4	4
174.0	0	1	1
175.0	0	4	4
176.0	0	7	7
177.0	0	3	3
178.0	0	2	2
179.0	0	3	3
180.0	0	3	3
181.0	0	4	4
182.0	0	4	4
183.0	0	8	8
184.0	0	3	3
185.0	0	5	5
186.0	0	3	3
187.0	0	5	5
188.0	0	7	7
189.0	0	9	9
190.0	0	3	3
191.0	0	2	2
192.0	0	1	1
193.0	0	1	1
194.0	0	2	2
195.0	0	8	8
196.0	0	1	1
197.0	0	3	3
198.0	0	6	6
199.0	0	1	1
200.0	0	4	4
201.0	0	3	3
203.0	0	6	6
204.0	0	3	3
205.0	0	7	7
206.0	0	3	3
207.0	0	2	2
208.0	0	3	3
209.0	0	2	2
210.0	0	7	7
211.0	0	3	3
212.0	0	4	4
213.0	0	1	1
214.0	0	2	2
215.0	0	1	1
216.0	0	3	3
217.0	0	4	4
218.0	0	3	3
219.0	0	3	3
220.0	0	6	6
221.0	0	2	2
222.0	0	1	1
223.0	0	4	4
224.0	0	4	4
225.0	0	2	2
226.0	0	3	3
227.0	0	3	3
228.0	0	4	4
229.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
234.0	0	1	1
236.0	0	3	3
237.0	0	4	4
238.0	0	4	4
239.0	0	4	4
240.0	0	1	1
241.0	0	1	1
242.0	0	2	2
243.0	0	3	3
244.0	0	2	2
245.0	0	3	3
246.0	0	7	7
247.0	0	1	1
249.0	0	2	2
250.0	0	3	3
251.0	0	2	2
253.0	0	2	2
254.0	0	1	1
255.0	0	6	6
257.0	0	2	2
258.0	0	2	2
259.0	0	3	3
260.0	0	3	3
261.0	0	2	2
262.0	0	1	1
263.0	0	2	2
264.0	0	3	3
266.0	0	1	1
268.0	0	1	1
270.0	0	2	2
272.0	0	1	1
273.0	0	3	3
274.0	0	5	5
277.0	0	1	1
278.0	0	1	1
279.0	0	5	5
280.0	0	2	2
281.0	0	1	1
283.0	0	4	4
284.0	0	3	3
285.0	0	1	1
286.0	0	2	2
288.0	0	3	3
289.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	1	1
296.0	0	1	1
297.0	0	3	3
299.0	0	1	1
300.0	0	1	1
302.0	0	2	2
304.0	0	1	1
305.0	0	2	2
307.0	0	2	2
308.0	0	4	4
309.0	0	2	2
310.0	0	1	1
311.0	0	2	2
312.0	0	2	2
314.0	0	3	3
315.0	0	1	1
317.0	0	2	2
319.0	0	1	1
321.0	0	1	1
322.0	0	2	2
323.0	0	1	1
326.0	0	1	1
328.0	0	2	2
329.0	0	1	1
332.0	0	1	1
334.0	0	1	1
335.0	0	1	1
339.0	0	1	1
340.0	0	1	1
341.0	0	2	2
342.0	0	3	3
344.0	0	2	2
345.0	0	2	2
346.0	0	2	2
349.0	0	1	1
350.0	0	2	2
352.0	0	2	2
355.0	0	2	2
362.0	0	1	1
363.0	0	3	3
365.0	0	3	3
368.0	0	1	1
374.0	0	2	2
377.0	0	1	1
381.0	0	1	1
382.0	0	1	1
385.0	0	3	3
396.0	0	1	1
400.0	0	1	1
401.0	0	2	2
402.0	0	2	2
406.0	0	1	1
410.0	0	1	1
412.0	0	1	1
417.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	1	1
424.0	0	1	1
425.0	0	1	1
428.0	0	1	1
430.0	0	2	2
434.0	0	2	2
435.0	0	1	1
438.0	0	1	1
439.0	0	2	2
448.0	0	1	1
454.0	0	1	1
457.0	0	2	2
459.0	0	1	1
465.0	0	1	1
472.0	0	1	1
484.0	0	1	1
492.0	0	2	2
494.0	0	1	1
507.0	0	1	1
510.0	0	1	1
520.0	0	1	1
522.0	0	1	1
523.0	0	1	1
536.0	0	1	1
542.0	0	2	2
551.0	0	1	1
556.0	0	1	1
559.0	0	1	1
590.0	0	1	1
627.0	0	1	1
641.0	0	1	1
653.0	0	1	1
660.0	0	1	1
681.0	0	1	1
683.0	0	1	1
695.0	0	1	1
716.0	0	1	1
722.0	0	1	1
724.0	0	1	1
728.0	0	1	1
748.0	0	1	1
756.0	0	1	1
770.0	0	1	1
778.0	0	1	1
819.0	0	1	1
880.0	0	1	1
882.0	0	1	1
935.0	0	1	1
977.0	0	1	1
996.0	0	1	1
1072.0	0	1	1
1075.0	0	1	1
1127.0	0	1	1
1137.0	0	1	1
1202.0	0	1	1
1208.0	0	1	1
1297.0	0	1	1
1300.0	0	1	1
1312.0	0	1	1
1326.0	0	1	1
1337.0	0	1	1
1338.0	0	1	1
1393.0	0	1	1
1496.0	0	1	1
1645.0	0	1	1
1745.0	0	2	2