## 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_supernatant_TA1uM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_TA1uM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_TA1uM_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 03:41:19 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	753	17650790	17559270	0	661	2716887	0	0.15394	51287550

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	13893297	13893297
2.0	1.70882	706129	706129
3.0	2.211246	142339	142339
4.0	2.567376	61559	61559
5.0	2.819808	33981	33981
6.0	2.998736	21352	21352
7.0	3.125565	14221	14221
8.0	3.215463	10223	10223
9.0	3.279185	7734	7734
10.0	3.324352	5892	5892
11.0	3.356368	4637	4637
12.0	3.379061	3683	3683
13.0	3.395146	3064	3064
14.0	3.406548	2541	2541
15.0	3.41463	2131	2131
16.0	3.420358	1830	1830
17.0	3.424419	1590	1590
18.0	3.427297	1371	1371
19.0	3.429337	1188	1188
20.0	3.430783	1120	1120
21.0	3.431808	944	944
22.0	3.432535	862	862
23.0	3.43305	720	720
24.0	3.433415	650	650
25.0	3.433673	621	621
26.0	3.433857	561	561
27.0	3.433987	502	502
28.0	3.434079	520	520
29.0	3.434144	466	466
30.0	3.43419	409	409
31.0	3.434223	358	358
32.0	3.434247	336	336
33.0	3.434263	311	311
34.0	3.434275	284	284
35.0	3.434283	279	279
36.0	3.434289	235	235
37.0	3.434293	238	238
38.0	3.434296	228	228
39.0	3.434298	187	187
40.0	3.4343	195	195
41.0	3.434301	169	169
42.0	3.434301	196	196
43.0	3.434302	146	146
44.0	3.434302	162	162
45.0	3.434302	136	136
46.0	3.434303	147	147
47.0	3.434303	136	136
48.0	3.434303	132	132
49.0	3.434303	134	134
50.0	3.434303	107	107
51.0	3.434303	112	112
52.0	3.434303	116	116
53.0	3.434303	95	95
54.0	3.434303	94	94
55.0	3.434303	92	92
56.0	3.434303	96	96
57.0	3.434303	81	81
58.0	3.434303	68	68
59.0	3.434303	72	72
60.0	3.434303	84	84
61.0	3.434303	59	59
62.0	3.434303	57	57
63.0	3.434303	76	76
64.0	3.434303	63	63
65.0	3.434303	61	61
66.0	3.434303	45	45
67.0	3.434303	54	54
68.0	3.434303	49	49
69.0	3.434303	42	42
70.0	3.434303	44	44
71.0	3.434303	46	46
72.0	3.434303	34	34
73.0	3.434303	32	32
74.0	3.434303	37	37
75.0	3.434303	42	42
76.0	3.434303	45	45
77.0	3.434303	40	40
78.0	3.434303	40	40
79.0	3.434303	35	35
80.0	3.434303	32	32
81.0	3.434303	32	32
82.0	3.434303	30	30
83.0	3.434303	38	38
84.0	3.434303	34	34
85.0	3.434303	35	35
86.0	3.434303	30	30
87.0	3.434303	26	26
88.0	3.434303	33	33
89.0	3.434303	31	31
90.0	3.434303	31	31
91.0	3.434303	19	19
92.0	3.434303	25	25
93.0	3.434303	20	20
94.0	3.434303	21	21
95.0	3.434303	30	30
96.0	3.434303	24	24
97.0	3.434303	23	23
98.0	3.434303	22	22
99.0	3.434303	15	15
100.0	3.434303	20	20
101.0	0	25	25
102.0	0	16	16
103.0	0	17	17
104.0	0	23	23
105.0	0	17	17
106.0	0	14	14
107.0	0	17	17
108.0	0	25	25
109.0	0	14	14
110.0	0	11	11
111.0	0	12	12
112.0	0	19	19
113.0	0	22	22
114.0	0	17	17
115.0	0	17	17
116.0	0	11	11
117.0	0	14	14
118.0	0	16	16
119.0	0	10	10
120.0	0	15	15
121.0	0	18	18
122.0	0	16	16
123.0	0	10	10
124.0	0	12	12
125.0	0	14	14
126.0	0	13	13
127.0	0	13	13
128.0	0	11	11
129.0	0	13	13
130.0	0	13	13
131.0	0	14	14
132.0	0	10	10
133.0	0	13	13
134.0	0	10	10
135.0	0	10	10
136.0	0	9	9
137.0	0	13	13
138.0	0	11	11
139.0	0	12	12
140.0	0	6	6
141.0	0	12	12
142.0	0	9	9
143.0	0	10	10
144.0	0	9	9
145.0	0	8	8
146.0	0	8	8
147.0	0	6	6
148.0	0	8	8
149.0	0	9	9
150.0	0	7	7
151.0	0	7	7
152.0	0	7	7
153.0	0	8	8
154.0	0	13	13
155.0	0	4	4
156.0	0	7	7
157.0	0	7	7
158.0	0	7	7
159.0	0	1	1
160.0	0	10	10
161.0	0	10	10
162.0	0	6	6
163.0	0	7	7
164.0	0	4	4
165.0	0	10	10
166.0	0	3	3
167.0	0	4	4
168.0	0	3	3
169.0	0	8	8
170.0	0	3	3
171.0	0	5	5
172.0	0	11	11
173.0	0	5	5
174.0	0	3	3
175.0	0	9	9
176.0	0	4	4
177.0	0	3	3
178.0	0	12	12
179.0	0	2	2
180.0	0	3	3
181.0	0	6	6
182.0	0	2	2
183.0	0	2	2
184.0	0	6	6
185.0	0	4	4
186.0	0	4	4
187.0	0	2	2
188.0	0	3	3
189.0	0	1	1
190.0	0	5	5
191.0	0	5	5
192.0	0	4	4
193.0	0	2	2
194.0	0	2	2
195.0	0	5	5
196.0	0	2	2
197.0	0	3	3
198.0	0	1	1
199.0	0	5	5
200.0	0	3	3
201.0	0	5	5
202.0	0	4	4
203.0	0	3	3
204.0	0	5	5
205.0	0	1	1
206.0	0	3	3
207.0	0	5	5
208.0	0	4	4
209.0	0	4	4
210.0	0	1	1
211.0	0	2	2
212.0	0	2	2
213.0	0	4	4
214.0	0	1	1
215.0	0	2	2
216.0	0	3	3
217.0	0	7	7
218.0	0	2	2
219.0	0	4	4
220.0	0	1	1
221.0	0	5	5
222.0	0	3	3
223.0	0	3	3
224.0	0	1	1
225.0	0	3	3
226.0	0	3	3
227.0	0	1	1
228.0	0	2	2
229.0	0	4	4
230.0	0	1	1
231.0	0	3	3
232.0	0	2	2
233.0	0	2	2
234.0	0	4	4
235.0	0	1	1
236.0	0	3	3
237.0	0	4	4
238.0	0	3	3
239.0	0	1	1
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	5	5
244.0	0	1	1
245.0	0	2	2
246.0	0	3	3
247.0	0	2	2
248.0	0	3	3
249.0	0	2	2
250.0	0	1	1
251.0	0	2	2
252.0	0	2	2
253.0	0	2	2
254.0	0	1	1
256.0	0	2	2
257.0	0	1	1
258.0	0	3	3
259.0	0	2	2
260.0	0	2	2
261.0	0	1	1
262.0	0	2	2
263.0	0	1	1
264.0	0	4	4
265.0	0	1	1
266.0	0	2	2
268.0	0	2	2
272.0	0	3	3
274.0	0	1	1
275.0	0	2	2
276.0	0	1	1
279.0	0	3	3
280.0	0	2	2
281.0	0	1	1
282.0	0	2	2
284.0	0	1	1
287.0	0	1	1
288.0	0	1	1
289.0	0	2	2
292.0	0	1	1
293.0	0	1	1
294.0	0	2	2
295.0	0	1	1
298.0	0	4	4
299.0	0	1	1
300.0	0	1	1
303.0	0	1	1
305.0	0	3	3
306.0	0	3	3
307.0	0	2	2
308.0	0	1	1
310.0	0	1	1
314.0	0	2	2
315.0	0	1	1
316.0	0	2	2
317.0	0	1	1
318.0	0	4	4
321.0	0	1	1
322.0	0	2	2
323.0	0	1	1
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
328.0	0	1	1
332.0	0	1	1
333.0	0	3	3
334.0	0	1	1
335.0	0	2	2
336.0	0	2	2
341.0	0	2	2
345.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	1	1
355.0	0	1	1
358.0	0	1	1
359.0	0	1	1
361.0	0	1	1
363.0	0	1	1
367.0	0	1	1
368.0	0	2	2
369.0	0	2	2
370.0	0	2	2
373.0	0	3	3
374.0	0	1	1
375.0	0	2	2
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
381.0	0	1	1
385.0	0	1	1
386.0	0	1	1
390.0	0	1	1
396.0	0	2	2
402.0	0	2	2
403.0	0	1	1
411.0	0	1	1
413.0	0	1	1
417.0	0	1	1
419.0	0	1	1
420.0	0	1	1
427.0	0	1	1
430.0	0	1	1
433.0	0	1	1
439.0	0	1	1
445.0	0	1	1
453.0	0	1	1
457.0	0	2	2
458.0	0	1	1
459.0	0	2	2
470.0	0	1	1
476.0	0	1	1
479.0	0	1	1
485.0	0	1	1
497.0	0	2	2
499.0	0	1	1
501.0	0	1	1
513.0	0	1	1
515.0	0	1	1
519.0	0	1	1
521.0	0	1	1
528.0	0	1	1
529.0	0	1	1
538.0	0	2	2
544.0	0	1	1
548.0	0	1	1
551.0	0	1	1
555.0	0	1	1
580.0	0	1	1
588.0	0	1	1
589.0	0	1	1
592.0	0	1	1
597.0	0	2	2
599.0	0	1	1
606.0	0	1	1
608.0	0	1	1
615.0	0	1	1
640.0	0	1	1
643.0	0	1	1
650.0	0	1	1
661.0	0	1	1
662.0	0	1	1
675.0	0	1	1
684.0	0	1	1
688.0	0	1	1
691.0	0	1	1
693.0	0	1	1
696.0	0	1	1
704.0	0	1	1
734.0	0	1	1
738.0	0	1	1
740.0	0	1	1
750.0	0	1	1
756.0	0	1	1
758.0	0	1	1
761.0	0	1	1
775.0	0	1	1
831.0	0	1	1
869.0	0	1	1
877.0	0	1	1
887.0	0	1	1
896.0	0	1	1
897.0	0	1	1
932.0	0	1	1
953.0	0	1	1
970.0	0	1	1
1065.0	0	1	1
1092.0	0	1	1
1119.0	0	1	1
1178.0	0	1	1
1333.0	0	1	1
1428.0	0	1	1
1545.0	0	1	1
1635.0	0	1	1
1643.0	0	1	1
2546.0	0	1	1
3016.0	0	1	1