## 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_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uMTA100nM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uMTA100nM_2.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 10:32:32 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	1320	40279814	27656148	0	1177	6880066	0	0.170819	104062261

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30383046	30383046
2.0	1.679041	2182344	2182344
3.0	2.140137	383682	383682
4.0	2.45324	150053	150053
5.0	2.66585	80594	80594
6.0	2.810221	49869	49869
7.0	2.908254	33527	33527
8.0	2.974823	23755	23755
9.0	3.020026	17782	17782
10.0	3.050721	13452	13452
11.0	3.071564	10629	10629
12.0	3.085717	8369	8369
13.0	3.095327	7078	7078
14.0	3.101853	5628	5628
15.0	3.106285	4893	4893
16.0	3.109294	4148	4148
17.0	3.111337	3616	3616
18.0	3.112725	3073	3073
19.0	3.113667	2692	2692
20.0	3.114307	2325	2325
21.0	3.114741	2006	2006
22.0	3.115036	1836	1836
23.0	3.115236	1631	1631
24.0	3.115372	1518	1518
25.0	3.115465	1238	1238
26.0	3.115527	1185	1185
27.0	3.11557	1052	1052
28.0	3.115599	965	965
29.0	3.115619	923	923
30.0	3.115632	828	828
31.0	3.115641	758	758
32.0	3.115647	694	694
33.0	3.115651	614	614
34.0	3.115654	618	618
35.0	3.115656	563	563
36.0	3.115657	566	566
37.0	3.115658	504	504
38.0	3.115659	488	488
39.0	3.115659	460	460
40.0	3.115659	392	392
41.0	3.11566	354	354
42.0	3.11566	328	328
43.0	3.11566	314	314
44.0	3.11566	307	307
45.0	3.11566	278	278
46.0	3.11566	277	277
47.0	3.11566	279	279
48.0	3.11566	245	245
49.0	3.11566	260	260
50.0	3.11566	224	224
51.0	3.11566	209	209
52.0	3.11566	193	193
53.0	3.11566	203	203
54.0	3.11566	184	184
55.0	3.11566	163	163
56.0	3.11566	166	166
57.0	3.11566	182	182
58.0	3.11566	141	141
59.0	3.11566	141	141
60.0	3.11566	151	151
61.0	3.11566	124	124
62.0	3.11566	136	136
63.0	3.11566	133	133
64.0	3.11566	106	106
65.0	3.11566	125	125
66.0	3.11566	115	115
67.0	3.11566	108	108
68.0	3.11566	111	111
69.0	3.11566	94	94
70.0	3.11566	91	91
71.0	3.11566	104	104
72.0	3.11566	88	88
73.0	3.11566	101	101
74.0	3.11566	78	78
75.0	3.11566	85	85
76.0	3.11566	78	78
77.0	3.11566	80	80
78.0	3.11566	80	80
79.0	3.11566	82	82
80.0	3.11566	75	75
81.0	3.11566	72	72
82.0	3.11566	68	68
83.0	3.11566	72	72
84.0	3.11566	58	58
85.0	3.11566	65	65
86.0	3.11566	66	66
87.0	3.11566	73	73
88.0	3.11566	52	52
89.0	3.11566	49	49
90.0	3.11566	42	42
91.0	3.11566	52	52
92.0	3.11566	50	50
93.0	3.11566	52	52
94.0	3.11566	50	50
95.0	3.11566	46	46
96.0	3.11566	50	50
97.0	3.11566	48	48
98.0	3.11566	48	48
99.0	3.11566	42	42
100.0	3.11566	39	39
101.0	0	31	31
102.0	0	38	38
103.0	0	44	44
104.0	0	42	42
105.0	0	34	34
106.0	0	32	32
107.0	0	33	33
108.0	0	31	31
109.0	0	28	28
110.0	0	27	27
111.0	0	25	25
112.0	0	26	26
113.0	0	27	27
114.0	0	29	29
115.0	0	31	31
116.0	0	35	35
117.0	0	22	22
118.0	0	20	20
119.0	0	26	26
120.0	0	25	25
121.0	0	25	25
122.0	0	20	20
123.0	0	25	25
124.0	0	18	18
125.0	0	22	22
126.0	0	29	29
127.0	0	17	17
128.0	0	19	19
129.0	0	25	25
130.0	0	24	24
131.0	0	18	18
132.0	0	26	26
133.0	0	16	16
134.0	0	17	17
135.0	0	16	16
136.0	0	13	13
137.0	0	22	22
138.0	0	20	20
139.0	0	12	12
140.0	0	11	11
141.0	0	16	16
142.0	0	14	14
143.0	0	17	17
144.0	0	14	14
145.0	0	18	18
146.0	0	18	18
147.0	0	17	17
148.0	0	17	17
149.0	0	16	16
150.0	0	13	13
151.0	0	19	19
152.0	0	13	13
153.0	0	7	7
154.0	0	13	13
155.0	0	19	19
156.0	0	10	10
157.0	0	14	14
158.0	0	11	11
159.0	0	14	14
160.0	0	13	13
161.0	0	17	17
162.0	0	10	10
163.0	0	10	10
164.0	0	10	10
165.0	0	19	19
166.0	0	21	21
167.0	0	9	9
168.0	0	8	8
169.0	0	6	6
170.0	0	7	7
171.0	0	12	12
172.0	0	13	13
173.0	0	13	13
174.0	0	17	17
175.0	0	8	8
176.0	0	16	16
177.0	0	10	10
178.0	0	12	12
179.0	0	8	8
180.0	0	8	8
181.0	0	8	8
182.0	0	5	5
183.0	0	11	11
184.0	0	7	7
185.0	0	5	5
186.0	0	10	10
187.0	0	8	8
188.0	0	10	10
189.0	0	14	14
190.0	0	11	11
191.0	0	5	5
192.0	0	6	6
193.0	0	7	7
194.0	0	12	12
195.0	0	10	10
196.0	0	7	7
197.0	0	12	12
198.0	0	13	13
199.0	0	9	9
200.0	0	6	6
201.0	0	13	13
202.0	0	8	8
203.0	0	2	2
204.0	0	11	11
205.0	0	8	8
206.0	0	8	8
207.0	0	10	10
208.0	0	10	10
209.0	0	4	4
210.0	0	9	9
211.0	0	6	6
212.0	0	5	5
213.0	0	8	8
214.0	0	8	8
215.0	0	5	5
216.0	0	3	3
217.0	0	11	11
218.0	0	7	7
219.0	0	4	4
220.0	0	3	3
221.0	0	5	5
222.0	0	4	4
223.0	0	4	4
224.0	0	3	3
225.0	0	6	6
226.0	0	1	1
227.0	0	2	2
228.0	0	9	9
229.0	0	7	7
230.0	0	9	9
231.0	0	3	3
232.0	0	8	8
233.0	0	3	3
234.0	0	6	6
235.0	0	2	2
236.0	0	6	6
237.0	0	5	5
238.0	0	9	9
239.0	0	4	4
240.0	0	11	11
241.0	0	5	5
242.0	0	5	5
243.0	0	2	2
244.0	0	6	6
245.0	0	3	3
246.0	0	6	6
247.0	0	4	4
248.0	0	4	4
249.0	0	2	2
250.0	0	4	4
251.0	0	4	4
252.0	0	5	5
253.0	0	5	5
254.0	0	2	2
255.0	0	2	2
256.0	0	6	6
257.0	0	2	2
258.0	0	2	2
259.0	0	8	8
260.0	0	5	5
261.0	0	1	1
262.0	0	3	3
263.0	0	3	3
264.0	0	8	8
265.0	0	4	4
266.0	0	6	6
267.0	0	4	4
268.0	0	3	3
269.0	0	3	3
270.0	0	5	5
271.0	0	4	4
272.0	0	5	5
274.0	0	1	1
275.0	0	6	6
276.0	0	8	8
277.0	0	3	3
278.0	0	5	5
279.0	0	3	3
280.0	0	2	2
281.0	0	5	5
282.0	0	3	3
283.0	0	5	5
284.0	0	4	4
285.0	0	1	1
286.0	0	1	1
287.0	0	3	3
288.0	0	2	2
289.0	0	10	10
291.0	0	1	1
292.0	0	3	3
293.0	0	3	3
294.0	0	3	3
295.0	0	2	2
296.0	0	3	3
298.0	0	3	3
299.0	0	3	3
300.0	0	4	4
301.0	0	2	2
302.0	0	5	5
304.0	0	4	4
305.0	0	1	1
306.0	0	2	2
307.0	0	1	1
308.0	0	6	6
309.0	0	1	1
310.0	0	2	2
311.0	0	3	3
312.0	0	3	3
313.0	0	3	3
314.0	0	3	3
315.0	0	2	2
316.0	0	2	2
317.0	0	1	1
318.0	0	3	3
319.0	0	3	3
320.0	0	2	2
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
324.0	0	3	3
325.0	0	4	4
326.0	0	2	2
327.0	0	5	5
328.0	0	2	2
329.0	0	1	1
330.0	0	3	3
331.0	0	3	3
332.0	0	5	5
333.0	0	2	2
334.0	0	2	2
335.0	0	2	2
337.0	0	3	3
338.0	0	2	2
339.0	0	3	3
340.0	0	4	4
341.0	0	1	1
342.0	0	4	4
343.0	0	2	2
344.0	0	3	3
345.0	0	2	2
346.0	0	2	2
347.0	0	1	1
348.0	0	2	2
349.0	0	3	3
350.0	0	1	1
352.0	0	2	2
353.0	0	1	1
354.0	0	4	4
355.0	0	2	2
356.0	0	2	2
357.0	0	4	4
358.0	0	4	4
359.0	0	3	3
360.0	0	2	2
361.0	0	3	3
362.0	0	2	2
363.0	0	3	3
364.0	0	5	5
365.0	0	1	1
366.0	0	1	1
367.0	0	3	3
368.0	0	1	1
369.0	0	2	2
370.0	0	2	2
371.0	0	3	3
372.0	0	6	6
373.0	0	3	3
374.0	0	3	3
375.0	0	2	2
376.0	0	1	1
378.0	0	2	2
379.0	0	1	1
380.0	0	3	3
382.0	0	5	5
383.0	0	1	1
384.0	0	1	1
385.0	0	2	2
386.0	0	1	1
387.0	0	2	2
388.0	0	2	2
389.0	0	3	3
391.0	0	2	2
392.0	0	1	1
396.0	0	2	2
398.0	0	2	2
399.0	0	3	3
401.0	0	2	2
402.0	0	3	3
403.0	0	2	2
404.0	0	2	2
406.0	0	1	1
407.0	0	2	2
408.0	0	1	1
409.0	0	3	3
411.0	0	3	3
412.0	0	1	1
413.0	0	1	1
414.0	0	1	1
415.0	0	1	1
416.0	0	2	2
417.0	0	3	3
418.0	0	1	1
419.0	0	2	2
420.0	0	2	2
421.0	0	2	2
422.0	0	1	1
423.0	0	1	1
425.0	0	2	2
427.0	0	1	1
428.0	0	4	4
431.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	1	1
435.0	0	2	2
436.0	0	1	1
437.0	0	1	1
439.0	0	3	3
440.0	0	2	2
441.0	0	1	1
442.0	0	1	1
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
449.0	0	1	1
452.0	0	2	2
456.0	0	3	3
457.0	0	1	1
458.0	0	1	1
459.0	0	2	2
460.0	0	2	2
462.0	0	1	1
465.0	0	4	4
469.0	0	2	2
470.0	0	2	2
471.0	0	2	2
472.0	0	1	1
474.0	0	1	1
476.0	0	1	1
478.0	0	2	2
481.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
486.0	0	1	1
487.0	0	4	4
489.0	0	2	2
490.0	0	1	1
491.0	0	1	1
493.0	0	2	2
494.0	0	1	1
498.0	0	2	2
499.0	0	1	1
500.0	0	1	1
501.0	0	2	2
502.0	0	1	1
503.0	0	2	2
504.0	0	3	3
505.0	0	1	1
506.0	0	1	1
508.0	0	1	1
509.0	0	1	1
510.0	0	1	1
515.0	0	2	2
516.0	0	1	1
518.0	0	1	1
520.0	0	1	1
522.0	0	1	1
523.0	0	1	1
526.0	0	1	1
531.0	0	2	2
532.0	0	1	1
534.0	0	1	1
536.0	0	1	1
543.0	0	2	2
545.0	0	1	1
547.0	0	1	1
548.0	0	1	1
550.0	0	1	1
554.0	0	2	2
555.0	0	1	1
560.0	0	1	1
563.0	0	1	1
566.0	0	1	1
567.0	0	2	2
569.0	0	2	2
570.0	0	1	1
571.0	0	1	1
572.0	0	1	1
573.0	0	1	1
576.0	0	1	1
577.0	0	1	1
579.0	0	1	1
595.0	0	1	1
596.0	0	1	1
607.0	0	1	1
612.0	0	1	1
613.0	0	2	2
614.0	0	1	1
615.0	0	1	1
619.0	0	1	1
620.0	0	1	1
623.0	0	1	1
626.0	0	2	2
629.0	0	1	1
632.0	0	1	1
634.0	0	1	1
637.0	0	1	1
640.0	0	1	1
641.0	0	1	1
642.0	0	1	1
646.0	0	1	1
650.0	0	1	1
652.0	0	1	1
658.0	0	1	1
659.0	0	2	2
663.0	0	1	1
664.0	0	1	1
671.0	0	2	2
681.0	0	1	1
697.0	0	1	1
708.0	0	2	2
711.0	0	1	1
715.0	0	1	1
717.0	0	2	2
727.0	0	1	1
734.0	0	1	1
735.0	0	1	1
742.0	0	1	1
750.0	0	1	1
752.0	0	1	1
756.0	0	1	1
762.0	0	1	1
764.0	0	1	1
794.0	0	1	1
800.0	0	1	1
814.0	0	2	2
819.0	0	2	2
842.0	0	1	1
843.0	0	1	1
849.0	0	1	1
861.0	0	1	1
868.0	0	1	1
881.0	0	1	1
882.0	0	1	1
888.0	0	1	1
891.0	0	1	1
893.0	0	1	1
894.0	0	1	1
895.0	0	1	1
900.0	0	1	1
911.0	0	2	2
938.0	0	1	1
947.0	0	1	1
954.0	0	1	1
956.0	0	1	1
962.0	0	1	1
986.0	0	1	1
1013.0	0	1	1
1020.0	0	1	1
1049.0	0	1	1
1061.0	0	1	1
1064.0	0	1	1
1077.0	0	1	1
1078.0	0	1	1
1083.0	0	1	1
1088.0	0	1	1
1119.0	0	1	1
1184.0	0	1	1
1246.0	0	1	1
1296.0	0	1	1
1309.0	0	1	1
1311.0	0	1	1
1325.0	0	1	1
1369.0	0	1	1
1377.0	0	1	1
1398.0	0	1	1
1414.0	0	1	1
1437.0	0	1	1
1442.0	0	1	1
1551.0	0	1	1
1581.0	0	1	1
1589.0	0	1	1
1647.0	0	1	1
1649.0	0	1	1
1700.0	0	1	1
1724.0	0	1	1
1848.0	0	1	1
1852.0	0	1	1
2023.0	0	1	1
2037.0	0	1	1
2100.0	0	1	1
2139.0	0	1	1
2152.0	0	1	1
2364.0	0	1	1
2794.0	0	1	1
2948.0	0	1	1
3265.0	0	1	1
3289.0	0	1	1
3400.0	0	1	1
3490.0	0	1	1
4268.0	0	1	1