## 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-D1_adherent_TA_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D1_adherent_TA_DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D1_adherent_TA_DMSO_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 02:13:43 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	1230	23950461	71598311	0	1056	6076995	0	0.253747	38820079

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	16046324	16046324
2.0	1.539582	1226821	1226821
3.0	1.830731	222194	222194
4.0	1.987829	96875	96875
5.0	2.072597	57643	57643
6.0	2.118336	39308	39308
7.0	2.143016	28148	28148
8.0	2.156333	21404	21404
9.0	2.163518	16787	16787
10.0	2.167395	13204	13204
11.0	2.169487	11022	11022
12.0	2.170616	9066	9066
13.0	2.171225	7803	7803
14.0	2.171554	6606	6606
15.0	2.171731	5695	5695
16.0	2.171827	4990	4990
17.0	2.171879	4340	4340
18.0	2.171906	4015	4015
19.0	2.171921	3454	3454
20.0	2.17193	3020	3020
21.0	2.171934	2782	2782
22.0	2.171936	2538	2538
23.0	2.171938	2245	2245
24.0	2.171938	2025	2025
25.0	2.171939	1872	1872
26.0	2.171939	1698	1698
27.0	2.171939	1615	1615
28.0	2.171939	1419	1419
29.0	2.171939	1316	1316
30.0	2.171939	1246	1246
31.0	2.171939	1207	1207
32.0	2.171939	1064	1064
33.0	2.171939	1021	1021
34.0	2.171939	974	974
35.0	2.171939	904	904
36.0	2.171939	845	845
37.0	2.171939	771	771
38.0	2.171939	706	706
39.0	2.171939	688	688
40.0	2.171939	680	680
41.0	2.171939	594	594
42.0	2.171939	558	558
43.0	2.171939	545	545
44.0	2.171939	481	481
45.0	2.171939	491	491
46.0	2.171939	426	426
47.0	2.171939	463	463
48.0	2.171939	436	436
49.0	2.171939	411	411
50.0	2.171939	376	376
51.0	2.171939	355	355
52.0	2.171939	362	362
53.0	2.171939	360	360
54.0	2.171939	353	353
55.0	2.171939	304	304
56.0	2.171939	318	318
57.0	2.171939	307	307
58.0	2.171939	237	237
59.0	2.171939	277	277
60.0	2.171939	229	229
61.0	2.171939	239	239
62.0	2.171939	219	219
63.0	2.171939	229	229
64.0	2.171939	206	206
65.0	2.171939	185	185
66.0	2.171939	180	180
67.0	2.171939	178	178
68.0	2.171939	166	166
69.0	2.171939	185	185
70.0	2.171939	171	171
71.0	2.171939	157	157
72.0	2.171939	166	166
73.0	2.171939	163	163
74.0	2.171939	141	141
75.0	2.171939	142	142
76.0	2.171939	131	131
77.0	2.171939	115	115
78.0	2.171939	145	145
79.0	2.171939	136	136
80.0	2.171939	109	109
81.0	2.171939	139	139
82.0	2.171939	115	115
83.0	2.171939	118	118
84.0	2.171939	104	104
85.0	2.171939	98	98
86.0	2.171939	114	114
87.0	2.171939	113	113
88.0	2.171939	98	98
89.0	2.171939	95	95
90.0	2.171939	91	91
91.0	2.171939	64	64
92.0	2.171939	92	92
93.0	2.171939	73	73
94.0	2.171939	103	103
95.0	2.171939	71	71
96.0	2.171939	86	86
97.0	2.171939	83	83
98.0	2.171939	58	58
99.0	2.171939	63	63
100.0	2.171939	59	59
101.0	0	75	75
102.0	0	75	75
103.0	0	69	69
104.0	0	48	48
105.0	0	53	53
106.0	0	48	48
107.0	0	53	53
108.0	0	65	65
109.0	0	66	66
110.0	0	60	60
111.0	0	58	58
112.0	0	64	64
113.0	0	44	44
114.0	0	53	53
115.0	0	45	45
116.0	0	44	44
117.0	0	48	48
118.0	0	54	54
119.0	0	42	42
120.0	0	43	43
121.0	0	60	60
122.0	0	37	37
123.0	0	51	51
124.0	0	38	38
125.0	0	46	46
126.0	0	32	32
127.0	0	42	42
128.0	0	35	35
129.0	0	36	36
130.0	0	33	33
131.0	0	27	27
132.0	0	46	46
133.0	0	28	28
134.0	0	36	36
135.0	0	36	36
136.0	0	29	29
137.0	0	30	30
138.0	0	33	33
139.0	0	30	30
140.0	0	25	25
141.0	0	33	33
142.0	0	25	25
143.0	0	39	39
144.0	0	21	21
145.0	0	31	31
146.0	0	32	32
147.0	0	18	18
148.0	0	26	26
149.0	0	19	19
150.0	0	18	18
151.0	0	28	28
152.0	0	19	19
153.0	0	26	26
154.0	0	21	21
155.0	0	22	22
156.0	0	18	18
157.0	0	26	26
158.0	0	32	32
159.0	0	23	23
160.0	0	13	13
161.0	0	21	21
162.0	0	18	18
163.0	0	27	27
164.0	0	17	17
165.0	0	18	18
166.0	0	26	26
167.0	0	23	23
168.0	0	17	17
169.0	0	16	16
170.0	0	21	21
171.0	0	20	20
172.0	0	22	22
173.0	0	24	24
174.0	0	12	12
175.0	0	14	14
176.0	0	15	15
177.0	0	10	10
178.0	0	12	12
179.0	0	16	16
180.0	0	14	14
181.0	0	17	17
182.0	0	13	13
183.0	0	15	15
184.0	0	20	20
185.0	0	10	10
186.0	0	14	14
187.0	0	17	17
188.0	0	19	19
189.0	0	10	10
190.0	0	15	15
191.0	0	11	11
192.0	0	9	9
193.0	0	15	15
194.0	0	22	22
195.0	0	8	8
196.0	0	12	12
197.0	0	11	11
198.0	0	13	13
199.0	0	5	5
200.0	0	12	12
201.0	0	13	13
202.0	0	6	6
203.0	0	7	7
204.0	0	12	12
205.0	0	9	9
206.0	0	10	10
207.0	0	16	16
208.0	0	12	12
209.0	0	9	9
210.0	0	15	15
211.0	0	12	12
212.0	0	13	13
213.0	0	12	12
214.0	0	11	11
215.0	0	14	14
216.0	0	6	6
217.0	0	9	9
218.0	0	6	6
219.0	0	12	12
220.0	0	11	11
221.0	0	7	7
222.0	0	6	6
223.0	0	7	7
224.0	0	9	9
225.0	0	11	11
226.0	0	7	7
227.0	0	4	4
228.0	0	2	2
229.0	0	10	10
230.0	0	2	2
231.0	0	6	6
232.0	0	2	2
233.0	0	6	6
234.0	0	9	9
235.0	0	8	8
236.0	0	10	10
237.0	0	6	6
238.0	0	9	9
239.0	0	6	6
240.0	0	9	9
241.0	0	3	3
242.0	0	7	7
243.0	0	5	5
244.0	0	4	4
245.0	0	3	3
246.0	0	8	8
247.0	0	6	6
248.0	0	7	7
249.0	0	7	7
250.0	0	3	3
251.0	0	3	3
252.0	0	8	8
253.0	0	4	4
254.0	0	6	6
255.0	0	4	4
256.0	0	7	7
257.0	0	1	1
258.0	0	9	9
259.0	0	6	6
260.0	0	11	11
261.0	0	4	4
262.0	0	5	5
263.0	0	7	7
264.0	0	3	3
265.0	0	7	7
266.0	0	6	6
267.0	0	2	2
268.0	0	6	6
269.0	0	1	1
270.0	0	1	1
271.0	0	4	4
272.0	0	3	3
273.0	0	3	3
274.0	0	5	5
275.0	0	3	3
276.0	0	4	4
277.0	0	3	3
279.0	0	1	1
280.0	0	4	4
281.0	0	2	2
282.0	0	7	7
283.0	0	5	5
284.0	0	2	2
285.0	0	4	4
286.0	0	2	2
287.0	0	3	3
288.0	0	2	2
289.0	0	6	6
290.0	0	2	2
291.0	0	3	3
293.0	0	5	5
294.0	0	3	3
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	4	4
299.0	0	3	3
300.0	0	3	3
301.0	0	4	4
302.0	0	2	2
303.0	0	3	3
304.0	0	2	2
305.0	0	3	3
306.0	0	2	2
307.0	0	3	3
308.0	0	4	4
309.0	0	2	2
310.0	0	5	5
311.0	0	4	4
312.0	0	4	4
313.0	0	2	2
314.0	0	6	6
315.0	0	7	7
316.0	0	4	4
317.0	0	2	2
318.0	0	2	2
319.0	0	2	2
320.0	0	4	4
321.0	0	4	4
322.0	0	4	4
323.0	0	5	5
324.0	0	3	3
326.0	0	2	2
327.0	0	5	5
328.0	0	4	4
329.0	0	5	5
330.0	0	4	4
331.0	0	3	3
333.0	0	1	1
334.0	0	2	2
335.0	0	2	2
336.0	0	4	4
337.0	0	3	3
338.0	0	3	3
339.0	0	2	2
340.0	0	6	6
341.0	0	3	3
342.0	0	2	2
344.0	0	3	3
345.0	0	3	3
346.0	0	1	1
347.0	0	2	2
348.0	0	1	1
349.0	0	3	3
350.0	0	2	2
351.0	0	1	1
354.0	0	2	2
355.0	0	1	1
356.0	0	1	1
357.0	0	2	2
358.0	0	3	3
359.0	0	4	4
360.0	0	1	1
361.0	0	2	2
364.0	0	3	3
365.0	0	2	2
366.0	0	1	1
367.0	0	2	2
369.0	0	1	1
370.0	0	1	1
371.0	0	2	2
372.0	0	5	5
373.0	0	5	5
374.0	0	3	3
375.0	0	3	3
376.0	0	3	3
377.0	0	3	3
379.0	0	1	1
380.0	0	1	1
381.0	0	1	1
383.0	0	2	2
384.0	0	2	2
386.0	0	1	1
387.0	0	1	1
390.0	0	2	2
391.0	0	3	3
392.0	0	2	2
393.0	0	4	4
394.0	0	2	2
396.0	0	1	1
398.0	0	1	1
399.0	0	3	3
400.0	0	1	1
401.0	0	3	3
404.0	0	2	2
405.0	0	1	1
406.0	0	2	2
407.0	0	1	1
408.0	0	2	2
409.0	0	2	2
410.0	0	1	1
413.0	0	3	3
414.0	0	1	1
415.0	0	2	2
416.0	0	2	2
419.0	0	3	3
420.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	2	2
425.0	0	3	3
426.0	0	3	3
427.0	0	1	1
428.0	0	2	2
430.0	0	1	1
435.0	0	1	1
436.0	0	2	2
437.0	0	1	1
438.0	0	3	3
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	1	1
444.0	0	3	3
445.0	0	1	1
447.0	0	2	2
451.0	0	2	2
452.0	0	2	2
453.0	0	2	2
455.0	0	1	1
457.0	0	2	2
458.0	0	1	1
459.0	0	2	2
460.0	0	2	2
462.0	0	4	4
463.0	0	1	1
465.0	0	1	1
466.0	0	1	1
468.0	0	1	1
469.0	0	1	1
470.0	0	1	1
473.0	0	1	1
476.0	0	1	1
477.0	0	2	2
478.0	0	1	1
479.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	2	2
487.0	0	1	1
488.0	0	3	3
491.0	0	1	1
495.0	0	1	1
496.0	0	2	2
497.0	0	3	3
499.0	0	1	1
500.0	0	2	2
503.0	0	1	1
506.0	0	1	1
507.0	0	2	2
508.0	0	1	1
510.0	0	1	1
511.0	0	1	1
514.0	0	1	1
515.0	0	2	2
517.0	0	2	2
520.0	0	1	1
521.0	0	1	1
524.0	0	1	1
527.0	0	2	2
530.0	0	2	2
534.0	0	1	1
536.0	0	1	1
538.0	0	3	3
539.0	0	1	1
541.0	0	1	1
546.0	0	2	2
547.0	0	1	1
548.0	0	3	3
552.0	0	1	1
553.0	0	1	1
554.0	0	2	2
558.0	0	1	1
561.0	0	2	2
562.0	0	1	1
563.0	0	1	1
564.0	0	1	1
565.0	0	1	1
567.0	0	2	2
569.0	0	1	1
575.0	0	1	1
578.0	0	1	1
579.0	0	2	2
580.0	0	1	1
581.0	0	1	1
590.0	0	1	1
592.0	0	3	3
597.0	0	1	1
598.0	0	1	1
599.0	0	1	1
603.0	0	1	1
605.0	0	1	1
609.0	0	1	1
610.0	0	1	1
621.0	0	1	1
624.0	0	1	1
625.0	0	3	3
626.0	0	1	1
633.0	0	2	2
643.0	0	1	1
644.0	0	2	2
651.0	0	1	1
652.0	0	1	1
654.0	0	1	1
657.0	0	1	1
659.0	0	1	1
661.0	0	2	2
664.0	0	2	2
666.0	0	1	1
670.0	0	1	1
671.0	0	1	1
686.0	0	1	1
687.0	0	1	1
688.0	0	1	1
689.0	0	1	1
691.0	0	1	1
698.0	0	1	1
705.0	0	2	2
706.0	0	1	1
710.0	0	1	1
712.0	0	1	1
716.0	0	1	1
717.0	0	1	1
720.0	0	1	1
727.0	0	1	1
732.0	0	2	2
736.0	0	1	1
739.0	0	1	1
746.0	0	1	1
747.0	0	1	1
758.0	0	1	1
768.0	0	1	1
769.0	0	1	1
779.0	0	1	1
788.0	0	1	1
790.0	0	1	1
794.0	0	1	1
796.0	0	1	1
804.0	0	1	1
806.0	0	1	1
813.0	0	1	1
838.0	0	1	1
843.0	0	1	1
844.0	0	1	1
850.0	0	1	1
866.0	0	1	1
875.0	0	1	1
881.0	0	1	1
884.0	0	1	1
886.0	0	1	1
891.0	0	1	1
898.0	0	1	1
908.0	0	1	1
911.0	0	1	1
915.0	0	1	1
926.0	0	1	1
931.0	0	1	1
960.0	0	1	1
983.0	0	1	1
996.0	0	1	1
1007.0	0	1	1
1012.0	0	1	1
1026.0	0	1	1
1035.0	0	1	1
1050.0	0	1	1
1117.0	0	1	1
1148.0	0	1	1
1168.0	0	1	1
1213.0	0	1	1
1257.0	0	1	1
1293.0	0	1	1
1312.0	0	1	1
1379.0	0	1	1
1411.0	0	1	1
1493.0	0	1	1
1535.0	0	1	1
1710.0	0	1	1
1799.0	0	1	1
1977.0	0	1	1
2199.0	0	2	2
2796.0	0	1	1
3200.0	0	1	1
3298.0	0	1	1
4256.0	0	1	1