## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/ChC_13/ChC_13_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/ChC_13/ChC_13_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/ChC_13/ChC_13_dedup_metrics.txt CREATE_INDEX=true    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 10 15:41:00 NOVT 2025

## 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	60711	26016881	845938	115341	41761	2143665	0	0.083101	149081776

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22760415	22760415
2.0	1.839865	892511	892511
3.0	2.545238	108151	108151
4.0	3.137656	38591	38591
5.0	3.635208	20159	20159
6.0	4.053083	12171	12171
7.0	4.404043	8197	8197
8.0	4.698801	5622	5622
9.0	4.946359	4091	4091
10.0	5.154273	3191	3191
11.0	5.328893	2488	2488
12.0	5.475551	1993	1993
13.0	5.598723	1556	1556
14.0	5.702172	1384	1384
15.0	5.789054	1119	1119
16.0	5.862024	983	983
17.0	5.923308	838	838
18.0	5.974779	716	716
19.0	6.018008	645	645
20.0	6.054314	541	541
21.0	6.084806	468	468
22.0	6.110415	437	437
23.0	6.131924	427	427
24.0	6.149988	386	386
25.0	6.165159	317	317
26.0	6.177901	280	280
27.0	6.188603	262	262
28.0	6.197591	261	261
29.0	6.205139	213	213
30.0	6.211479	220	220
31.0	6.216804	172	172
32.0	6.221276	169	169
33.0	6.225031	160	160
34.0	6.228186	161	161
35.0	6.230835	147	147
36.0	6.23306	126	126
37.0	6.234929	113	113
38.0	6.236498	116	116
39.0	6.237816	119	119
40.0	6.238923	116	116
41.0	6.239853	105	105
42.0	6.240634	89	89
43.0	6.24129	83	83
44.0	6.241841	80	80
45.0	6.242303	87	87
46.0	6.242692	82	82
47.0	6.243018	73	73
48.0	6.243292	69	69
49.0	6.243522	56	56
50.0	6.243716	79	79
51.0	6.243878	62	62
52.0	6.244014	57	57
53.0	6.244129	44	44
54.0	6.244225	62	62
55.0	6.244306	56	56
56.0	6.244374	44	44
57.0	6.244431	55	55
58.0	6.244478	60	60
59.0	6.244519	45	45
60.0	6.244552	40	40
61.0	6.244581	39	39
62.0	6.244605	44	44
63.0	6.244625	43	43
64.0	6.244641	34	34
65.0	6.244656	42	42
66.0	6.244667	37	37
67.0	6.244677	38	38
68.0	6.244686	25	25
69.0	6.244693	30	30
70.0	6.244699	30	30
71.0	6.244704	24	24
72.0	6.244708	24	24
73.0	6.244711	29	29
74.0	6.244714	27	27
75.0	6.244717	25	25
76.0	6.244719	31	31
77.0	6.24472	25	25
78.0	6.244722	22	22
79.0	6.244723	26	26
80.0	6.244724	30	30
81.0	6.244725	19	19
82.0	6.244726	29	29
83.0	6.244726	28	28
84.0	6.244727	14	14
85.0	6.244727	18	18
86.0	6.244728	17	17
87.0	6.244728	17	17
88.0	6.244728	18	18
89.0	6.244728	15	15
90.0	6.244729	13	13
91.0	6.244729	14	14
92.0	6.244729	12	12
93.0	6.244729	18	18
94.0	6.244729	16	16
95.0	6.244729	15	15
96.0	6.244729	13	13
97.0	6.244729	12	12
98.0	6.244729	13	13
99.0	6.244729	16	16
100.0	6.244729	13	13
101.0	0	14	14
102.0	0	14	14
103.0	0	13	13
104.0	0	11	11
105.0	0	9	9
106.0	0	10	10
107.0	0	16	16
108.0	0	7	7
109.0	0	15	15
110.0	0	7	7
111.0	0	4	4
112.0	0	15	15
113.0	0	12	12
114.0	0	14	14
115.0	0	10	10
116.0	0	15	15
117.0	0	8	8
118.0	0	9	9
119.0	0	7	7
120.0	0	10	10
121.0	0	11	11
122.0	0	3	3
123.0	0	4	4
124.0	0	12	12
125.0	0	3	3
126.0	0	6	6
127.0	0	9	9
128.0	0	6	6
129.0	0	10	10
130.0	0	9	9
131.0	0	6	6
132.0	0	13	13
133.0	0	4	4
134.0	0	8	8
135.0	0	9	9
136.0	0	5	5
137.0	0	5	5
138.0	0	8	8
139.0	0	7	7
140.0	0	7	7
141.0	0	5	5
142.0	0	4	4
143.0	0	6	6
144.0	0	7	7
145.0	0	5	5
146.0	0	3	3
147.0	0	3	3
148.0	0	4	4
149.0	0	2	2
150.0	0	1	1
151.0	0	3	3
152.0	0	5	5
153.0	0	7	7
154.0	0	4	4
155.0	0	2	2
156.0	0	6	6
157.0	0	7	7
158.0	0	2	2
159.0	0	7	7
160.0	0	7	7
161.0	0	4	4
162.0	0	2	2
163.0	0	7	7
164.0	0	2	2
165.0	0	5	5
166.0	0	4	4
167.0	0	2	2
168.0	0	6	6
169.0	0	6	6
170.0	0	2	2
171.0	0	6	6
172.0	0	3	3
173.0	0	1	1
174.0	0	1	1
175.0	0	4	4
176.0	0	6	6
177.0	0	4	4
178.0	0	3	3
179.0	0	6	6
180.0	0	3	3
181.0	0	6	6
182.0	0	2	2
183.0	0	2	2
184.0	0	2	2
185.0	0	2	2
186.0	0	4	4
187.0	0	3	3
188.0	0	3	3
189.0	0	3	3
190.0	0	4	4
191.0	0	5	5
192.0	0	2	2
193.0	0	4	4
194.0	0	5	5
195.0	0	2	2
196.0	0	4	4
197.0	0	4	4
198.0	0	4	4
199.0	0	1	1
201.0	0	4	4
202.0	0	1	1
203.0	0	5	5
204.0	0	3	3
205.0	0	1	1
206.0	0	2	2
207.0	0	3	3
208.0	0	1	1
210.0	0	2	2
211.0	0	4	4
212.0	0	2	2
213.0	0	2	2
214.0	0	3	3
215.0	0	4	4
216.0	0	2	2
217.0	0	3	3
218.0	0	4	4
220.0	0	2	2
221.0	0	2	2
223.0	0	2	2
224.0	0	1	1
225.0	0	2	2
226.0	0	4	4
227.0	0	1	1
228.0	0	1	1
229.0	0	2	2
230.0	0	3	3
231.0	0	3	3
232.0	0	1	1
233.0	0	4	4
234.0	0	2	2
235.0	0	1	1
236.0	0	2	2
237.0	0	2	2
238.0	0	1	1
239.0	0	1	1
244.0	0	4	4
245.0	0	1	1
246.0	0	1	1
247.0	0	1	1
248.0	0	2	2
249.0	0	2	2
250.0	0	1	1
251.0	0	3	3
253.0	0	3	3
255.0	0	1	1
257.0	0	1	1
258.0	0	2	2
260.0	0	2	2
261.0	0	3	3
263.0	0	1	1
264.0	0	1	1
266.0	0	2	2
267.0	0	3	3
268.0	0	1	1
271.0	0	2	2
274.0	0	3	3
275.0	0	2	2
276.0	0	2	2
277.0	0	2	2
281.0	0	1	1
282.0	0	3	3
284.0	0	1	1
285.0	0	1	1
286.0	0	1	1
287.0	0	1	1
288.0	0	2	2
290.0	0	2	2
291.0	0	3	3
292.0	0	2	2
294.0	0	1	1
295.0	0	1	1
300.0	0	4	4
301.0	0	2	2
308.0	0	1	1
309.0	0	1	1
311.0	0	1	1
313.0	0	4	4
315.0	0	2	2
319.0	0	3	3
323.0	0	3	3
325.0	0	1	1
329.0	0	1	1
331.0	0	1	1
332.0	0	2	2
333.0	0	1	1
334.0	0	3	3
336.0	0	1	1
337.0	0	2	2
338.0	0	2	2
339.0	0	2	2
340.0	0	1	1
341.0	0	1	1
344.0	0	1	1
348.0	0	1	1
349.0	0	2	2
350.0	0	1	1
359.0	0	1	1
360.0	0	1	1
361.0	0	1	1
365.0	0	1	1
372.0	0	1	1
374.0	0	1	1
377.0	0	3	3
379.0	0	1	1
380.0	0	1	1
381.0	0	2	2
383.0	0	1	1
390.0	0	1	1
396.0	0	1	1
401.0	0	1	1
403.0	0	1	1
405.0	0	1	1
406.0	0	1	1
411.0	0	2	2
416.0	0	1	1
418.0	0	2	2
420.0	0	2	2
427.0	0	1	1
430.0	0	1	1
431.0	0	1	1
432.0	0	1	1
434.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
439.0	0	1	1
440.0	0	1	1
444.0	0	1	1
454.0	0	1	1
455.0	0	1	1
457.0	0	1	1
461.0	0	1	1
465.0	0	1	1
472.0	0	1	1
474.0	0	1	1
475.0	0	1	1
497.0	0	2	2
501.0	0	1	1
505.0	0	1	1
508.0	0	1	1
514.0	0	1	1
517.0	0	1	1
521.0	0	1	1
532.0	0	1	1
535.0	0	1	1
548.0	0	1	1
551.0	0	1	1
556.0	0	1	1
568.0	0	1	1
572.0	0	1	1
582.0	0	1	1
583.0	0	1	1
587.0	0	1	1
596.0	0	1	1
597.0	0	2	2
599.0	0	1	1
611.0	0	2	2
616.0	0	1	1
617.0	0	1	1
623.0	0	1	1
629.0	0	1	1
633.0	0	1	1
638.0	0	1	1
639.0	0	1	1
661.0	0	1	1
662.0	0	2	2
664.0	0	1	1
669.0	0	1	1
673.0	0	1	1
675.0	0	1	1
684.0	0	1	1
688.0	0	2	2
692.0	0	1	1
703.0	0	1	1
763.0	0	1	1
770.0	0	1	1
788.0	0	1	1
800.0	0	1	1
807.0	0	1	1
817.0	0	1	1
818.0	0	1	1
819.0	0	1	1
830.0	0	1	1
861.0	0	1	1
882.0	0	1	1
885.0	0	1	1
917.0	0	1	1
932.0	0	1	1
940.0	0	1	1
1114.0	0	1	1
1128.0	0	1	1
1226.0	0	1	1
1325.0	0	1	1
1337.0	0	1	1
1454.0	0	1	1
1525.0	0	1	1
1844.0	0	1	1
1920.0	0	1	1
1951.0	0	1	1
2151.0	0	1	1