## 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-RU1uMTA100nM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/star/GRCh38.p13-RU1uMTA100nM_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results/qc/markdup/GRCh38.p13-RU1uMTA100nM_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 10:21:19 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	931	43132414	18945077	0	748	6900133	0	0.159983	120011890

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	33239016	33239016
2.0	1.698094	2114492	2114492
3.0	2.18543	394192	394192
4.0	2.525636	159775	159775
5.0	2.763132	87220	87220
6.0	2.928926	53507	53507
7.0	3.044667	36175	36175
8.0	3.125464	25915	25915
9.0	3.181869	19112	19112
10.0	3.221244	14910	14910
11.0	3.248732	11572	11572
12.0	3.267921	9456	9456
13.0	3.281317	7599	7599
14.0	3.290668	6195	6195
15.0	3.297197	5364	5364
16.0	3.301754	4580	4580
17.0	3.304935	3880	3880
18.0	3.307156	3332	3332
19.0	3.308707	3007	3007
20.0	3.309789	2553	2553
21.0	3.310545	2302	2302
22.0	3.311072	2039	2039
23.0	3.31144	1825	1825
24.0	3.311697	1592	1592
25.0	3.311877	1412	1412
26.0	3.312002	1268	1268
27.0	3.31209	1226	1226
28.0	3.312151	1133	1133
29.0	3.312193	1028	1028
30.0	3.312223	903	903
31.0	3.312244	790	790
32.0	3.312258	756	756
33.0	3.312268	685	685
34.0	3.312276	675	675
35.0	3.31228	597	597
36.0	3.312284	545	545
37.0	3.312286	493	493
38.0	3.312288	432	432
39.0	3.312289	400	400
40.0	3.31229	396	396
41.0	3.312291	402	402
42.0	3.312291	398	398
43.0	3.312291	343	343
44.0	3.312291	321	321
45.0	3.312292	297	297
46.0	3.312292	306	306
47.0	3.312292	302	302
48.0	3.312292	231	231
49.0	3.312292	269	269
50.0	3.312292	212	212
51.0	3.312292	214	214
52.0	3.312292	186	186
53.0	3.312292	222	222
54.0	3.312292	198	198
55.0	3.312292	173	173
56.0	3.312292	167	167
57.0	3.312292	167	167
58.0	3.312292	152	152
59.0	3.312292	144	144
60.0	3.312292	138	138
61.0	3.312292	134	134
62.0	3.312292	130	130
63.0	3.312292	124	124
64.0	3.312292	98	98
65.0	3.312292	115	115
66.0	3.312292	125	125
67.0	3.312292	116	116
68.0	3.312292	101	101
69.0	3.312292	100	100
70.0	3.312292	114	114
71.0	3.312292	75	75
72.0	3.312292	86	86
73.0	3.312292	74	74
74.0	3.312292	85	85
75.0	3.312292	87	87
76.0	3.312292	77	77
77.0	3.312292	61	61
78.0	3.312292	70	70
79.0	3.312292	65	65
80.0	3.312292	85	85
81.0	3.312292	62	62
82.0	3.312292	71	71
83.0	3.312292	61	61
84.0	3.312292	62	62
85.0	3.312292	49	49
86.0	3.312292	67	67
87.0	3.312292	48	48
88.0	3.312292	51	51
89.0	3.312292	47	47
90.0	3.312292	51	51
91.0	3.312292	51	51
92.0	3.312292	40	40
93.0	3.312292	39	39
94.0	3.312292	41	41
95.0	3.312292	46	46
96.0	3.312292	47	47
97.0	3.312292	48	48
98.0	3.312292	29	29
99.0	3.312292	39	39
100.0	3.312292	32	32
101.0	0	37	37
102.0	0	35	35
103.0	0	26	26
104.0	0	23	23
105.0	0	36	36
106.0	0	35	35
107.0	0	35	35
108.0	0	35	35
109.0	0	33	33
110.0	0	27	27
111.0	0	30	30
112.0	0	18	18
113.0	0	25	25
114.0	0	21	21
115.0	0	22	22
116.0	0	5	5
117.0	0	24	24
118.0	0	27	27
119.0	0	27	27
120.0	0	18	18
121.0	0	20	20
122.0	0	22	22
123.0	0	23	23
124.0	0	21	21
125.0	0	28	28
126.0	0	17	17
127.0	0	27	27
128.0	0	16	16
129.0	0	12	12
130.0	0	20	20
131.0	0	18	18
132.0	0	14	14
133.0	0	19	19
134.0	0	16	16
135.0	0	10	10
136.0	0	15	15
137.0	0	12	12
138.0	0	18	18
139.0	0	14	14
140.0	0	14	14
141.0	0	12	12
142.0	0	13	13
143.0	0	18	18
144.0	0	14	14
145.0	0	20	20
146.0	0	19	19
147.0	0	13	13
148.0	0	7	7
149.0	0	10	10
150.0	0	18	18
151.0	0	14	14
152.0	0	9	9
153.0	0	11	11
154.0	0	14	14
155.0	0	11	11
156.0	0	12	12
157.0	0	11	11
158.0	0	15	15
159.0	0	15	15
160.0	0	9	9
161.0	0	10	10
162.0	0	8	8
163.0	0	11	11
164.0	0	12	12
165.0	0	14	14
166.0	0	8	8
167.0	0	10	10
168.0	0	10	10
169.0	0	5	5
170.0	0	4	4
171.0	0	15	15
172.0	0	10	10
173.0	0	15	15
174.0	0	7	7
175.0	0	7	7
176.0	0	6	6
177.0	0	7	7
178.0	0	6	6
179.0	0	12	12
180.0	0	10	10
181.0	0	12	12
182.0	0	9	9
183.0	0	7	7
184.0	0	4	4
185.0	0	7	7
186.0	0	5	5
187.0	0	9	9
188.0	0	8	8
189.0	0	9	9
190.0	0	2	2
191.0	0	9	9
192.0	0	8	8
193.0	0	9	9
194.0	0	9	9
195.0	0	9	9
196.0	0	5	5
197.0	0	5	5
198.0	0	7	7
199.0	0	6	6
200.0	0	7	7
201.0	0	8	8
202.0	0	6	6
203.0	0	4	4
204.0	0	2	2
205.0	0	2	2
206.0	0	5	5
207.0	0	7	7
208.0	0	3	3
209.0	0	13	13
210.0	0	1	1
211.0	0	2	2
212.0	0	4	4
213.0	0	2	2
214.0	0	6	6
215.0	0	6	6
216.0	0	3	3
217.0	0	6	6
218.0	0	6	6
219.0	0	7	7
220.0	0	8	8
221.0	0	4	4
222.0	0	3	3
223.0	0	2	2
224.0	0	3	3
225.0	0	7	7
226.0	0	2	2
227.0	0	4	4
228.0	0	4	4
229.0	0	6	6
230.0	0	6	6
231.0	0	5	5
232.0	0	8	8
233.0	0	4	4
234.0	0	4	4
235.0	0	4	4
236.0	0	3	3
237.0	0	7	7
238.0	0	5	5
239.0	0	7	7
240.0	0	3	3
241.0	0	6	6
242.0	0	5	5
243.0	0	4	4
244.0	0	2	2
245.0	0	3	3
246.0	0	5	5
247.0	0	5	5
248.0	0	6	6
249.0	0	1	1
250.0	0	1	1
251.0	0	3	3
252.0	0	2	2
253.0	0	2	2
254.0	0	6	6
255.0	0	3	3
256.0	0	3	3
257.0	0	3	3
258.0	0	3	3
259.0	0	2	2
260.0	0	6	6
261.0	0	4	4
262.0	0	3	3
263.0	0	2	2
264.0	0	7	7
265.0	0	3	3
266.0	0	6	6
267.0	0	2	2
268.0	0	1	1
269.0	0	4	4
270.0	0	2	2
271.0	0	5	5
272.0	0	1	1
273.0	0	3	3
274.0	0	4	4
275.0	0	2	2
276.0	0	3	3
277.0	0	4	4
278.0	0	1	1
279.0	0	4	4
280.0	0	2	2
281.0	0	5	5
282.0	0	2	2
283.0	0	2	2
284.0	0	4	4
285.0	0	5	5
286.0	0	4	4
287.0	0	1	1
288.0	0	4	4
290.0	0	4	4
291.0	0	6	6
292.0	0	5	5
293.0	0	5	5
294.0	0	3	3
296.0	0	3	3
297.0	0	4	4
299.0	0	2	2
301.0	0	2	2
302.0	0	2	2
303.0	0	1	1
304.0	0	3	3
305.0	0	3	3
306.0	0	3	3
307.0	0	3	3
308.0	0	1	1
309.0	0	1	1
310.0	0	6	6
311.0	0	3	3
312.0	0	2	2
313.0	0	4	4
314.0	0	2	2
315.0	0	2	2
317.0	0	1	1
318.0	0	2	2
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	1	1
325.0	0	3	3
326.0	0	3	3
327.0	0	3	3
329.0	0	2	2
330.0	0	1	1
334.0	0	3	3
335.0	0	2	2
337.0	0	2	2
338.0	0	1	1
339.0	0	1	1
340.0	0	2	2
343.0	0	2	2
346.0	0	1	1
348.0	0	1	1
349.0	0	4	4
351.0	0	2	2
352.0	0	1	1
353.0	0	1	1
359.0	0	2	2
360.0	0	2	2
361.0	0	4	4
366.0	0	2	2
367.0	0	5	5
368.0	0	2	2
369.0	0	1	1
370.0	0	2	2
372.0	0	2	2
373.0	0	2	2
375.0	0	1	1
376.0	0	1	1
377.0	0	1	1
378.0	0	2	2
379.0	0	1	1
380.0	0	1	1
383.0	0	2	2
384.0	0	1	1
385.0	0	2	2
386.0	0	2	2
387.0	0	4	4
392.0	0	1	1
393.0	0	1	1
396.0	0	1	1
397.0	0	2	2
398.0	0	1	1
402.0	0	1	1
404.0	0	1	1
405.0	0	1	1
406.0	0	1	1
407.0	0	2	2
409.0	0	1	1
410.0	0	1	1
412.0	0	1	1
414.0	0	1	1
416.0	0	3	3
417.0	0	1	1
420.0	0	1	1
422.0	0	1	1
426.0	0	2	2
427.0	0	1	1
428.0	0	2	2
432.0	0	1	1
435.0	0	2	2
438.0	0	1	1
439.0	0	2	2
441.0	0	1	1
443.0	0	1	1
445.0	0	1	1
446.0	0	2	2
447.0	0	1	1
448.0	0	3	3
451.0	0	1	1
452.0	0	1	1
453.0	0	1	1
455.0	0	1	1
457.0	0	1	1
458.0	0	2	2
460.0	0	1	1
461.0	0	1	1
463.0	0	1	1
464.0	0	1	1
467.0	0	1	1
469.0	0	1	1
470.0	0	1	1
472.0	0	2	2
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
476.0	0	2	2
477.0	0	1	1
478.0	0	1	1
480.0	0	1	1
481.0	0	1	1
482.0	0	1	1
486.0	0	1	1
490.0	0	1	1
492.0	0	1	1
494.0	0	1	1
496.0	0	1	1
498.0	0	3	3
500.0	0	1	1
502.0	0	1	1
504.0	0	1	1
506.0	0	2	2
510.0	0	1	1
516.0	0	1	1
517.0	0	1	1
520.0	0	1	1
524.0	0	1	1
528.0	0	1	1
530.0	0	1	1
531.0	0	1	1
532.0	0	2	2
533.0	0	1	1
538.0	0	1	1
542.0	0	1	1
544.0	0	1	1
547.0	0	1	1
548.0	0	2	2
549.0	0	1	1
552.0	0	1	1
557.0	0	1	1
569.0	0	1	1
571.0	0	1	1
573.0	0	1	1
574.0	0	1	1
575.0	0	2	2
582.0	0	1	1
596.0	0	1	1
603.0	0	2	2
616.0	0	1	1
620.0	0	1	1
625.0	0	1	1
640.0	0	1	1
641.0	0	1	1
642.0	0	2	2
644.0	0	1	1
645.0	0	1	1
657.0	0	1	1
658.0	0	1	1
661.0	0	1	1
682.0	0	1	1
683.0	0	1	1
685.0	0	2	2
693.0	0	1	1
707.0	0	1	1
711.0	0	1	1
724.0	0	1	1
725.0	0	1	1
728.0	0	1	1
757.0	0	1	1
764.0	0	1	1
767.0	0	1	1
772.0	0	1	1
780.0	0	1	1
782.0	0	2	2
784.0	0	1	1
785.0	0	1	1
811.0	0	1	1
852.0	0	1	1
864.0	0	1	1
868.0	0	1	1
890.0	0	1	1
927.0	0	1	1
955.0	0	1	1
963.0	0	1	1
995.0	0	1	1
1019.0	0	1	1
1077.0	0	2	2
1099.0	0	1	1
1102.0	0	1	1
1105.0	0	1	1
1119.0	0	1	1
1121.0	0	1	1
1151.0	0	1	1
1214.0	0	1	1
1272.0	0	1	1
1286.0	0	1	1
1306.0	0	1	1
1312.0	0	1	1
1343.0	0	1	1
1354.0	0	1	1
1414.0	0	1	1
1437.0	0	1	1
1451.0	0	1	1
1452.0	0	1	1
1581.0	0	1	1
1738.0	0	1	1
1752.0	0	1	1
1909.0	0	1	1
1957.0	0	1	1
2017.0	0	1	1
2076.0	0	1	1
2176.0	0	1	1
2196.0	0	1	1
2269.0	0	1	1