## 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-RU1uMTA1uM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uMTA1uM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uMTA1uM_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: Wed Oct 04 10:31:29 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	1194	40179900	33716327	0	1011	7910970	0	0.196898	88151019

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28700508	28700508
2.0	1.633936	2625164	2625164
3.0	2.03581	444176	444176
4.0	2.290573	162672	162672
5.0	2.452076	86987	86987
6.0	2.554459	54186	54186
7.0	2.619363	37162	37162
8.0	2.660508	26423	26423
9.0	2.686591	19938	19938
10.0	2.703127	15471	15471
11.0	2.713609	12101	12101
12.0	2.720254	9763	9763
13.0	2.724466	8056	8056
14.0	2.727137	6733	6733
15.0	2.72883	5762	5762
16.0	2.729903	4900	4900
17.0	2.730583	4255	4255
18.0	2.731015	3601	3601
19.0	2.731288	3195	3195
20.0	2.731461	2780	2780
21.0	2.731571	2435	2435
22.0	2.731641	2275	2275
23.0	2.731685	1988	1988
24.0	2.731713	1819	1819
25.0	2.731731	1646	1646
26.0	2.731742	1430	1430
27.0	2.731749	1308	1308
28.0	2.731754	1228	1228
29.0	2.731756	1139	1139
30.0	2.731758	1041	1041
31.0	2.731759	962	962
32.0	2.73176	873	873
33.0	2.731761	857	857
34.0	2.731761	714	714
35.0	2.731761	690	690
36.0	2.731761	638	638
37.0	2.731761	595	595
38.0	2.731761	525	525
39.0	2.731761	507	507
40.0	2.731761	454	454
41.0	2.731761	475	475
42.0	2.731761	430	430
43.0	2.731761	418	418
44.0	2.731761	343	343
45.0	2.731761	352	352
46.0	2.731761	369	369
47.0	2.731761	313	313
48.0	2.731761	289	289
49.0	2.731761	274	274
50.0	2.731761	274	274
51.0	2.731761	249	249
52.0	2.731761	241	241
53.0	2.731761	245	245
54.0	2.731761	217	217
55.0	2.731761	224	224
56.0	2.731761	205	205
57.0	2.731761	196	196
58.0	2.731761	165	165
59.0	2.731761	205	205
60.0	2.731761	170	170
61.0	2.731761	152	152
62.0	2.731761	187	187
63.0	2.731761	155	155
64.0	2.731761	141	141
65.0	2.731761	124	124
66.0	2.731761	128	128
67.0	2.731761	142	142
68.0	2.731761	115	115
69.0	2.731761	128	128
70.0	2.731761	116	116
71.0	2.731761	107	107
72.0	2.731761	100	100
73.0	2.731761	104	104
74.0	2.731761	109	109
75.0	2.731761	96	96
76.0	2.731761	97	97
77.0	2.731761	90	90
78.0	2.731761	73	73
79.0	2.731761	72	72
80.0	2.731761	90	90
81.0	2.731761	84	84
82.0	2.731761	66	66
83.0	2.731761	79	79
84.0	2.731761	52	52
85.0	2.731761	69	69
86.0	2.731761	54	54
87.0	2.731761	71	71
88.0	2.731761	71	71
89.0	2.731761	57	57
90.0	2.731761	58	58
91.0	2.731761	66	66
92.0	2.731761	62	62
93.0	2.731761	43	43
94.0	2.731761	53	53
95.0	2.731761	56	56
96.0	2.731761	57	57
97.0	2.731761	47	47
98.0	2.731761	50	50
99.0	2.731761	53	53
100.0	2.731761	55	55
101.0	0	55	55
102.0	0	52	52
103.0	0	28	28
104.0	0	35	35
105.0	0	37	37
106.0	0	52	52
107.0	0	40	40
108.0	0	42	42
109.0	0	39	39
110.0	0	39	39
111.0	0	29	29
112.0	0	32	32
113.0	0	38	38
114.0	0	34	34
115.0	0	27	27
116.0	0	35	35
117.0	0	35	35
118.0	0	28	28
119.0	0	28	28
120.0	0	28	28
121.0	0	28	28
122.0	0	21	21
123.0	0	19	19
124.0	0	29	29
125.0	0	21	21
126.0	0	19	19
127.0	0	27	27
128.0	0	32	32
129.0	0	15	15
130.0	0	27	27
131.0	0	22	22
132.0	0	20	20
133.0	0	28	28
134.0	0	20	20
135.0	0	25	25
136.0	0	20	20
137.0	0	28	28
138.0	0	15	15
139.0	0	23	23
140.0	0	19	19
141.0	0	22	22
142.0	0	19	19
143.0	0	19	19
144.0	0	17	17
145.0	0	10	10
146.0	0	19	19
147.0	0	12	12
148.0	0	18	18
149.0	0	17	17
150.0	0	12	12
151.0	0	15	15
152.0	0	14	14
153.0	0	19	19
154.0	0	17	17
155.0	0	12	12
156.0	0	4	4
157.0	0	8	8
158.0	0	15	15
159.0	0	16	16
160.0	0	15	15
161.0	0	8	8
162.0	0	19	19
163.0	0	10	10
164.0	0	12	12
165.0	0	6	6
166.0	0	16	16
167.0	0	12	12
168.0	0	9	9
169.0	0	19	19
170.0	0	11	11
171.0	0	19	19
172.0	0	9	9
173.0	0	10	10
174.0	0	14	14
175.0	0	13	13
176.0	0	9	9
177.0	0	10	10
178.0	0	11	11
179.0	0	11	11
180.0	0	10	10
181.0	0	7	7
182.0	0	9	9
183.0	0	9	9
184.0	0	7	7
185.0	0	7	7
186.0	0	6	6
187.0	0	9	9
188.0	0	6	6
189.0	0	6	6
190.0	0	10	10
191.0	0	11	11
192.0	0	7	7
193.0	0	8	8
194.0	0	13	13
195.0	0	15	15
196.0	0	10	10
197.0	0	11	11
198.0	0	6	6
199.0	0	7	7
200.0	0	6	6
201.0	0	6	6
202.0	0	5	5
203.0	0	9	9
204.0	0	10	10
205.0	0	6	6
206.0	0	7	7
207.0	0	11	11
208.0	0	5	5
209.0	0	3	3
210.0	0	6	6
211.0	0	7	7
212.0	0	5	5
213.0	0	7	7
214.0	0	6	6
215.0	0	4	4
216.0	0	4	4
217.0	0	8	8
218.0	0	5	5
219.0	0	6	6
220.0	0	8	8
221.0	0	4	4
222.0	0	12	12
223.0	0	3	3
224.0	0	4	4
225.0	0	5	5
226.0	0	3	3
227.0	0	6	6
228.0	0	2	2
229.0	0	10	10
230.0	0	5	5
231.0	0	9	9
232.0	0	3	3
233.0	0	9	9
234.0	0	8	8
235.0	0	5	5
236.0	0	9	9
237.0	0	3	3
238.0	0	4	4
239.0	0	5	5
240.0	0	3	3
241.0	0	11	11
242.0	0	8	8
243.0	0	4	4
244.0	0	3	3
245.0	0	1	1
246.0	0	5	5
247.0	0	3	3
248.0	0	5	5
249.0	0	8	8
250.0	0	10	10
251.0	0	5	5
252.0	0	3	3
253.0	0	3	3
254.0	0	5	5
255.0	0	2	2
256.0	0	6	6
257.0	0	5	5
258.0	0	4	4
259.0	0	2	2
260.0	0	1	1
261.0	0	4	4
262.0	0	3	3
263.0	0	4	4
264.0	0	2	2
265.0	0	2	2
266.0	0	2	2
267.0	0	1	1
268.0	0	3	3
269.0	0	7	7
270.0	0	1	1
271.0	0	3	3
272.0	0	4	4
273.0	0	2	2
274.0	0	4	4
275.0	0	5	5
276.0	0	3	3
277.0	0	3	3
278.0	0	7	7
279.0	0	3	3
280.0	0	2	2
281.0	0	3	3
282.0	0	3	3
283.0	0	2	2
284.0	0	2	2
285.0	0	2	2
286.0	0	2	2
287.0	0	2	2
288.0	0	3	3
289.0	0	5	5
290.0	0	4	4
291.0	0	6	6
292.0	0	1	1
293.0	0	4	4
294.0	0	5	5
295.0	0	2	2
296.0	0	4	4
297.0	0	4	4
298.0	0	3	3
299.0	0	3	3
300.0	0	3	3
301.0	0	3	3
302.0	0	1	1
303.0	0	2	2
304.0	0	2	2
305.0	0	4	4
306.0	0	1	1
307.0	0	3	3
308.0	0	1	1
309.0	0	2	2
310.0	0	1	1
311.0	0	3	3
312.0	0	3	3
313.0	0	2	2
314.0	0	4	4
315.0	0	1	1
316.0	0	2	2
317.0	0	4	4
318.0	0	2	2
319.0	0	1	1
320.0	0	5	5
321.0	0	4	4
322.0	0	3	3
323.0	0	2	2
324.0	0	6	6
329.0	0	1	1
330.0	0	1	1
331.0	0	5	5
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
335.0	0	3	3
336.0	0	3	3
337.0	0	2	2
338.0	0	2	2
340.0	0	2	2
341.0	0	1	1
342.0	0	1	1
343.0	0	1	1
344.0	0	2	2
345.0	0	2	2
346.0	0	2	2
348.0	0	1	1
349.0	0	1	1
350.0	0	3	3
352.0	0	1	1
353.0	0	3	3
354.0	0	1	1
355.0	0	1	1
356.0	0	2	2
357.0	0	2	2
358.0	0	1	1
359.0	0	1	1
360.0	0	2	2
361.0	0	4	4
362.0	0	2	2
364.0	0	1	1
365.0	0	3	3
366.0	0	3	3
367.0	0	2	2
368.0	0	1	1
369.0	0	2	2
370.0	0	2	2
371.0	0	2	2
372.0	0	1	1
373.0	0	3	3
374.0	0	1	1
375.0	0	2	2
376.0	0	1	1
377.0	0	1	1
378.0	0	4	4
379.0	0	4	4
380.0	0	2	2
381.0	0	3	3
383.0	0	2	2
385.0	0	1	1
386.0	0	1	1
387.0	0	3	3
388.0	0	3	3
389.0	0	1	1
390.0	0	1	1
392.0	0	1	1
393.0	0	1	1
395.0	0	2	2
397.0	0	1	1
398.0	0	1	1
400.0	0	1	1
401.0	0	1	1
402.0	0	2	2
403.0	0	3	3
404.0	0	1	1
405.0	0	2	2
407.0	0	1	1
408.0	0	3	3
409.0	0	1	1
410.0	0	1	1
411.0	0	2	2
414.0	0	3	3
415.0	0	1	1
416.0	0	1	1
417.0	0	3	3
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	2	2
422.0	0	1	1
424.0	0	1	1
425.0	0	2	2
428.0	0	1	1
429.0	0	2	2
431.0	0	1	1
436.0	0	2	2
438.0	0	1	1
439.0	0	2	2
441.0	0	2	2
442.0	0	1	1
443.0	0	3	3
445.0	0	1	1
446.0	0	1	1
448.0	0	1	1
449.0	0	3	3
452.0	0	1	1
453.0	0	1	1
454.0	0	1	1
457.0	0	1	1
459.0	0	1	1
460.0	0	1	1
461.0	0	1	1
462.0	0	2	2
464.0	0	1	1
465.0	0	1	1
467.0	0	2	2
468.0	0	1	1
469.0	0	1	1
472.0	0	1	1
473.0	0	2	2
474.0	0	1	1
476.0	0	1	1
477.0	0	2	2
478.0	0	2	2
480.0	0	2	2
481.0	0	1	1
482.0	0	2	2
484.0	0	1	1
487.0	0	1	1
490.0	0	1	1
493.0	0	2	2
494.0	0	2	2
497.0	0	1	1
499.0	0	3	3
500.0	0	1	1
502.0	0	1	1
503.0	0	2	2
505.0	0	1	1
506.0	0	1	1
508.0	0	1	1
509.0	0	2	2
510.0	0	1	1
512.0	0	1	1
513.0	0	2	2
515.0	0	1	1
518.0	0	2	2
521.0	0	2	2
522.0	0	2	2
524.0	0	1	1
525.0	0	1	1
530.0	0	1	1
534.0	0	3	3
535.0	0	1	1
536.0	0	1	1
539.0	0	1	1
540.0	0	2	2
543.0	0	1	1
544.0	0	1	1
545.0	0	2	2
548.0	0	1	1
553.0	0	1	1
554.0	0	1	1
555.0	0	1	1
558.0	0	1	1
559.0	0	3	3
565.0	0	2	2
569.0	0	1	1
570.0	0	1	1
571.0	0	1	1
574.0	0	1	1
582.0	0	1	1
583.0	0	1	1
587.0	0	1	1
591.0	0	1	1
594.0	0	1	1
597.0	0	1	1
599.0	0	1	1
600.0	0	1	1
601.0	0	1	1
617.0	0	1	1
627.0	0	1	1
632.0	0	1	1
637.0	0	1	1
641.0	0	1	1
642.0	0	1	1
647.0	0	1	1
648.0	0	3	3
653.0	0	2	2
654.0	0	3	3
655.0	0	1	1
658.0	0	1	1
671.0	0	1	1
685.0	0	1	1
687.0	0	1	1
704.0	0	1	1
706.0	0	1	1
707.0	0	1	1
708.0	0	1	1
710.0	0	1	1
716.0	0	1	1
717.0	0	2	2
719.0	0	1	1
726.0	0	1	1
728.0	0	1	1
729.0	0	1	1
737.0	0	1	1
740.0	0	1	1
747.0	0	1	1
770.0	0	1	1
772.0	0	1	1
781.0	0	1	1
785.0	0	1	1
795.0	0	1	1
823.0	0	1	1
825.0	0	1	1
826.0	0	1	1
892.0	0	1	1
919.0	0	1	1
928.0	0	1	1
936.0	0	1	1
948.0	0	1	1
949.0	0	1	1
957.0	0	1	1
988.0	0	1	1
999.0	0	1	1
1031.0	0	1	1
1040.0	0	1	1
1065.0	0	1	1
1067.0	0	1	1
1082.0	0	1	1
1091.0	0	1	1
1099.0	0	1	1
1118.0	0	1	1
1137.0	0	1	1
1158.0	0	1	1
1162.0	0	1	1
1167.0	0	1	1
1176.0	0	1	1
1184.0	0	1	1
1200.0	0	1	1
1253.0	0	1	1
1255.0	0	1	1
1293.0	0	1	1
1321.0	0	1	1
1355.0	0	1	1
1363.0	0	1	1
1372.0	0	1	1
1381.0	0	1	1
1383.0	0	1	1
1493.0	0	1	1
1608.0	0	1	1
1637.0	0	1	1
1665.0	0	1	1
1678.0	0	1	1
1828.0	0	1	1
1844.0	0	1	1
1857.0	0	1	1
1860.0	0	2	2
2101.0	0	1	1
2111.0	0	1	1
2230.0	0	1	1
2241.0	0	1	1
2280.0	0	1	1
2367.0	0	1	1
2418.0	0	1	1
2472.0	0	1	1
2475.0	0	1	1
2494.0	0	1	1
2666.0	0	1	1
2789.0	0	1	1
2899.0	0	1	1
3233.0	0	1	1
3736.0	0	1	1