## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Sep 22 17:43:35 CEST 2022

## 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	972499	41672408	0	1187981	701869	6934751	0	0.172816	110894635

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	31968941	31968941
2.0	1.686751	1816063	1816063
3.0	2.158377	409111	409111
4.0	2.482267	181188	181188
5.0	2.704699	100663	100663
6.0	2.857454	62037	62037
7.0	2.962359	41671	41671
8.0	3.034402	29262	29262
9.0	3.083878	21627	21627
10.0	3.117856	16216	16216
11.0	3.14119	12904	12904
12.0	3.157215	10104	10104
13.0	3.16822	8078	8078
14.0	3.175777	6633	6633
15.0	3.180968	5509	5509
16.0	3.184532	4729	4729
17.0	3.18698	3920	3920
18.0	3.188661	3429	3429
19.0	3.189815	2934	2934
20.0	3.190608	2495	2495
21.0	3.191153	2293	2293
22.0	3.191527	2005	2005
23.0	3.191783	1698	1698
24.0	3.19196	1551	1551
25.0	3.192081	1391	1391
26.0	3.192164	1303	1303
27.0	3.192221	1143	1143
28.0	3.19226	1045	1045
29.0	3.192287	939	939
30.0	3.192306	862	862
31.0	3.192319	833	833
32.0	3.192327	714	714
33.0	3.192333	740	740
34.0	3.192337	626	626
35.0	3.19234	594	594
36.0	3.192342	489	489
37.0	3.192343	521	521
38.0	3.192344	468	468
39.0	3.192345	475	475
40.0	3.192345	425	425
41.0	3.192346	392	392
42.0	3.192346	357	357
43.0	3.192346	323	323
44.0	3.192346	324	324
45.0	3.192346	307	307
46.0	3.192346	301	301
47.0	3.192346	276	276
48.0	3.192346	224	224
49.0	3.192346	243	243
50.0	3.192346	240	240
51.0	3.192346	236	236
52.0	3.192346	188	188
53.0	3.192346	176	176
54.0	3.192346	176	176
55.0	3.192346	185	185
56.0	3.192346	158	158
57.0	3.192346	139	139
58.0	3.192346	151	151
59.0	3.192346	146	146
60.0	3.192346	140	140
61.0	3.192346	155	155
62.0	3.192346	138	138
63.0	3.192346	117	117
64.0	3.192346	107	107
65.0	3.192346	103	103
66.0	3.192346	113	113
67.0	3.192346	109	109
68.0	3.192346	107	107
69.0	3.192346	105	105
70.0	3.192346	109	109
71.0	3.192346	99	99
72.0	3.192346	96	96
73.0	3.192346	86	86
74.0	3.192346	95	95
75.0	3.192346	69	69
76.0	3.192346	80	80
77.0	3.192346	95	95
78.0	3.192346	65	65
79.0	3.192346	67	67
80.0	3.192346	74	74
81.0	3.192346	59	59
82.0	3.192346	63	63
83.0	3.192346	48	48
84.0	3.192346	61	61
85.0	3.192346	50	50
86.0	3.192346	47	47
87.0	3.192346	63	63
88.0	3.192346	61	61
89.0	3.192346	64	64
90.0	3.192346	41	41
91.0	3.192346	45	45
92.0	3.192346	49	49
93.0	3.192346	33	33
94.0	3.192346	55	55
95.0	3.192346	43	43
96.0	3.192346	44	44
97.0	3.192346	48	48
98.0	3.192346	49	49
99.0	3.192346	38	38
100.0	3.192346	36	36
101.0	0	34	34
102.0	0	30	30
103.0	0	43	43
104.0	0	24	24
105.0	0	39	39
106.0	0	20	20
107.0	0	30	30
108.0	0	34	34
109.0	0	28	28
110.0	0	28	28
111.0	0	31	31
112.0	0	34	34
113.0	0	33	33
114.0	0	23	23
115.0	0	29	29
116.0	0	23	23
117.0	0	18	18
118.0	0	26	26
119.0	0	19	19
120.0	0	28	28
121.0	0	23	23
122.0	0	21	21
123.0	0	20	20
124.0	0	26	26
125.0	0	33	33
126.0	0	21	21
127.0	0	16	16
128.0	0	18	18
129.0	0	14	14
130.0	0	23	23
131.0	0	11	11
132.0	0	22	22
133.0	0	18	18
134.0	0	15	15
135.0	0	23	23
136.0	0	21	21
137.0	0	18	18
138.0	0	16	16
139.0	0	23	23
140.0	0	18	18
141.0	0	17	17
142.0	0	22	22
143.0	0	16	16
144.0	0	10	10
145.0	0	17	17
146.0	0	18	18
147.0	0	14	14
148.0	0	20	20
149.0	0	12	12
150.0	0	7	7
151.0	0	13	13
152.0	0	9	9
153.0	0	13	13
154.0	0	12	12
155.0	0	16	16
156.0	0	12	12
157.0	0	13	13
158.0	0	11	11
159.0	0	20	20
160.0	0	8	8
161.0	0	9	9
162.0	0	7	7
163.0	0	12	12
164.0	0	5	5
165.0	0	9	9
166.0	0	12	12
167.0	0	13	13
168.0	0	11	11
169.0	0	11	11
170.0	0	9	9
171.0	0	13	13
172.0	0	8	8
173.0	0	13	13
174.0	0	8	8
175.0	0	9	9
176.0	0	4	4
177.0	0	6	6
178.0	0	8	8
179.0	0	10	10
180.0	0	8	8
181.0	0	13	13
182.0	0	7	7
183.0	0	8	8
184.0	0	10	10
185.0	0	6	6
186.0	0	8	8
187.0	0	9	9
188.0	0	9	9
189.0	0	9	9
190.0	0	8	8
191.0	0	3	3
192.0	0	6	6
193.0	0	10	10
194.0	0	4	4
195.0	0	11	11
196.0	0	7	7
197.0	0	4	4
198.0	0	7	7
199.0	0	7	7
200.0	0	7	7
201.0	0	8	8
202.0	0	5	5
203.0	0	7	7
204.0	0	9	9
205.0	0	3	3
206.0	0	9	9
207.0	0	8	8
208.0	0	8	8
209.0	0	5	5
210.0	0	4	4
211.0	0	3	3
212.0	0	5	5
213.0	0	5	5
214.0	0	9	9
215.0	0	7	7
216.0	0	7	7
217.0	0	7	7
218.0	0	9	9
219.0	0	7	7
220.0	0	13	13
221.0	0	6	6
222.0	0	7	7
223.0	0	5	5
224.0	0	3	3
225.0	0	3	3
226.0	0	5	5
227.0	0	6	6
228.0	0	7	7
229.0	0	7	7
230.0	0	9	9
231.0	0	4	4
232.0	0	2	2
233.0	0	8	8
234.0	0	7	7
235.0	0	4	4
236.0	0	6	6
237.0	0	4	4
238.0	0	5	5
239.0	0	5	5
240.0	0	2	2
241.0	0	4	4
242.0	0	6	6
243.0	0	8	8
244.0	0	3	3
245.0	0	5	5
246.0	0	3	3
247.0	0	4	4
248.0	0	3	3
249.0	0	3	3
250.0	0	1	1
251.0	0	4	4
252.0	0	6	6
253.0	0	4	4
254.0	0	8	8
255.0	0	4	4
256.0	0	2	2
257.0	0	8	8
258.0	0	1	1
259.0	0	4	4
260.0	0	5	5
261.0	0	5	5
262.0	0	2	2
263.0	0	2	2
264.0	0	3	3
265.0	0	3	3
266.0	0	2	2
267.0	0	6	6
268.0	0	5	5
269.0	0	5	5
270.0	0	4	4
271.0	0	1	1
272.0	0	5	5
273.0	0	3	3
274.0	0	3	3
275.0	0	2	2
276.0	0	2	2
277.0	0	2	2
278.0	0	3	3
279.0	0	2	2
280.0	0	2	2
281.0	0	3	3
282.0	0	2	2
283.0	0	2	2
284.0	0	1	1
285.0	0	3	3
286.0	0	3	3
287.0	0	3	3
288.0	0	3	3
289.0	0	2	2
290.0	0	3	3
291.0	0	2	2
292.0	0	4	4
293.0	0	6	6
294.0	0	3	3
296.0	0	1	1
297.0	0	3	3
298.0	0	4	4
299.0	0	1	1
300.0	0	4	4
301.0	0	2	2
302.0	0	1	1
303.0	0	2	2
304.0	0	3	3
305.0	0	1	1
306.0	0	4	4
307.0	0	2	2
308.0	0	2	2
309.0	0	1	1
310.0	0	2	2
311.0	0	2	2
312.0	0	4	4
313.0	0	4	4
314.0	0	3	3
315.0	0	2	2
316.0	0	1	1
317.0	0	3	3
318.0	0	3	3
319.0	0	2	2
320.0	0	1	1
321.0	0	1	1
322.0	0	1	1
323.0	0	4	4
324.0	0	4	4
325.0	0	2	2
326.0	0	1	1
328.0	0	2	2
329.0	0	3	3
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
334.0	0	2	2
335.0	0	1	1
336.0	0	1	1
338.0	0	1	1
341.0	0	3	3
342.0	0	1	1
343.0	0	1	1
344.0	0	1	1
345.0	0	3	3
348.0	0	3	3
349.0	0	1	1
350.0	0	1	1
355.0	0	1	1
356.0	0	1	1
358.0	0	1	1
359.0	0	3	3
362.0	0	1	1
363.0	0	3	3
364.0	0	2	2
365.0	0	1	1
367.0	0	1	1
370.0	0	2	2
371.0	0	2	2
372.0	0	3	3
373.0	0	1	1
374.0	0	3	3
375.0	0	2	2
376.0	0	3	3
377.0	0	2	2
378.0	0	1	1
379.0	0	1	1
380.0	0	2	2
381.0	0	1	1
382.0	0	2	2
387.0	0	1	1
392.0	0	2	2
393.0	0	1	1
394.0	0	1	1
397.0	0	1	1
398.0	0	2	2
399.0	0	1	1
401.0	0	1	1
402.0	0	1	1
403.0	0	2	2
404.0	0	1	1
406.0	0	3	3
407.0	0	2	2
408.0	0	3	3
409.0	0	1	1
412.0	0	1	1
413.0	0	2	2
415.0	0	1	1
417.0	0	1	1
420.0	0	2	2
423.0	0	1	1
429.0	0	1	1
431.0	0	1	1
433.0	0	2	2
434.0	0	1	1
438.0	0	1	1
439.0	0	1	1
442.0	0	1	1
444.0	0	1	1
446.0	0	1	1
447.0	0	1	1
448.0	0	1	1
453.0	0	1	1
456.0	0	1	1
458.0	0	2	2
460.0	0	1	1
466.0	0	1	1
467.0	0	1	1
471.0	0	1	1
473.0	0	1	1
474.0	0	1	1
477.0	0	2	2
479.0	0	1	1
481.0	0	2	2
484.0	0	1	1
486.0	0	3	3
492.0	0	1	1
495.0	0	1	1
505.0	0	1	1
508.0	0	1	1
517.0	0	1	1
520.0	0	1	1
521.0	0	4	4
522.0	0	2	2
523.0	0	1	1
527.0	0	1	1
528.0	0	1	1
529.0	0	1	1
532.0	0	1	1
534.0	0	2	2
537.0	0	1	1
539.0	0	1	1
543.0	0	1	1
545.0	0	1	1
550.0	0	1	1
551.0	0	2	2
552.0	0	2	2
555.0	0	1	1
556.0	0	1	1
558.0	0	1	1
560.0	0	1	1
562.0	0	2	2
565.0	0	1	1
571.0	0	1	1
578.0	0	1	1
580.0	0	2	2
581.0	0	1	1
582.0	0	1	1
583.0	0	1	1
586.0	0	1	1
589.0	0	1	1
591.0	0	1	1
596.0	0	1	1
597.0	0	1	1
598.0	0	1	1
602.0	0	1	1
606.0	0	2	2
608.0	0	1	1
609.0	0	1	1
613.0	0	2	2
617.0	0	1	1
621.0	0	1	1
626.0	0	1	1
628.0	0	1	1
631.0	0	1	1
640.0	0	1	1
648.0	0	1	1
654.0	0	1	1
658.0	0	1	1
664.0	0	1	1
666.0	0	1	1
669.0	0	1	1
675.0	0	1	1
682.0	0	1	1
685.0	0	1	1
686.0	0	1	1
697.0	0	2	2
698.0	0	1	1
701.0	0	1	1
709.0	0	1	1
711.0	0	1	1
718.0	0	1	1
720.0	0	1	1
723.0	0	1	1
724.0	0	1	1
730.0	0	1	1
731.0	0	1	1
733.0	0	1	1
752.0	0	1	1
764.0	0	1	1
769.0	0	1	1
775.0	0	1	1
778.0	0	1	1
789.0	0	2	2
790.0	0	2	2
793.0	0	1	1
799.0	0	1	1
823.0	0	1	1
830.0	0	1	1
833.0	0	1	1
837.0	0	1	1
851.0	0	1	1
861.0	0	1	1
862.0	0	1	1
869.0	0	1	1
877.0	0	1	1
882.0	0	1	1
885.0	0	1	1
887.0	0	1	1
889.0	0	1	1
895.0	0	1	1
897.0	0	1	1
898.0	0	1	1
899.0	0	1	1
909.0	0	1	1
917.0	0	1	1
922.0	0	1	1
940.0	0	1	1
947.0	0	1	1
949.0	0	1	1
990.0	0	1	1
1012.0	0	1	1
1028.0	0	1	1
1035.0	0	1	1
1045.0	0	1	1
1053.0	0	1	1
1078.0	0	1	1
1120.0	0	1	1
1121.0	0	1	1
1141.0	0	1	1
1149.0	0	1	1
1171.0	0	1	1
1206.0	0	1	1
1265.0	0	1	1
1270.0	0	1	1
1319.0	0	1	1
1470.0	0	1	1
1561.0	0	1	1
1562.0	0	1	1
1694.0	0	1	1