## 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_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uM_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uM_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 10:43:10 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	833	37344290	28021255	0	708	6487503	0	0.173729	94636915

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28366076	28366076
2.0	1.673946	1724859	1724859
3.0	2.128148	327390	327390
4.0	2.434256	138230	138230
5.0	2.640556	76739	76739
6.0	2.779591	48268	48268
7.0	2.873293	32895	32895
8.0	2.936443	23870	23870
9.0	2.979003	17804	17804
10.0	3.007686	13617	13617
11.0	3.027016	10745	10745
12.0	3.040044	8867	8867
13.0	3.048824	7256	7256
14.0	3.054742	6080	6080
15.0	3.058729	5038	5038
16.0	3.061417	4392	4392
17.0	3.063228	3714	3714
18.0	3.064449	3297	3297
19.0	3.065272	2798	2798
20.0	3.065826	2470	2470
21.0	3.0662	2176	2176
22.0	3.066452	1973	1973
23.0	3.066622	1781	1781
24.0	3.066736	1588	1588
25.0	3.066813	1511	1511
26.0	3.066865	1236	1236
27.0	3.0669	1193	1193
28.0	3.066924	1060	1060
29.0	3.06694	987	987
30.0	3.06695	841	841
31.0	3.066957	840	840
32.0	3.066962	796	796
33.0	3.066966	723	723
34.0	3.066968	678	678
35.0	3.066969	636	636
36.0	3.06697	608	608
37.0	3.066971	529	529
38.0	3.066971	516	516
39.0	3.066972	475	475
40.0	3.066972	437	437
41.0	3.066972	402	402
42.0	3.066972	395	395
43.0	3.066972	371	371
44.0	3.066972	343	343
45.0	3.066972	330	330
46.0	3.066972	304	304
47.0	3.066972	272	272
48.0	3.066972	283	283
49.0	3.066972	310	310
50.0	3.066972	257	257
51.0	3.066972	271	271
52.0	3.066972	228	228
53.0	3.066972	220	220
54.0	3.066972	218	218
55.0	3.066972	189	189
56.0	3.066972	214	214
57.0	3.066972	185	185
58.0	3.066972	168	168
59.0	3.066972	154	154
60.0	3.066972	164	164
61.0	3.066972	155	155
62.0	3.066972	155	155
63.0	3.066972	135	135
64.0	3.066972	139	139
65.0	3.066972	127	127
66.0	3.066972	120	120
67.0	3.066972	133	133
68.0	3.066972	115	115
69.0	3.066972	113	113
70.0	3.066972	98	98
71.0	3.066972	109	109
72.0	3.066972	101	101
73.0	3.066972	102	102
74.0	3.066972	98	98
75.0	3.066972	99	99
76.0	3.066972	84	84
77.0	3.066972	100	100
78.0	3.066972	83	83
79.0	3.066972	91	91
80.0	3.066972	85	85
81.0	3.066972	83	83
82.0	3.066972	69	69
83.0	3.066972	74	74
84.0	3.066972	72	72
85.0	3.066972	71	71
86.0	3.066972	57	57
87.0	3.066972	64	64
88.0	3.066972	51	51
89.0	3.066972	64	64
90.0	3.066972	62	62
91.0	3.066972	39	39
92.0	3.066972	56	56
93.0	3.066972	71	71
94.0	3.066972	59	59
95.0	3.066972	54	54
96.0	3.066972	59	59
97.0	3.066972	46	46
98.0	3.066972	50	50
99.0	3.066972	44	44
100.0	3.066972	35	35
101.0	0	65	65
102.0	0	49	49
103.0	0	42	42
104.0	0	40	40
105.0	0	48	48
106.0	0	52	52
107.0	0	41	41
108.0	0	44	44
109.0	0	44	44
110.0	0	32	32
111.0	0	29	29
112.0	0	27	27
113.0	0	24	24
114.0	0	46	46
115.0	0	36	36
116.0	0	29	29
117.0	0	31	31
118.0	0	31	31
119.0	0	30	30
120.0	0	34	34
121.0	0	31	31
122.0	0	24	24
123.0	0	32	32
124.0	0	35	35
125.0	0	20	20
126.0	0	34	34
127.0	0	22	22
128.0	0	24	24
129.0	0	28	28
130.0	0	25	25
131.0	0	19	19
132.0	0	15	15
133.0	0	24	24
134.0	0	19	19
135.0	0	20	20
136.0	0	19	19
137.0	0	18	18
138.0	0	22	22
139.0	0	21	21
140.0	0	18	18
141.0	0	19	19
142.0	0	10	10
143.0	0	20	20
144.0	0	17	17
145.0	0	9	9
146.0	0	17	17
147.0	0	21	21
148.0	0	20	20
149.0	0	12	12
150.0	0	28	28
151.0	0	17	17
152.0	0	19	19
153.0	0	10	10
154.0	0	8	8
155.0	0	7	7
156.0	0	14	14
157.0	0	16	16
158.0	0	12	12
159.0	0	16	16
160.0	0	13	13
161.0	0	8	8
162.0	0	13	13
163.0	0	17	17
164.0	0	5	5
165.0	0	14	14
166.0	0	22	22
167.0	0	18	18
168.0	0	11	11
169.0	0	9	9
170.0	0	16	16
171.0	0	14	14
172.0	0	16	16
173.0	0	11	11
174.0	0	15	15
175.0	0	10	10
176.0	0	9	9
177.0	0	10	10
178.0	0	12	12
179.0	0	13	13
180.0	0	14	14
181.0	0	11	11
182.0	0	16	16
183.0	0	10	10
184.0	0	13	13
185.0	0	12	12
186.0	0	13	13
187.0	0	10	10
188.0	0	3	3
189.0	0	10	10
190.0	0	8	8
191.0	0	8	8
192.0	0	10	10
193.0	0	6	6
194.0	0	7	7
195.0	0	6	6
196.0	0	8	8
197.0	0	10	10
198.0	0	9	9
199.0	0	10	10
200.0	0	11	11
201.0	0	8	8
202.0	0	5	5
203.0	0	8	8
204.0	0	6	6
205.0	0	7	7
206.0	0	4	4
207.0	0	5	5
208.0	0	9	9
209.0	0	8	8
210.0	0	7	7
211.0	0	6	6
212.0	0	14	14
213.0	0	9	9
214.0	0	6	6
215.0	0	5	5
216.0	0	9	9
217.0	0	7	7
218.0	0	6	6
219.0	0	6	6
220.0	0	6	6
221.0	0	11	11
222.0	0	6	6
223.0	0	6	6
224.0	0	5	5
225.0	0	12	12
226.0	0	8	8
227.0	0	6	6
228.0	0	6	6
229.0	0	7	7
230.0	0	9	9
231.0	0	9	9
232.0	0	8	8
233.0	0	5	5
234.0	0	5	5
235.0	0	3	3
236.0	0	9	9
237.0	0	6	6
238.0	0	6	6
239.0	0	8	8
240.0	0	10	10
241.0	0	6	6
242.0	0	10	10
243.0	0	5	5
244.0	0	7	7
245.0	0	3	3
246.0	0	7	7
247.0	0	5	5
248.0	0	4	4
249.0	0	4	4
250.0	0	4	4
251.0	0	4	4
252.0	0	6	6
253.0	0	7	7
254.0	0	5	5
255.0	0	3	3
256.0	0	2	2
257.0	0	4	4
258.0	0	1	1
259.0	0	6	6
260.0	0	5	5
261.0	0	4	4
262.0	0	6	6
263.0	0	5	5
264.0	0	5	5
265.0	0	5	5
266.0	0	1	1
267.0	0	5	5
268.0	0	6	6
269.0	0	2	2
270.0	0	3	3
271.0	0	3	3
272.0	0	3	3
273.0	0	1	1
274.0	0	5	5
275.0	0	6	6
276.0	0	1	1
277.0	0	4	4
278.0	0	4	4
279.0	0	2	2
280.0	0	3	3
281.0	0	8	8
282.0	0	4	4
283.0	0	6	6
284.0	0	8	8
285.0	0	6	6
286.0	0	2	2
287.0	0	4	4
288.0	0	2	2
289.0	0	3	3
291.0	0	3	3
292.0	0	3	3
293.0	0	6	6
294.0	0	4	4
295.0	0	4	4
296.0	0	2	2
297.0	0	3	3
298.0	0	3	3
299.0	0	4	4
300.0	0	5	5
301.0	0	2	2
302.0	0	2	2
303.0	0	3	3
304.0	0	4	4
305.0	0	6	6
306.0	0	3	3
307.0	0	1	1
308.0	0	1	1
309.0	0	2	2
311.0	0	2	2
312.0	0	1	1
314.0	0	3	3
317.0	0	2	2
318.0	0	7	7
319.0	0	4	4
321.0	0	2	2
322.0	0	3	3
323.0	0	4	4
324.0	0	3	3
325.0	0	2	2
326.0	0	6	6
327.0	0	2	2
328.0	0	2	2
329.0	0	2	2
330.0	0	5	5
332.0	0	4	4
333.0	0	3	3
334.0	0	1	1
335.0	0	3	3
337.0	0	3	3
339.0	0	1	1
340.0	0	5	5
341.0	0	4	4
342.0	0	2	2
343.0	0	2	2
344.0	0	2	2
345.0	0	2	2
347.0	0	8	8
348.0	0	4	4
349.0	0	2	2
350.0	0	2	2
351.0	0	2	2
352.0	0	3	3
353.0	0	3	3
354.0	0	2	2
355.0	0	3	3
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
359.0	0	2	2
360.0	0	1	1
361.0	0	5	5
362.0	0	2	2
363.0	0	1	1
365.0	0	5	5
366.0	0	3	3
367.0	0	3	3
368.0	0	4	4
369.0	0	2	2
370.0	0	2	2
371.0	0	2	2
372.0	0	1	1
373.0	0	4	4
374.0	0	2	2
375.0	0	2	2
376.0	0	3	3
377.0	0	5	5
378.0	0	3	3
379.0	0	1	1
381.0	0	3	3
382.0	0	3	3
383.0	0	2	2
384.0	0	1	1
385.0	0	3	3
386.0	0	1	1
387.0	0	3	3
388.0	0	2	2
389.0	0	4	4
390.0	0	1	1
391.0	0	3	3
392.0	0	2	2
394.0	0	2	2
395.0	0	3	3
396.0	0	2	2
397.0	0	2	2
398.0	0	1	1
399.0	0	2	2
402.0	0	2	2
404.0	0	1	1
407.0	0	1	1
408.0	0	1	1
409.0	0	2	2
411.0	0	2	2
413.0	0	1	1
415.0	0	4	4
416.0	0	1	1
417.0	0	2	2
418.0	0	2	2
419.0	0	2	2
422.0	0	2	2
423.0	0	2	2
424.0	0	1	1
425.0	0	4	4
426.0	0	3	3
427.0	0	1	1
428.0	0	3	3
430.0	0	1	1
431.0	0	1	1
432.0	0	2	2
433.0	0	2	2
435.0	0	1	1
436.0	0	1	1
438.0	0	1	1
439.0	0	2	2
440.0	0	1	1
441.0	0	1	1
442.0	0	2	2
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
446.0	0	1	1
447.0	0	2	2
448.0	0	1	1
450.0	0	1	1
451.0	0	2	2
452.0	0	2	2
453.0	0	2	2
457.0	0	1	1
459.0	0	1	1
460.0	0	1	1
461.0	0	1	1
463.0	0	3	3
464.0	0	1	1
466.0	0	3	3
468.0	0	3	3
469.0	0	2	2
471.0	0	1	1
472.0	0	3	3
473.0	0	1	1
474.0	0	4	4
476.0	0	3	3
477.0	0	1	1
478.0	0	1	1
479.0	0	3	3
480.0	0	1	1
483.0	0	2	2
484.0	0	3	3
485.0	0	1	1
486.0	0	1	1
487.0	0	2	2
488.0	0	1	1
489.0	0	1	1
490.0	0	2	2
491.0	0	2	2
493.0	0	2	2
494.0	0	1	1
495.0	0	1	1
496.0	0	1	1
497.0	0	2	2
499.0	0	1	1
506.0	0	1	1
510.0	0	1	1
511.0	0	1	1
514.0	0	1	1
515.0	0	2	2
516.0	0	3	3
518.0	0	1	1
521.0	0	1	1
522.0	0	1	1
526.0	0	1	1
527.0	0	1	1
529.0	0	1	1
530.0	0	1	1
531.0	0	2	2
535.0	0	2	2
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
550.0	0	1	1
551.0	0	1	1
553.0	0	2	2
554.0	0	1	1
557.0	0	3	3
560.0	0	1	1
563.0	0	1	1
565.0	0	1	1
568.0	0	3	3
571.0	0	1	1
572.0	0	1	1
573.0	0	1	1
575.0	0	1	1
579.0	0	1	1
582.0	0	1	1
584.0	0	2	2
586.0	0	1	1
589.0	0	1	1
590.0	0	1	1
591.0	0	1	1
596.0	0	1	1
599.0	0	1	1
603.0	0	1	1
610.0	0	1	1
616.0	0	1	1
617.0	0	1	1
618.0	0	1	1
619.0	0	3	3
620.0	0	1	1
623.0	0	1	1
625.0	0	1	1
628.0	0	1	1
629.0	0	1	1
631.0	0	1	1
632.0	0	2	2
633.0	0	1	1
635.0	0	1	1
637.0	0	1	1
639.0	0	1	1
645.0	0	1	1
646.0	0	2	2
648.0	0	1	1
650.0	0	1	1
651.0	0	1	1
654.0	0	2	2
657.0	0	2	2
662.0	0	1	1
668.0	0	1	1
669.0	0	2	2
671.0	0	1	1
674.0	0	1	1
678.0	0	1	1
679.0	0	1	1
684.0	0	1	1
685.0	0	1	1
689.0	0	1	1
695.0	0	1	1
713.0	0	1	1
714.0	0	1	1
715.0	0	1	1
719.0	0	1	1
729.0	0	1	1
737.0	0	1	1
742.0	0	1	1
746.0	0	1	1
747.0	0	1	1
750.0	0	1	1
752.0	0	1	1
753.0	0	1	1
754.0	0	1	1
755.0	0	1	1
763.0	0	1	1
769.0	0	1	1
773.0	0	2	2
774.0	0	1	1
779.0	0	1	1
787.0	0	1	1
791.0	0	2	2
792.0	0	1	1
796.0	0	1	1
797.0	0	1	1
798.0	0	1	1
813.0	0	2	2
815.0	0	1	1
819.0	0	1	1
820.0	0	1	1
821.0	0	1	1
826.0	0	1	1
828.0	0	1	1
831.0	0	2	2
845.0	0	1	1
856.0	0	1	1
858.0	0	1	1
859.0	0	1	1
861.0	0	1	1
880.0	0	1	1
883.0	0	1	1
909.0	0	1	1
910.0	0	1	1
911.0	0	1	1
912.0	0	1	1
915.0	0	1	1
922.0	0	2	2
927.0	0	1	1
932.0	0	1	1
943.0	0	1	1
952.0	0	1	1
964.0	0	1	1
970.0	0	1	1
1015.0	0	1	1
1016.0	0	1	1
1022.0	0	1	1
1035.0	0	1	1
1043.0	0	1	1
1064.0	0	1	1
1081.0	0	2	2
1085.0	0	1	1
1105.0	0	1	1
1128.0	0	1	1
1137.0	0	1	1
1147.0	0	1	1
1182.0	0	1	1
1197.0	0	1	1
1218.0	0	1	1
1255.0	0	1	1
1257.0	0	2	2
1261.0	0	1	1
1299.0	0	1	1
1307.0	0	1	1
1328.0	0	1	1
1414.0	0	1	1
1457.0	0	1	1
1510.0	0	1	1
1532.0	0	1	1
1561.0	0	1	1
1564.0	0	1	1
1636.0	0	1	1
1684.0	0	1	1
1706.0	0	1	1
1785.0	0	1	1
1804.0	0	1	1
1807.0	0	1	1
1819.0	0	1	1
1898.0	0	1	1
1914.0	0	1	1
1989.0	0	1	1
2020.0	0	1	1
2047.0	0	1	1
2070.0	0	1	1
2114.0	0	1	1
2140.0	0	1	1
2175.0	0	1	1
2267.0	0	1	1
2431.0	0	1	1
2650.0	0	1	1
2655.0	0	1	1
2921.0	0	1	1
3303.0	0	1	1
3342.0	0	1	1
3481.0	0	1	1
4331.0	0	1	1