## 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/star/GRCh38.p13-RU1uMTA100nM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uMTA100nM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uMTA100nM_3.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: Wed Oct 04 10:41:50 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	696	40336812	24389805	0	577	6976739	0	0.172968	102732252

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30597919	30597919
2.0	1.675272	1933278	1933278
3.0	2.131263	361392	361392
4.0	2.439182	149634	149634
5.0	2.64711	82357	82357
6.0	2.787519	51520	51520
7.0	2.882332	35203	35203
8.0	2.946357	25542	25542
9.0	2.989592	18606	18606
10.0	3.018787	14420	14420
11.0	3.038501	11415	11415
12.0	3.051814	9282	9282
13.0	3.060803	7489	7489
14.0	3.066874	6166	6166
15.0	3.070973	5247	5247
16.0	3.073741	4388	4388
17.0	3.07561	3896	3896
18.0	3.076872	3336	3336
19.0	3.077725	2946	2946
20.0	3.0783	2621	2621
21.0	3.078689	2421	2421
22.0	3.078951	1986	1986
23.0	3.079129	1866	1866
24.0	3.079248	1679	1679
25.0	3.079329	1515	1515
26.0	3.079384	1342	1342
27.0	3.079421	1261	1261
28.0	3.079445	1157	1157
29.0	3.079462	998	998
30.0	3.079474	895	895
31.0	3.079481	859	859
32.0	3.079486	840	840
33.0	3.07949	709	709
34.0	3.079492	638	638
35.0	3.079494	609	609
36.0	3.079495	566	566
37.0	3.079496	545	545
38.0	3.079496	528	528
39.0	3.079497	462	462
40.0	3.079497	445	445
41.0	3.079497	414	414
42.0	3.079497	398	398
43.0	3.079497	312	312
44.0	3.079497	393	393
45.0	3.079497	345	345
46.0	3.079497	319	319
47.0	3.079497	290	290
48.0	3.079497	288	288
49.0	3.079497	277	277
50.0	3.079497	278	278
51.0	3.079497	247	247
52.0	3.079497	210	210
53.0	3.079497	229	229
54.0	3.079497	179	179
55.0	3.079497	207	207
56.0	3.079497	184	184
57.0	3.079497	200	200
58.0	3.079497	192	192
59.0	3.079497	165	165
60.0	3.079497	155	155
61.0	3.079497	194	194
62.0	3.079497	142	142
63.0	3.079497	134	134
64.0	3.079497	130	130
65.0	3.079497	145	145
66.0	3.079497	128	128
67.0	3.079497	126	126
68.0	3.079497	134	134
69.0	3.079497	122	122
70.0	3.079497	117	117
71.0	3.079497	109	109
72.0	3.079497	133	133
73.0	3.079497	95	95
74.0	3.079497	96	96
75.0	3.079497	102	102
76.0	3.079497	81	81
77.0	3.079497	102	102
78.0	3.079497	71	71
79.0	3.079497	74	74
80.0	3.079497	63	63
81.0	3.079497	70	70
82.0	3.079497	85	85
83.0	3.079497	68	68
84.0	3.079497	85	85
85.0	3.079497	72	72
86.0	3.079497	61	61
87.0	3.079497	72	72
88.0	3.079497	68	68
89.0	3.079497	70	70
90.0	3.079497	65	65
91.0	3.079497	55	55
92.0	3.079497	59	59
93.0	3.079497	62	62
94.0	3.079497	54	54
95.0	3.079497	48	48
96.0	3.079497	54	54
97.0	3.079497	58	58
98.0	3.079497	45	45
99.0	3.079497	44	44
100.0	3.079497	54	54
101.0	0	36	36
102.0	0	54	54
103.0	0	43	43
104.0	0	59	59
105.0	0	54	54
106.0	0	42	42
107.0	0	35	35
108.0	0	40	40
109.0	0	22	22
110.0	0	28	28
111.0	0	37	37
112.0	0	39	39
113.0	0	44	44
114.0	0	33	33
115.0	0	33	33
116.0	0	26	26
117.0	0	35	35
118.0	0	26	26
119.0	0	32	32
120.0	0	24	24
121.0	0	39	39
122.0	0	31	31
123.0	0	28	28
124.0	0	31	31
125.0	0	29	29
126.0	0	23	23
127.0	0	30	30
128.0	0	22	22
129.0	0	30	30
130.0	0	25	25
131.0	0	14	14
132.0	0	23	23
133.0	0	29	29
134.0	0	27	27
135.0	0	23	23
136.0	0	21	21
137.0	0	24	24
138.0	0	27	27
139.0	0	22	22
140.0	0	19	19
141.0	0	19	19
142.0	0	23	23
143.0	0	13	13
144.0	0	18	18
145.0	0	21	21
146.0	0	15	15
147.0	0	20	20
148.0	0	16	16
149.0	0	18	18
150.0	0	25	25
151.0	0	20	20
152.0	0	16	16
153.0	0	12	12
154.0	0	9	9
155.0	0	15	15
156.0	0	19	19
157.0	0	10	10
158.0	0	20	20
159.0	0	13	13
160.0	0	14	14
161.0	0	12	12
162.0	0	19	19
163.0	0	15	15
164.0	0	12	12
165.0	0	13	13
166.0	0	13	13
167.0	0	13	13
168.0	0	5	5
169.0	0	20	20
170.0	0	17	17
171.0	0	12	12
172.0	0	7	7
173.0	0	12	12
174.0	0	10	10
175.0	0	14	14
176.0	0	12	12
177.0	0	6	6
178.0	0	10	10
179.0	0	13	13
180.0	0	12	12
181.0	0	11	11
182.0	0	21	21
183.0	0	12	12
184.0	0	11	11
185.0	0	16	16
186.0	0	8	8
187.0	0	10	10
188.0	0	10	10
189.0	0	13	13
190.0	0	8	8
191.0	0	7	7
192.0	0	17	17
193.0	0	10	10
194.0	0	10	10
195.0	0	10	10
196.0	0	7	7
197.0	0	6	6
198.0	0	12	12
199.0	0	13	13
200.0	0	9	9
201.0	0	14	14
202.0	0	4	4
203.0	0	11	11
204.0	0	14	14
205.0	0	5	5
206.0	0	8	8
207.0	0	7	7
208.0	0	7	7
209.0	0	7	7
210.0	0	7	7
211.0	0	7	7
212.0	0	7	7
213.0	0	5	5
214.0	0	8	8
215.0	0	12	12
216.0	0	18	18
217.0	0	7	7
218.0	0	9	9
219.0	0	10	10
220.0	0	7	7
221.0	0	13	13
222.0	0	12	12
223.0	0	5	5
224.0	0	10	10
225.0	0	8	8
226.0	0	7	7
227.0	0	8	8
228.0	0	6	6
229.0	0	4	4
230.0	0	4	4
231.0	0	2	2
232.0	0	3	3
233.0	0	5	5
234.0	0	6	6
235.0	0	7	7
236.0	0	5	5
237.0	0	7	7
238.0	0	9	9
239.0	0	5	5
240.0	0	7	7
241.0	0	7	7
242.0	0	2	2
243.0	0	2	2
244.0	0	4	4
245.0	0	6	6
246.0	0	3	3
247.0	0	5	5
248.0	0	7	7
249.0	0	8	8
250.0	0	5	5
251.0	0	9	9
252.0	0	5	5
253.0	0	7	7
254.0	0	3	3
255.0	0	7	7
256.0	0	4	4
257.0	0	6	6
258.0	0	3	3
259.0	0	7	7
260.0	0	4	4
261.0	0	6	6
262.0	0	3	3
263.0	0	5	5
264.0	0	8	8
265.0	0	4	4
266.0	0	5	5
267.0	0	2	2
268.0	0	2	2
269.0	0	5	5
270.0	0	2	2
271.0	0	2	2
272.0	0	4	4
273.0	0	4	4
274.0	0	7	7
275.0	0	5	5
276.0	0	5	5
277.0	0	7	7
278.0	0	3	3
279.0	0	1	1
280.0	0	8	8
281.0	0	6	6
282.0	0	6	6
283.0	0	3	3
284.0	0	3	3
285.0	0	6	6
286.0	0	2	2
287.0	0	3	3
288.0	0	7	7
289.0	0	3	3
290.0	0	4	4
291.0	0	3	3
292.0	0	4	4
293.0	0	1	1
294.0	0	3	3
295.0	0	2	2
296.0	0	4	4
297.0	0	3	3
298.0	0	2	2
299.0	0	5	5
300.0	0	2	2
301.0	0	2	2
302.0	0	2	2
303.0	0	3	3
304.0	0	5	5
305.0	0	5	5
306.0	0	7	7
307.0	0	2	2
308.0	0	4	4
309.0	0	5	5
310.0	0	2	2
311.0	0	3	3
312.0	0	3	3
313.0	0	4	4
314.0	0	2	2
315.0	0	2	2
316.0	0	2	2
317.0	0	5	5
318.0	0	1	1
319.0	0	3	3
320.0	0	1	1
321.0	0	3	3
322.0	0	3	3
323.0	0	3	3
324.0	0	1	1
325.0	0	4	4
326.0	0	2	2
328.0	0	3	3
329.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	4	4
333.0	0	6	6
334.0	0	4	4
335.0	0	3	3
336.0	0	2	2
337.0	0	3	3
338.0	0	3	3
339.0	0	1	1
340.0	0	3	3
341.0	0	3	3
342.0	0	5	5
343.0	0	4	4
344.0	0	3	3
345.0	0	5	5
346.0	0	4	4
347.0	0	3	3
348.0	0	5	5
349.0	0	1	1
350.0	0	2	2
351.0	0	1	1
353.0	0	4	4
354.0	0	6	6
355.0	0	6	6
356.0	0	2	2
358.0	0	2	2
359.0	0	2	2
360.0	0	1	1
361.0	0	4	4
363.0	0	1	1
364.0	0	4	4
365.0	0	4	4
366.0	0	3	3
367.0	0	2	2
368.0	0	3	3
369.0	0	2	2
370.0	0	3	3
371.0	0	3	3
372.0	0	2	2
373.0	0	1	1
374.0	0	3	3
375.0	0	4	4
376.0	0	3	3
377.0	0	3	3
378.0	0	2	2
379.0	0	4	4
380.0	0	1	1
381.0	0	6	6
382.0	0	1	1
383.0	0	4	4
384.0	0	1	1
385.0	0	2	2
386.0	0	2	2
387.0	0	3	3
389.0	0	2	2
390.0	0	3	3
392.0	0	3	3
393.0	0	6	6
394.0	0	4	4
395.0	0	1	1
396.0	0	3	3
398.0	0	1	1
399.0	0	1	1
400.0	0	4	4
401.0	0	2	2
402.0	0	2	2
405.0	0	2	2
406.0	0	2	2
407.0	0	2	2
408.0	0	1	1
409.0	0	3	3
411.0	0	3	3
412.0	0	2	2
413.0	0	1	1
414.0	0	3	3
415.0	0	1	1
416.0	0	2	2
418.0	0	1	1
420.0	0	3	3
421.0	0	1	1
422.0	0	2	2
423.0	0	2	2
424.0	0	1	1
425.0	0	1	1
426.0	0	3	3
427.0	0	2	2
428.0	0	2	2
429.0	0	2	2
430.0	0	3	3
431.0	0	3	3
433.0	0	4	4
434.0	0	2	2
437.0	0	1	1
438.0	0	2	2
440.0	0	2	2
441.0	0	1	1
442.0	0	2	2
443.0	0	5	5
444.0	0	2	2
445.0	0	1	1
446.0	0	2	2
447.0	0	1	1
448.0	0	1	1
450.0	0	1	1
451.0	0	2	2
452.0	0	1	1
453.0	0	2	2
454.0	0	2	2
455.0	0	2	2
458.0	0	1	1
460.0	0	2	2
461.0	0	1	1
462.0	0	2	2
463.0	0	1	1
465.0	0	2	2
466.0	0	2	2
468.0	0	2	2
469.0	0	2	2
471.0	0	1	1
474.0	0	1	1
475.0	0	1	1
477.0	0	1	1
478.0	0	1	1
481.0	0	2	2
482.0	0	1	1
485.0	0	2	2
486.0	0	2	2
487.0	0	1	1
488.0	0	2	2
489.0	0	1	1
490.0	0	1	1
491.0	0	1	1
492.0	0	1	1
493.0	0	1	1
494.0	0	4	4
497.0	0	2	2
499.0	0	1	1
500.0	0	2	2
501.0	0	2	2
503.0	0	1	1
504.0	0	1	1
505.0	0	2	2
506.0	0	1	1
507.0	0	1	1
508.0	0	1	1
511.0	0	1	1
512.0	0	1	1
513.0	0	1	1
515.0	0	1	1
516.0	0	3	3
517.0	0	1	1
518.0	0	1	1
519.0	0	1	1
521.0	0	1	1
522.0	0	1	1
523.0	0	1	1
527.0	0	2	2
529.0	0	2	2
530.0	0	1	1
531.0	0	1	1
533.0	0	1	1
539.0	0	2	2
541.0	0	1	1
542.0	0	3	3
544.0	0	1	1
546.0	0	1	1
547.0	0	2	2
548.0	0	1	1
549.0	0	1	1
551.0	0	1	1
552.0	0	1	1
556.0	0	1	1
558.0	0	1	1
559.0	0	3	3
561.0	0	1	1
562.0	0	2	2
565.0	0	1	1
566.0	0	1	1
568.0	0	1	1
569.0	0	1	1
571.0	0	3	3
573.0	0	1	1
575.0	0	1	1
576.0	0	1	1
578.0	0	1	1
579.0	0	1	1
581.0	0	1	1
582.0	0	1	1
583.0	0	2	2
586.0	0	1	1
587.0	0	1	1
597.0	0	1	1
598.0	0	1	1
606.0	0	2	2
608.0	0	2	2
609.0	0	1	1
615.0	0	1	1
616.0	0	1	1
617.0	0	5	5
619.0	0	1	1
620.0	0	1	1
621.0	0	1	1
624.0	0	1	1
625.0	0	1	1
627.0	0	2	2
630.0	0	1	1
636.0	0	2	2
638.0	0	1	1
643.0	0	1	1
645.0	0	1	1
647.0	0	1	1
648.0	0	1	1
649.0	0	1	1
655.0	0	1	1
657.0	0	1	1
659.0	0	1	1
666.0	0	3	3
669.0	0	2	2
671.0	0	1	1
676.0	0	1	1
677.0	0	1	1
678.0	0	2	2
682.0	0	1	1
683.0	0	1	1
684.0	0	1	1
685.0	0	1	1
686.0	0	1	1
688.0	0	1	1
691.0	0	1	1
702.0	0	1	1
705.0	0	2	2
711.0	0	1	1
717.0	0	1	1
725.0	0	2	2
727.0	0	1	1
728.0	0	1	1
730.0	0	2	2
737.0	0	1	1
743.0	0	1	1
746.0	0	2	2
759.0	0	1	1
761.0	0	1	1
764.0	0	1	1
767.0	0	1	1
772.0	0	1	1
773.0	0	1	1
776.0	0	1	1
783.0	0	1	1
784.0	0	1	1
795.0	0	2	2
796.0	0	1	1
798.0	0	1	1
805.0	0	1	1
810.0	0	1	1
812.0	0	1	1
814.0	0	1	1
834.0	0	1	1
840.0	0	1	1
848.0	0	1	1
850.0	0	1	1
852.0	0	1	1
862.0	0	1	1
876.0	0	1	1
879.0	0	1	1
883.0	0	1	1
906.0	0	1	1
919.0	0	1	1
930.0	0	1	1
933.0	0	1	1
934.0	0	1	1
937.0	0	1	1
963.0	0	1	1
968.0	0	1	1
973.0	0	1	1
995.0	0	1	1
1016.0	0	1	1
1018.0	0	1	1
1028.0	0	1	1
1032.0	0	1	1
1035.0	0	1	1
1052.0	0	1	1
1054.0	0	1	1
1069.0	0	1	1
1078.0	0	2	2
1100.0	0	1	1
1129.0	0	1	1
1155.0	0	1	1
1171.0	0	1	1
1180.0	0	1	1
1183.0	0	1	1
1197.0	0	1	1
1198.0	0	1	1
1229.0	0	1	1
1236.0	0	1	1
1249.0	0	1	1
1289.0	0	1	1
1301.0	0	1	1
1336.0	0	1	1
1339.0	0	1	1
1347.0	0	1	1
1418.0	0	1	1
1459.0	0	1	1
1570.0	0	1	1
1593.0	0	1	1
1613.0	0	1	1
1614.0	0	1	1
1623.0	0	1	1
1682.0	0	1	1
1691.0	0	1	1
1749.0	0	1	1
1761.0	0	1	1
1784.0	0	1	1
1811.0	0	1	1
1818.0	0	1	1
1859.0	0	1	1
1927.0	0	1	1
1929.0	0	1	1
2007.0	0	1	1
2088.0	0	1	1
2143.0	0	1	1
2188.0	0	1	1
2190.0	0	1	1
2403.0	0	1	1
2412.0	0	1	1
2682.0	0	1	1
2687.0	0	1	1
2814.0	0	1	1
2899.0	0	1	1
2940.0	0	1	1
2992.0	0	1	1
3199.0	0	1	1
4547.0	0	1	1