## 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_plus_TA_100nM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/bwa-mem2/GRCh38-RU_1uM_plus_TA_100nM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/share_moldevbio/ghe_2022/results/qc/markdup/GRCh38-RU_1uM_plus_TA_100nM_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 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 19:05:07 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	1106520	43308440	0	1261320	825027	6461514	0	0.15672	130311007

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	33928498	33928498
2.0	1.717239	2077912	2077912
3.0	2.23167	385065	385065
4.0	2.60064	153826	153826
5.0	2.865279	82995	82995
6.0	3.055089	50755	50755
7.0	3.191227	34042	34042
8.0	3.288871	23972	23972
9.0	3.358905	17424	17424
10.0	3.409137	13649	13649
11.0	3.445164	10600	10600
12.0	3.471005	8476	8476
13.0	3.489538	6952	6952
14.0	3.502832	5665	5665
15.0	3.512366	4802	4802
16.0	3.519204	4052	4052
17.0	3.524109	3486	3486
18.0	3.527627	2924	2924
19.0	3.53015	2659	2659
20.0	3.53196	2296	2296
21.0	3.533258	1997	1997
22.0	3.534189	1793	1793
23.0	3.534857	1570	1570
24.0	3.535335	1363	1363
25.0	3.535679	1262	1262
26.0	3.535925	1151	1151
27.0	3.536102	1098	1098
28.0	3.536229	993	993
29.0	3.53632	868	868
30.0	3.536385	840	840
31.0	3.536432	691	691
32.0	3.536465	690	690
33.0	3.536489	583	583
34.0	3.536507	608	608
35.0	3.536519	562	562
36.0	3.536528	470	470
37.0	3.536534	447	447
38.0	3.536539	409	409
39.0	3.536542	383	383
40.0	3.536544	344	344
41.0	3.536546	361	361
42.0	3.536547	348	348
43.0	3.536548	320	320
44.0	3.536549	298	298
45.0	3.536549	251	251
46.0	3.536549	252	252
47.0	3.53655	240	240
48.0	3.53655	226	226
49.0	3.53655	233	233
50.0	3.53655	202	202
51.0	3.53655	201	201
52.0	3.53655	152	152
53.0	3.53655	186	186
54.0	3.53655	181	181
55.0	3.53655	141	141
56.0	3.53655	147	147
57.0	3.53655	139	139
58.0	3.53655	149	149
59.0	3.53655	136	136
60.0	3.53655	135	135
61.0	3.53655	119	119
62.0	3.53655	115	115
63.0	3.53655	117	117
64.0	3.53655	91	91
65.0	3.53655	95	95
66.0	3.53655	98	98
67.0	3.53655	88	88
68.0	3.53655	101	101
69.0	3.53655	91	91
70.0	3.53655	97	97
71.0	3.53655	74	74
72.0	3.53655	76	76
73.0	3.53655	64	64
74.0	3.53655	75	75
75.0	3.53655	75	75
76.0	3.53655	66	66
77.0	3.53655	66	66
78.0	3.53655	68	68
79.0	3.53655	68	68
80.0	3.53655	72	72
81.0	3.53655	62	62
82.0	3.53655	57	57
83.0	3.53655	60	60
84.0	3.53655	55	55
85.0	3.53655	64	64
86.0	3.53655	48	48
87.0	3.53655	42	42
88.0	3.53655	38	38
89.0	3.53655	48	48
90.0	3.53655	39	39
91.0	3.53655	48	48
92.0	3.53655	49	49
93.0	3.53655	31	31
94.0	3.53655	36	36
95.0	3.53655	39	39
96.0	3.53655	41	41
97.0	3.53655	34	34
98.0	3.53655	37	37
99.0	3.53655	31	31
100.0	3.53655	31	31
101.0	0	22	22
102.0	0	40	40
103.0	0	26	26
104.0	0	26	26
105.0	0	29	29
106.0	0	29	29
107.0	0	32	32
108.0	0	18	18
109.0	0	24	24
110.0	0	29	29
111.0	0	23	23
112.0	0	18	18
113.0	0	22	22
114.0	0	19	19
115.0	0	15	15
116.0	0	17	17
117.0	0	12	12
118.0	0	21	21
119.0	0	22	22
120.0	0	22	22
121.0	0	24	24
122.0	0	17	17
123.0	0	13	13
124.0	0	13	13
125.0	0	28	28
126.0	0	17	17
127.0	0	20	20
128.0	0	29	29
129.0	0	19	19
130.0	0	21	21
131.0	0	19	19
132.0	0	11	11
133.0	0	17	17
134.0	0	14	14
135.0	0	17	17
136.0	0	19	19
137.0	0	5	5
138.0	0	15	15
139.0	0	10	10
140.0	0	16	16
141.0	0	9	9
142.0	0	14	14
143.0	0	14	14
144.0	0	15	15
145.0	0	18	18
146.0	0	11	11
147.0	0	11	11
148.0	0	10	10
149.0	0	10	10
150.0	0	10	10
151.0	0	13	13
152.0	0	7	7
153.0	0	13	13
154.0	0	8	8
155.0	0	15	15
156.0	0	8	8
157.0	0	13	13
158.0	0	8	8
159.0	0	8	8
160.0	0	8	8
161.0	0	11	11
162.0	0	13	13
163.0	0	11	11
164.0	0	11	11
165.0	0	5	5
166.0	0	8	8
167.0	0	8	8
168.0	0	8	8
169.0	0	10	10
170.0	0	8	8
171.0	0	9	9
172.0	0	5	5
173.0	0	5	5
174.0	0	4	4
175.0	0	7	7
176.0	0	7	7
177.0	0	10	10
178.0	0	2	2
179.0	0	12	12
180.0	0	7	7
181.0	0	9	9
182.0	0	8	8
183.0	0	3	3
184.0	0	5	5
185.0	0	4	4
186.0	0	5	5
187.0	0	3	3
188.0	0	3	3
189.0	0	4	4
190.0	0	1	1
191.0	0	6	6
192.0	0	4	4
193.0	0	6	6
194.0	0	11	11
195.0	0	11	11
196.0	0	7	7
197.0	0	8	8
198.0	0	4	4
199.0	0	2	2
200.0	0	6	6
201.0	0	5	5
202.0	0	4	4
203.0	0	6	6
204.0	0	3	3
205.0	0	4	4
206.0	0	5	5
207.0	0	4	4
208.0	0	4	4
209.0	0	3	3
210.0	0	4	4
211.0	0	8	8
212.0	0	2	2
213.0	0	2	2
214.0	0	3	3
215.0	0	5	5
216.0	0	3	3
217.0	0	3	3
218.0	0	2	2
219.0	0	5	5
220.0	0	5	5
221.0	0	5	5
222.0	0	3	3
223.0	0	8	8
224.0	0	2	2
225.0	0	5	5
226.0	0	7	7
227.0	0	2	2
228.0	0	4	4
229.0	0	6	6
230.0	0	6	6
231.0	0	1	1
232.0	0	11	11
233.0	0	5	5
234.0	0	1	1
235.0	0	6	6
236.0	0	3	3
237.0	0	4	4
238.0	0	1	1
239.0	0	1	1
240.0	0	3	3
241.0	0	6	6
242.0	0	1	1
243.0	0	6	6
244.0	0	2	2
245.0	0	2	2
246.0	0	1	1
247.0	0	1	1
248.0	0	2	2
250.0	0	3	3
251.0	0	2	2
253.0	0	2	2
254.0	0	1	1
255.0	0	4	4
256.0	0	7	7
257.0	0	1	1
258.0	0	2	2
259.0	0	3	3
260.0	0	3	3
261.0	0	4	4
262.0	0	5	5
263.0	0	3	3
264.0	0	4	4
265.0	0	8	8
266.0	0	2	2
267.0	0	4	4
268.0	0	1	1
269.0	0	2	2
271.0	0	4	4
274.0	0	4	4
275.0	0	3	3
276.0	0	2	2
277.0	0	3	3
278.0	0	4	4
279.0	0	5	5
280.0	0	4	4
281.0	0	2	2
282.0	0	1	1
284.0	0	3	3
285.0	0	2	2
286.0	0	3	3
287.0	0	2	2
288.0	0	3	3
290.0	0	6	6
291.0	0	4	4
292.0	0	1	1
293.0	0	5	5
294.0	0	2	2
297.0	0	1	1
298.0	0	3	3
299.0	0	4	4
300.0	0	3	3
301.0	0	2	2
302.0	0	2	2
304.0	0	1	1
305.0	0	2	2
306.0	0	1	1
307.0	0	1	1
308.0	0	1	1
309.0	0	2	2
310.0	0	2	2
311.0	0	3	3
312.0	0	1	1
313.0	0	1	1
314.0	0	2	2
315.0	0	2	2
316.0	0	1	1
317.0	0	1	1
318.0	0	1	1
319.0	0	1	1
320.0	0	2	2
322.0	0	1	1
323.0	0	2	2
324.0	0	1	1
327.0	0	1	1
333.0	0	1	1
335.0	0	2	2
336.0	0	1	1
337.0	0	1	1
340.0	0	2	2
341.0	0	2	2
343.0	0	3	3
344.0	0	1	1
346.0	0	2	2
348.0	0	1	1
350.0	0	1	1
351.0	0	1	1
353.0	0	1	1
359.0	0	1	1
360.0	0	1	1
361.0	0	2	2
362.0	0	1	1
363.0	0	1	1
367.0	0	2	2
368.0	0	1	1
369.0	0	1	1
371.0	0	2	2
372.0	0	2	2
374.0	0	1	1
375.0	0	1	1
377.0	0	1	1
380.0	0	2	2
381.0	0	2	2
382.0	0	1	1
383.0	0	1	1
384.0	0	1	1
385.0	0	1	1
389.0	0	3	3
390.0	0	1	1
391.0	0	1	1
394.0	0	1	1
399.0	0	2	2
403.0	0	2	2
406.0	0	1	1
407.0	0	2	2
408.0	0	1	1
412.0	0	3	3
418.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	2	2
427.0	0	2	2
429.0	0	1	1
430.0	0	2	2
431.0	0	1	1
436.0	0	1	1
437.0	0	1	1
440.0	0	1	1
447.0	0	1	1
448.0	0	1	1
451.0	0	1	1
453.0	0	1	1
455.0	0	2	2
456.0	0	2	2
457.0	0	2	2
459.0	0	2	2
464.0	0	1	1
469.0	0	1	1
472.0	0	1	1
473.0	0	2	2
475.0	0	1	1
476.0	0	3	3
478.0	0	1	1
484.0	0	1	1
490.0	0	1	1
492.0	0	1	1
494.0	0	2	2
495.0	0	2	2
497.0	0	2	2
500.0	0	1	1
501.0	0	1	1
502.0	0	1	1
507.0	0	1	1
511.0	0	1	1
512.0	0	1	1
515.0	0	1	1
525.0	0	3	3
527.0	0	3	3
529.0	0	1	1
531.0	0	1	1
532.0	0	2	2
533.0	0	3	3
536.0	0	1	1
539.0	0	2	2
549.0	0	1	1
551.0	0	1	1
555.0	0	1	1
557.0	0	1	1
559.0	0	2	2
562.0	0	1	1
565.0	0	1	1
567.0	0	1	1
569.0	0	1	1
575.0	0	1	1
578.0	0	1	1
588.0	0	1	1
598.0	0	1	1
608.0	0	2	2
619.0	0	1	1
620.0	0	1	1
630.0	0	1	1
632.0	0	1	1
638.0	0	2	2
645.0	0	1	1
658.0	0	1	1
659.0	0	1	1
662.0	0	1	1
666.0	0	1	1
667.0	0	1	1
673.0	0	1	1
683.0	0	1	1
687.0	0	1	1
689.0	0	1	1
693.0	0	1	1
697.0	0	1	1
712.0	0	1	1
724.0	0	1	1
731.0	0	1	1
735.0	0	1	1
743.0	0	1	1
764.0	0	2	2
780.0	0	1	1
790.0	0	1	1
802.0	0	1	1
804.0	0	1	1
805.0	0	1	1
808.0	0	1	1
819.0	0	1	1
840.0	0	1	1
844.0	0	1	1
855.0	0	1	1
892.0	0	1	1
910.0	0	1	1
929.0	0	1	1
1005.0	0	1	1
1021.0	0	1	1
1078.0	0	1	1
1129.0	0	1	1
1158.0	0	1	1
1294.0	0	1	1
1313.0	0	1	1
1355.0	0	1	1
1460.0	0	1	1