## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/PrC_14/PrC_14_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/PrC_14/PrC_14_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-worksep/Alignment/Oncobox_rna/PrC_14/PrC_14_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: Thu Oct 09 18:07:13 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	176208	32781117	607435	325806	96124	2463646	0	0.076415	207022043

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	29112637	29112637
2.0	1.853554	951604	951604
3.0	2.582109	110458	110458
4.0	3.203971	45152	45152
5.0	3.734763	25438	25438
6.0	4.187824	16118	16118
7.0	4.574535	10875	10875
8.0	4.904615	7854	7854
9.0	5.186355	5782	5782
10.0	5.426836	4396	4396
11.0	5.6321	3552	3552
12.0	5.807304	2767	2767
13.0	5.956849	2314	2314
14.0	6.084495	1868	1868
15.0	6.193447	1609	1609
16.0	6.286444	1409	1409
17.0	6.365822	1191	1191
18.0	6.433575	1031	1031
19.0	6.491406	812	812
20.0	6.540768	747	747
21.0	6.582901	656	656
22.0	6.618864	610	610
23.0	6.649561	557	557
24.0	6.675762	492	492
25.0	6.698126	491	491
26.0	6.717214	407	407
27.0	6.733508	331	331
28.0	6.747415	305	305
29.0	6.759286	280	280
30.0	6.769418	262	262
31.0	6.778066	242	242
32.0	6.785448	243	243
33.0	6.791749	226	226
34.0	6.797127	176	176
35.0	6.801718	202	202
36.0	6.805636	173	173
37.0	6.80898	172	172
38.0	6.811835	140	140
39.0	6.814272	144	144
40.0	6.816351	143	143
41.0	6.818127	117	117
42.0	6.819642	137	137
43.0	6.820935	120	120
44.0	6.822039	100	100
45.0	6.822981	100	100
46.0	6.823786	108	108
47.0	6.824472	86	86
48.0	6.825058	90	90
49.0	6.825558	83	83
50.0	6.825985	83	83
51.0	6.82635	76	76
52.0	6.826661	68	68
53.0	6.826926	56	56
54.0	6.827153	71	71
55.0	6.827346	43	43
56.0	6.827511	60	60
57.0	6.827652	52	52
58.0	6.827772	75	75
59.0	6.827875	61	61
60.0	6.827963	55	55
61.0	6.828037	48	48
62.0	6.828101	48	48
63.0	6.828156	42	42
64.0	6.828202	46	46
65.0	6.828242	37	37
66.0	6.828276	46	46
67.0	6.828305	40	40
68.0	6.828329	36	36
69.0	6.828351	33	33
70.0	6.828369	37	37
71.0	6.828384	36	36
72.0	6.828397	34	34
73.0	6.828408	19	19
74.0	6.828418	28	28
75.0	6.828426	23	23
76.0	6.828433	19	19
77.0	6.828439	29	29
78.0	6.828444	30	30
79.0	6.828448	28	28
80.0	6.828452	16	16
81.0	6.828455	23	23
82.0	6.828458	33	33
83.0	6.82846	12	12
84.0	6.828462	11	11
85.0	6.828464	21	21
86.0	6.828465	23	23
87.0	6.828466	18	18
88.0	6.828467	17	17
89.0	6.828468	11	11
90.0	6.828469	17	17
91.0	6.82847	25	25
92.0	6.82847	15	15
93.0	6.828471	11	11
94.0	6.828471	13	13
95.0	6.828471	9	9
96.0	6.828472	16	16
97.0	6.828472	17	17
98.0	6.828472	14	14
99.0	6.828472	13	13
100.0	6.828472	18	18
101.0	0	15	15
102.0	0	11	11
103.0	0	13	13
104.0	0	17	17
105.0	0	21	21
106.0	0	14	14
107.0	0	9	9
108.0	0	13	13
109.0	0	14	14
110.0	0	7	7
111.0	0	13	13
112.0	0	8	8
113.0	0	10	10
114.0	0	11	11
115.0	0	13	13
116.0	0	5	5
117.0	0	13	13
118.0	0	11	11
119.0	0	7	7
120.0	0	11	11
121.0	0	12	12
122.0	0	5	5
123.0	0	9	9
124.0	0	8	8
125.0	0	8	8
126.0	0	11	11
127.0	0	6	6
128.0	0	6	6
129.0	0	8	8
130.0	0	9	9
131.0	0	6	6
132.0	0	8	8
133.0	0	7	7
134.0	0	6	6
135.0	0	4	4
136.0	0	6	6
137.0	0	6	6
138.0	0	11	11
139.0	0	11	11
140.0	0	7	7
141.0	0	5	5
142.0	0	6	6
143.0	0	9	9
144.0	0	4	4
145.0	0	6	6
146.0	0	6	6
147.0	0	5	5
148.0	0	2	2
149.0	0	4	4
150.0	0	2	2
151.0	0	3	3
152.0	0	4	4
153.0	0	4	4
154.0	0	8	8
155.0	0	3	3
156.0	0	5	5
157.0	0	5	5
158.0	0	5	5
159.0	0	5	5
160.0	0	4	4
161.0	0	5	5
162.0	0	6	6
163.0	0	4	4
164.0	0	3	3
166.0	0	2	2
167.0	0	5	5
168.0	0	3	3
169.0	0	4	4
170.0	0	7	7
171.0	0	3	3
172.0	0	5	5
173.0	0	1	1
174.0	0	6	6
175.0	0	5	5
176.0	0	5	5
177.0	0	2	2
178.0	0	1	1
179.0	0	4	4
180.0	0	4	4
181.0	0	2	2
182.0	0	4	4
183.0	0	6	6
184.0	0	4	4
185.0	0	3	3
186.0	0	5	5
187.0	0	5	5
188.0	0	3	3
189.0	0	4	4
190.0	0	2	2
191.0	0	6	6
192.0	0	2	2
194.0	0	3	3
195.0	0	2	2
196.0	0	2	2
198.0	0	3	3
199.0	0	2	2
200.0	0	2	2
201.0	0	1	1
202.0	0	3	3
203.0	0	5	5
204.0	0	2	2
205.0	0	4	4
207.0	0	6	6
208.0	0	2	2
209.0	0	2	2
210.0	0	2	2
211.0	0	2	2
212.0	0	1	1
213.0	0	1	1
214.0	0	2	2
215.0	0	2	2
216.0	0	1	1
217.0	0	3	3
218.0	0	3	3
219.0	0	2	2
220.0	0	2	2
221.0	0	1	1
222.0	0	2	2
223.0	0	2	2
224.0	0	1	1
225.0	0	2	2
226.0	0	3	3
227.0	0	4	4
228.0	0	2	2
229.0	0	1	1
230.0	0	3	3
231.0	0	2	2
232.0	0	1	1
233.0	0	2	2
234.0	0	2	2
238.0	0	2	2
239.0	0	4	4
240.0	0	2	2
241.0	0	2	2
242.0	0	3	3
243.0	0	1	1
244.0	0	2	2
245.0	0	4	4
246.0	0	2	2
249.0	0	1	1
250.0	0	2	2
251.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	3	3
256.0	0	1	1
257.0	0	1	1
258.0	0	2	2
260.0	0	1	1
262.0	0	1	1
263.0	0	1	1
264.0	0	2	2
265.0	0	1	1
268.0	0	1	1
270.0	0	2	2
274.0	0	2	2
275.0	0	1	1
276.0	0	1	1
278.0	0	1	1
279.0	0	1	1
280.0	0	4	4
283.0	0	1	1
284.0	0	2	2
285.0	0	1	1
286.0	0	2	2
288.0	0	1	1
289.0	0	1	1
291.0	0	2	2
292.0	0	1	1
293.0	0	3	3
294.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	2	2
301.0	0	1	1
303.0	0	1	1
304.0	0	1	1
307.0	0	2	2
308.0	0	1	1
309.0	0	3	3
312.0	0	3	3
314.0	0	1	1
320.0	0	1	1
322.0	0	2	2
323.0	0	2	2
324.0	0	1	1
326.0	0	1	1
327.0	0	2	2
329.0	0	1	1
332.0	0	1	1
334.0	0	3	3
336.0	0	2	2
337.0	0	1	1
338.0	0	1	1
340.0	0	1	1
343.0	0	2	2
349.0	0	1	1
351.0	0	1	1
354.0	0	3	3
355.0	0	1	1
356.0	0	2	2
357.0	0	1	1
359.0	0	1	1
360.0	0	2	2
364.0	0	1	1
366.0	0	1	1
369.0	0	1	1
376.0	0	1	1
381.0	0	1	1
382.0	0	1	1
385.0	0	1	1
386.0	0	1	1
387.0	0	1	1
388.0	0	2	2
389.0	0	2	2
400.0	0	2	2
401.0	0	1	1
402.0	0	1	1
403.0	0	1	1
404.0	0	1	1
405.0	0	2	2
407.0	0	1	1
410.0	0	1	1
416.0	0	2	2
417.0	0	1	1
418.0	0	1	1
420.0	0	1	1
422.0	0	2	2
424.0	0	2	2
428.0	0	1	1
429.0	0	1	1
433.0	0	1	1
434.0	0	1	1
439.0	0	1	1
442.0	0	1	1
444.0	0	1	1
447.0	0	1	1
448.0	0	1	1
451.0	0	1	1
452.0	0	1	1
453.0	0	1	1
455.0	0	1	1
457.0	0	3	3
459.0	0	1	1
460.0	0	1	1
463.0	0	1	1
464.0	0	1	1
465.0	0	1	1
471.0	0	1	1
474.0	0	1	1
476.0	0	1	1
478.0	0	2	2
480.0	0	1	1
486.0	0	2	2
490.0	0	1	1
491.0	0	1	1
495.0	0	1	1
501.0	0	2	2
510.0	0	1	1
513.0	0	2	2
514.0	0	1	1
516.0	0	1	1
529.0	0	1	1
531.0	0	2	2
538.0	0	1	1
543.0	0	1	1
552.0	0	1	1
555.0	0	1	1
556.0	0	1	1
565.0	0	1	1
567.0	0	1	1
568.0	0	1	1
574.0	0	1	1
580.0	0	1	1
582.0	0	1	1
589.0	0	1	1
591.0	0	1	1
601.0	0	1	1
605.0	0	1	1
608.0	0	2	2
613.0	0	1	1
617.0	0	1	1
636.0	0	2	2
644.0	0	1	1
647.0	0	1	1
652.0	0	2	2
667.0	0	1	1
673.0	0	1	1
677.0	0	1	1
683.0	0	1	1
686.0	0	1	1
688.0	0	1	1
690.0	0	1	1
696.0	0	1	1
700.0	0	1	1
701.0	0	1	1
711.0	0	1	1
742.0	0	1	1
749.0	0	1	1
764.0	0	1	1
766.0	0	1	1
773.0	0	1	1
808.0	0	1	1
826.0	0	1	1
869.0	0	1	1
918.0	0	1	1
955.0	0	1	1
993.0	0	1	1
1001.0	0	1	1
1005.0	0	1	1
1039.0	0	1	1
1057.0	0	1	1
1076.0	0	1	1
1083.0	0	1	1
1122.0	0	1	1
1137.0	0	1	1
1149.0	0	1	1
1156.0	0	1	1
1180.0	0	1	1
1231.0	0	1	1
1288.0	0	1	1
1339.0	0	1	1
1354.0	0	1	1
1502.0	0	1	1
1615.0	0	1	1