## 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-RU1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uM_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 10:25:30 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	1535	41424592	60886933	0	1385	8141265	0	0.196545	91073657

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30626728	30626728
2.0	1.634545	1700080	1700080
3.0	2.037192	373275	373275
4.0	2.29269	170340	170340
5.0	2.454815	98388	98388
6.0	2.55769	64419	64419
7.0	2.62297	43951	43951
8.0	2.664392	32589	32589
9.0	2.690677	24725	24725
10.0	2.707355	19303	19303
11.0	2.717939	15624	15624
12.0	2.724654	12629	12629
13.0	2.728916	10358	10358
14.0	2.73162	8758	8758
15.0	2.733335	7336	7336
16.0	2.734424	6338	6338
17.0	2.735115	5555	5555
18.0	2.735554	4892	4892
19.0	2.735832	4306	4306
20.0	2.736008	3736	3736
21.0	2.73612	3330	3330
22.0	2.736191	3042	3042
23.0	2.736236	2770	2770
24.0	2.736265	2422	2422
25.0	2.736283	2184	2184
26.0	2.736295	2024	2024
27.0	2.736302	1879	1879
28.0	2.736307	1654	1654
29.0	2.73631	1600	1600
30.0	2.736311	1390	1390
31.0	2.736313	1380	1380
32.0	2.736313	1262	1262
33.0	2.736314	1203	1203
34.0	2.736314	1018	1018
35.0	2.736314	951	951
36.0	2.736314	933	933
37.0	2.736315	867	867
38.0	2.736315	840	840
39.0	2.736315	792	792
40.0	2.736315	698	698
41.0	2.736315	611	611
42.0	2.736315	603	603
43.0	2.736315	597	597
44.0	2.736315	578	578
45.0	2.736315	524	524
46.0	2.736315	444	444
47.0	2.736315	496	496
48.0	2.736315	462	462
49.0	2.736315	406	406
50.0	2.736315	435	435
51.0	2.736315	353	353
52.0	2.736315	370	370
53.0	2.736315	322	322
54.0	2.736315	335	335
55.0	2.736315	343	343
56.0	2.736315	278	278
57.0	2.736315	291	291
58.0	2.736315	277	277
59.0	2.736315	264	264
60.0	2.736315	246	246
61.0	2.736315	256	256
62.0	2.736315	260	260
63.0	2.736315	216	216
64.0	2.736315	194	194
65.0	2.736315	223	223
66.0	2.736315	204	204
67.0	2.736315	203	203
68.0	2.736315	182	182
69.0	2.736315	163	163
70.0	2.736315	178	178
71.0	2.736315	177	177
72.0	2.736315	176	176
73.0	2.736315	145	145
74.0	2.736315	150	150
75.0	2.736315	154	154
76.0	2.736315	133	133
77.0	2.736315	135	135
78.0	2.736315	136	136
79.0	2.736315	119	119
80.0	2.736315	121	121
81.0	2.736315	121	121
82.0	2.736315	120	120
83.0	2.736315	116	116
84.0	2.736315	106	106
85.0	2.736315	101	101
86.0	2.736315	107	107
87.0	2.736315	100	100
88.0	2.736315	100	100
89.0	2.736315	93	93
90.0	2.736315	94	94
91.0	2.736315	74	74
92.0	2.736315	81	81
93.0	2.736315	99	99
94.0	2.736315	80	80
95.0	2.736315	89	89
96.0	2.736315	79	79
97.0	2.736315	73	73
98.0	2.736315	66	66
99.0	2.736315	60	60
100.0	2.736315	65	65
101.0	0	59	59
102.0	0	55	55
103.0	0	68	68
104.0	0	63	63
105.0	0	45	45
106.0	0	63	63
107.0	0	64	64
108.0	0	56	56
109.0	0	49	49
110.0	0	53	53
111.0	0	50	50
112.0	0	46	46
113.0	0	60	60
114.0	0	60	60
115.0	0	62	62
116.0	0	50	50
117.0	0	44	44
118.0	0	45	45
119.0	0	44	44
120.0	0	46	46
121.0	0	42	42
122.0	0	38	38
123.0	0	50	50
124.0	0	39	39
125.0	0	32	32
126.0	0	44	44
127.0	0	40	40
128.0	0	35	35
129.0	0	34	34
130.0	0	39	39
131.0	0	34	34
132.0	0	30	30
133.0	0	39	39
134.0	0	27	27
135.0	0	35	35
136.0	0	27	27
137.0	0	37	37
138.0	0	37	37
139.0	0	33	33
140.0	0	30	30
141.0	0	31	31
142.0	0	30	30
143.0	0	25	25
144.0	0	19	19
145.0	0	27	27
146.0	0	27	27
147.0	0	30	30
148.0	0	32	32
149.0	0	24	24
150.0	0	21	21
151.0	0	20	20
152.0	0	20	20
153.0	0	27	27
154.0	0	29	29
155.0	0	21	21
156.0	0	28	28
157.0	0	23	23
158.0	0	22	22
159.0	0	20	20
160.0	0	20	20
161.0	0	18	18
162.0	0	14	14
163.0	0	22	22
164.0	0	9	9
165.0	0	27	27
166.0	0	19	19
167.0	0	19	19
168.0	0	13	13
169.0	0	21	21
170.0	0	15	15
171.0	0	19	19
172.0	0	15	15
173.0	0	19	19
174.0	0	16	16
175.0	0	17	17
176.0	0	7	7
177.0	0	17	17
178.0	0	18	18
179.0	0	13	13
180.0	0	11	11
181.0	0	11	11
182.0	0	24	24
183.0	0	14	14
184.0	0	16	16
185.0	0	13	13
186.0	0	13	13
187.0	0	18	18
188.0	0	14	14
189.0	0	19	19
190.0	0	8	8
191.0	0	16	16
192.0	0	14	14
193.0	0	13	13
194.0	0	12	12
195.0	0	9	9
196.0	0	11	11
197.0	0	13	13
198.0	0	12	12
199.0	0	11	11
200.0	0	10	10
201.0	0	7	7
202.0	0	11	11
203.0	0	12	12
204.0	0	15	15
205.0	0	5	5
206.0	0	6	6
207.0	0	8	8
208.0	0	10	10
209.0	0	11	11
210.0	0	9	9
211.0	0	5	5
212.0	0	10	10
213.0	0	8	8
214.0	0	10	10
215.0	0	10	10
216.0	0	7	7
217.0	0	7	7
218.0	0	8	8
219.0	0	15	15
220.0	0	10	10
221.0	0	9	9
222.0	0	10	10
223.0	0	7	7
224.0	0	7	7
225.0	0	8	8
226.0	0	14	14
227.0	0	17	17
228.0	0	6	6
229.0	0	5	5
230.0	0	11	11
231.0	0	9	9
232.0	0	6	6
233.0	0	5	5
234.0	0	4	4
235.0	0	14	14
236.0	0	6	6
237.0	0	7	7
238.0	0	6	6
239.0	0	10	10
240.0	0	7	7
241.0	0	7	7
242.0	0	6	6
243.0	0	6	6
244.0	0	2	2
245.0	0	6	6
246.0	0	9	9
247.0	0	8	8
248.0	0	6	6
249.0	0	8	8
250.0	0	9	9
251.0	0	1	1
252.0	0	5	5
253.0	0	5	5
254.0	0	8	8
255.0	0	7	7
256.0	0	5	5
257.0	0	9	9
258.0	0	6	6
259.0	0	7	7
260.0	0	4	4
261.0	0	4	4
262.0	0	5	5
263.0	0	2	2
264.0	0	4	4
265.0	0	6	6
266.0	0	8	8
267.0	0	7	7
268.0	0	6	6
269.0	0	8	8
270.0	0	6	6
271.0	0	9	9
272.0	0	5	5
273.0	0	9	9
274.0	0	2	2
275.0	0	6	6
276.0	0	4	4
277.0	0	7	7
278.0	0	5	5
279.0	0	1	1
280.0	0	2	2
281.0	0	2	2
282.0	0	6	6
283.0	0	3	3
284.0	0	7	7
285.0	0	2	2
286.0	0	3	3
287.0	0	1	1
288.0	0	4	4
289.0	0	4	4
290.0	0	11	11
291.0	0	4	4
292.0	0	5	5
293.0	0	2	2
294.0	0	4	4
295.0	0	1	1
296.0	0	6	6
297.0	0	3	3
298.0	0	5	5
300.0	0	2	2
301.0	0	3	3
302.0	0	4	4
303.0	0	3	3
304.0	0	4	4
305.0	0	8	8
306.0	0	5	5
307.0	0	8	8
308.0	0	4	4
310.0	0	2	2
311.0	0	5	5
312.0	0	7	7
313.0	0	6	6
314.0	0	7	7
315.0	0	3	3
316.0	0	1	1
317.0	0	1	1
318.0	0	4	4
319.0	0	4	4
320.0	0	2	2
321.0	0	4	4
322.0	0	5	5
323.0	0	3	3
324.0	0	2	2
325.0	0	5	5
326.0	0	5	5
327.0	0	4	4
328.0	0	2	2
329.0	0	4	4
330.0	0	1	1
331.0	0	3	3
333.0	0	3	3
334.0	0	3	3
335.0	0	4	4
336.0	0	4	4
337.0	0	1	1
338.0	0	1	1
339.0	0	4	4
340.0	0	2	2
341.0	0	3	3
342.0	0	4	4
343.0	0	1	1
344.0	0	1	1
345.0	0	4	4
346.0	0	1	1
347.0	0	4	4
348.0	0	1	1
349.0	0	6	6
350.0	0	4	4
351.0	0	1	1
352.0	0	1	1
353.0	0	1	1
354.0	0	4	4
355.0	0	3	3
356.0	0	3	3
357.0	0	1	1
358.0	0	5	5
360.0	0	4	4
361.0	0	2	2
363.0	0	2	2
364.0	0	2	2
365.0	0	3	3
366.0	0	4	4
367.0	0	3	3
368.0	0	1	1
369.0	0	2	2
370.0	0	1	1
371.0	0	4	4
372.0	0	5	5
376.0	0	3	3
377.0	0	1	1
378.0	0	2	2
379.0	0	2	2
380.0	0	3	3
381.0	0	1	1
382.0	0	4	4
383.0	0	1	1
384.0	0	3	3
385.0	0	2	2
386.0	0	2	2
388.0	0	3	3
389.0	0	1	1
390.0	0	2	2
391.0	0	2	2
392.0	0	2	2
393.0	0	1	1
394.0	0	1	1
395.0	0	1	1
397.0	0	3	3
398.0	0	2	2
399.0	0	4	4
401.0	0	4	4
402.0	0	1	1
405.0	0	2	2
406.0	0	3	3
407.0	0	1	1
408.0	0	3	3
410.0	0	1	1
411.0	0	6	6
412.0	0	2	2
413.0	0	2	2
414.0	0	1	1
415.0	0	2	2
417.0	0	1	1
418.0	0	1	1
419.0	0	3	3
420.0	0	2	2
422.0	0	1	1
423.0	0	1	1
424.0	0	1	1
426.0	0	1	1
429.0	0	3	3
430.0	0	3	3
431.0	0	2	2
432.0	0	2	2
433.0	0	2	2
434.0	0	2	2
435.0	0	1	1
437.0	0	1	1
438.0	0	2	2
439.0	0	3	3
440.0	0	3	3
441.0	0	1	1
443.0	0	2	2
444.0	0	3	3
445.0	0	2	2
446.0	0	3	3
447.0	0	2	2
449.0	0	2	2
451.0	0	2	2
452.0	0	1	1
453.0	0	3	3
454.0	0	2	2
456.0	0	2	2
457.0	0	1	1
458.0	0	1	1
461.0	0	3	3
462.0	0	1	1
465.0	0	1	1
468.0	0	1	1
469.0	0	2	2
471.0	0	2	2
473.0	0	1	1
474.0	0	2	2
475.0	0	2	2
476.0	0	2	2
478.0	0	2	2
479.0	0	2	2
480.0	0	1	1
482.0	0	2	2
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
486.0	0	2	2
488.0	0	1	1
489.0	0	1	1
491.0	0	1	1
493.0	0	1	1
494.0	0	3	3
495.0	0	3	3
496.0	0	1	1
497.0	0	1	1
498.0	0	1	1
499.0	0	1	1
500.0	0	1	1
501.0	0	1	1
504.0	0	1	1
505.0	0	2	2
507.0	0	1	1
509.0	0	1	1
511.0	0	1	1
512.0	0	1	1
514.0	0	1	1
515.0	0	2	2
519.0	0	1	1
520.0	0	1	1
521.0	0	2	2
522.0	0	2	2
524.0	0	3	3
527.0	0	1	1
529.0	0	1	1
530.0	0	1	1
531.0	0	1	1
532.0	0	2	2
533.0	0	1	1
534.0	0	1	1
537.0	0	1	1
539.0	0	2	2
543.0	0	1	1
546.0	0	1	1
548.0	0	1	1
551.0	0	1	1
553.0	0	2	2
558.0	0	2	2
564.0	0	1	1
565.0	0	1	1
566.0	0	1	1
567.0	0	1	1
568.0	0	1	1
569.0	0	1	1
571.0	0	1	1
576.0	0	2	2
577.0	0	1	1
578.0	0	1	1
579.0	0	2	2
582.0	0	3	3
592.0	0	1	1
594.0	0	1	1
595.0	0	3	3
596.0	0	1	1
597.0	0	1	1
599.0	0	1	1
602.0	0	1	1
603.0	0	1	1
604.0	0	1	1
605.0	0	1	1
607.0	0	2	2
610.0	0	1	1
612.0	0	1	1
613.0	0	1	1
614.0	0	1	1
617.0	0	1	1
619.0	0	2	2
621.0	0	1	1
623.0	0	1	1
624.0	0	2	2
626.0	0	2	2
628.0	0	2	2
630.0	0	1	1
633.0	0	1	1
637.0	0	1	1
638.0	0	1	1
639.0	0	1	1
640.0	0	1	1
641.0	0	1	1
649.0	0	1	1
650.0	0	2	2
651.0	0	1	1
657.0	0	1	1
658.0	0	1	1
660.0	0	2	2
661.0	0	1	1
662.0	0	1	1
667.0	0	1	1
671.0	0	1	1
672.0	0	2	2
679.0	0	1	1
684.0	0	2	2
703.0	0	1	1
704.0	0	1	1
706.0	0	2	2
708.0	0	2	2
709.0	0	1	1
710.0	0	1	1
721.0	0	1	1
723.0	0	1	1
724.0	0	1	1
728.0	0	1	1
731.0	0	1	1
733.0	0	1	1
745.0	0	1	1
761.0	0	1	1
762.0	0	1	1
763.0	0	1	1
765.0	0	1	1
768.0	0	1	1
770.0	0	2	2
774.0	0	1	1
775.0	0	1	1
777.0	0	1	1
778.0	0	1	1
784.0	0	1	1
785.0	0	1	1
794.0	0	1	1
813.0	0	2	2
819.0	0	1	1
824.0	0	1	1
827.0	0	1	1
848.0	0	1	1
851.0	0	1	1
855.0	0	1	1
856.0	0	1	1
870.0	0	1	1
874.0	0	1	1
877.0	0	1	1
882.0	0	1	1
885.0	0	1	1
886.0	0	1	1
897.0	0	1	1
898.0	0	1	1
900.0	0	1	1
923.0	0	1	1
934.0	0	1	1
940.0	0	1	1
956.0	0	1	1
957.0	0	1	1
972.0	0	1	1
995.0	0	1	1
1012.0	0	1	1
1013.0	0	1	1
1018.0	0	1	1
1052.0	0	1	1
1074.0	0	1	1
1085.0	0	1	1
1120.0	0	1	1
1133.0	0	1	1
1138.0	0	1	1
1140.0	0	1	1
1159.0	0	1	1
1165.0	0	1	1
1211.0	0	1	1
1224.0	0	1	1
1230.0	0	1	1
1259.0	0	1	1
1260.0	0	1	1
1288.0	0	1	1
1318.0	0	1	1
1322.0	0	1	1
1347.0	0	1	1
1358.0	0	1	1
1375.0	0	1	1
1379.0	0	1	1
1387.0	0	1	1
1402.0	0	1	1
1404.0	0	1	1
1419.0	0	1	1
1454.0	0	1	1
1493.0	0	1	1
1540.0	0	1	1
1550.0	0	1	1
1557.0	0	1	1
1573.0	0	1	1
1592.0	0	1	1
1603.0	0	1	1
1620.0	0	1	1
1645.0	0	2	2
1682.0	0	1	1
1695.0	0	1	1
1720.0	0	1	1
1891.0	0	1	1
1973.0	0	1	1
2238.0	0	1	1
2239.0	0	1	1
2289.0	0	1	1
2295.0	0	1	1
2329.0	0	1	1
2460.0	0	1	1
2695.0	0	1	1
2704.0	0	1	1
3619.0	0	1	1