## 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_no_replicates/star/GRCh38.p13-D18_supernatant_TA_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_supernatant_TA_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D18_supernatant_TA_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 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: Fri Oct 06 01:39:41 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	1456	24738228	22307536	0	1301	3550607	0	0.143549	77719571

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	19835155	19835155
2.0	1.727384	978240	978240
3.0	2.256471	159833	159833
4.0	2.64132	65989	65989
5.0	2.921253	36292	36292
6.0	3.124872	23151	23151
7.0	3.272981	15843	15843
8.0	3.380713	11691	11691
9.0	3.459076	8497	8497
10.0	3.516075	6754	6754
11.0	3.557536	5431	5431
12.0	3.587694	4346	4346
13.0	3.60963	3598	3598
14.0	3.625586	3038	3038
15.0	3.637192	2631	2631
16.0	3.645634	2212	2212
17.0	3.651775	1878	1878
18.0	3.656242	1623	1623
19.0	3.659491	1427	1427
20.0	3.661854	1261	1261
21.0	3.663573	1159	1159
22.0	3.664823	1078	1078
23.0	3.665733	902	902
24.0	3.666394	889	889
25.0	3.666875	765	765
26.0	3.667225	699	699
27.0	3.66748	633	633
28.0	3.667665	617	617
29.0	3.6678	548	548
30.0	3.667898	495	495
31.0	3.667969	464	464
32.0	3.668021	446	446
33.0	3.668059	412	412
34.0	3.668086	393	393
35.0	3.668106	345	345
36.0	3.668121	325	325
37.0	3.668131	300	300
38.0	3.668139	296	296
39.0	3.668144	251	251
40.0	3.668149	255	255
41.0	3.668152	212	212
42.0	3.668154	212	212
43.0	3.668155	207	207
44.0	3.668156	194	194
45.0	3.668157	208	208
46.0	3.668158	204	204
47.0	3.668158	162	162
48.0	3.668159	173	173
49.0	3.668159	167	167
50.0	3.668159	144	144
51.0	3.668159	130	130
52.0	3.668159	152	152
53.0	3.668159	145	145
54.0	3.668159	140	140
55.0	3.668159	106	106
56.0	3.668159	124	124
57.0	3.668159	128	128
58.0	3.668159	117	117
59.0	3.668159	124	124
60.0	3.668159	98	98
61.0	3.668159	102	102
62.0	3.668159	77	77
63.0	3.668159	75	75
64.0	3.668159	76	76
65.0	3.668159	78	78
66.0	3.668159	88	88
67.0	3.668159	96	96
68.0	3.668159	65	65
69.0	3.668159	75	75
70.0	3.668159	63	63
71.0	3.668159	90	90
72.0	3.668159	60	60
73.0	3.668159	68	68
74.0	3.668159	68	68
75.0	3.668159	54	54
76.0	3.668159	56	56
77.0	3.668159	67	67
78.0	3.668159	45	45
79.0	3.668159	56	56
80.0	3.668159	40	40
81.0	3.668159	41	41
82.0	3.668159	53	53
83.0	3.668159	39	39
84.0	3.668159	43	43
85.0	3.668159	40	40
86.0	3.668159	42	42
87.0	3.668159	44	44
88.0	3.668159	46	46
89.0	3.668159	48	48
90.0	3.668159	33	33
91.0	3.668159	43	43
92.0	3.668159	34	34
93.0	3.668159	37	37
94.0	3.668159	33	33
95.0	3.668159	28	28
96.0	3.668159	31	31
97.0	3.668159	29	29
98.0	3.668159	25	25
99.0	3.668159	35	35
100.0	3.668159	36	36
101.0	0	29	29
102.0	0	25	25
103.0	0	29	29
104.0	0	23	23
105.0	0	18	18
106.0	0	29	29
107.0	0	20	20
108.0	0	33	33
109.0	0	22	22
110.0	0	18	18
111.0	0	25	25
112.0	0	15	15
113.0	0	26	26
114.0	0	22	22
115.0	0	22	22
116.0	0	18	18
117.0	0	21	21
118.0	0	14	14
119.0	0	26	26
120.0	0	21	21
121.0	0	23	23
122.0	0	20	20
123.0	0	19	19
124.0	0	13	13
125.0	0	20	20
126.0	0	15	15
127.0	0	22	22
128.0	0	15	15
129.0	0	15	15
130.0	0	14	14
131.0	0	18	18
132.0	0	13	13
133.0	0	10	10
134.0	0	18	18
135.0	0	19	19
136.0	0	18	18
137.0	0	9	9
138.0	0	15	15
139.0	0	12	12
140.0	0	16	16
141.0	0	18	18
142.0	0	13	13
143.0	0	15	15
144.0	0	16	16
145.0	0	8	8
146.0	0	15	15
147.0	0	16	16
148.0	0	7	7
149.0	0	9	9
150.0	0	13	13
151.0	0	19	19
152.0	0	16	16
153.0	0	6	6
154.0	0	10	10
155.0	0	13	13
156.0	0	14	14
157.0	0	10	10
158.0	0	8	8
159.0	0	4	4
160.0	0	11	11
161.0	0	10	10
162.0	0	5	5
163.0	0	3	3
164.0	0	6	6
165.0	0	8	8
166.0	0	14	14
167.0	0	12	12
168.0	0	8	8
169.0	0	9	9
170.0	0	14	14
171.0	0	11	11
172.0	0	9	9
173.0	0	16	16
174.0	0	5	5
175.0	0	11	11
176.0	0	12	12
177.0	0	5	5
178.0	0	8	8
179.0	0	8	8
180.0	0	11	11
181.0	0	15	15
182.0	0	7	7
183.0	0	13	13
184.0	0	11	11
185.0	0	7	7
186.0	0	8	8
187.0	0	8	8
188.0	0	5	5
189.0	0	10	10
190.0	0	6	6
191.0	0	8	8
192.0	0	5	5
193.0	0	7	7
194.0	0	10	10
195.0	0	5	5
196.0	0	7	7
197.0	0	2	2
198.0	0	4	4
199.0	0	8	8
200.0	0	4	4
201.0	0	7	7
202.0	0	5	5
203.0	0	8	8
204.0	0	7	7
205.0	0	3	3
206.0	0	7	7
207.0	0	6	6
208.0	0	5	5
209.0	0	5	5
210.0	0	6	6
211.0	0	6	6
212.0	0	8	8
213.0	0	6	6
214.0	0	5	5
215.0	0	7	7
216.0	0	8	8
217.0	0	10	10
218.0	0	9	9
219.0	0	7	7
220.0	0	4	4
221.0	0	7	7
222.0	0	6	6
223.0	0	6	6
224.0	0	8	8
225.0	0	4	4
226.0	0	6	6
227.0	0	5	5
228.0	0	2	2
229.0	0	6	6
230.0	0	10	10
231.0	0	5	5
232.0	0	3	3
233.0	0	4	4
234.0	0	5	5
235.0	0	5	5
236.0	0	4	4
237.0	0	5	5
238.0	0	5	5
239.0	0	7	7
240.0	0	4	4
241.0	0	6	6
242.0	0	3	3
243.0	0	4	4
244.0	0	5	5
245.0	0	2	2
246.0	0	2	2
247.0	0	4	4
248.0	0	3	3
249.0	0	3	3
250.0	0	6	6
251.0	0	1	1
252.0	0	1	1
253.0	0	3	3
254.0	0	5	5
255.0	0	4	4
256.0	0	7	7
257.0	0	9	9
258.0	0	4	4
259.0	0	4	4
260.0	0	5	5
261.0	0	6	6
262.0	0	5	5
263.0	0	5	5
264.0	0	4	4
266.0	0	3	3
267.0	0	5	5
268.0	0	2	2
269.0	0	1	1
270.0	0	1	1
271.0	0	2	2
272.0	0	3	3
273.0	0	4	4
274.0	0	3	3
276.0	0	1	1
277.0	0	2	2
278.0	0	3	3
279.0	0	3	3
280.0	0	6	6
281.0	0	3	3
282.0	0	1	1
283.0	0	2	2
284.0	0	1	1
285.0	0	3	3
286.0	0	2	2
287.0	0	7	7
288.0	0	3	3
289.0	0	3	3
290.0	0	1	1
291.0	0	1	1
292.0	0	5	5
294.0	0	2	2
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	4	4
300.0	0	4	4
301.0	0	4	4
302.0	0	4	4
303.0	0	1	1
306.0	0	2	2
307.0	0	2	2
309.0	0	1	1
310.0	0	2	2
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	4	4
319.0	0	3	3
320.0	0	6	6
322.0	0	2	2
323.0	0	5	5
325.0	0	5	5
326.0	0	1	1
327.0	0	2	2
328.0	0	2	2
329.0	0	2	2
330.0	0	2	2
331.0	0	2	2
332.0	0	5	5
333.0	0	3	3
334.0	0	2	2
335.0	0	1	1
336.0	0	2	2
338.0	0	1	1
339.0	0	4	4
340.0	0	3	3
341.0	0	4	4
342.0	0	3	3
348.0	0	2	2
351.0	0	2	2
352.0	0	1	1
353.0	0	2	2
354.0	0	3	3
356.0	0	1	1
357.0	0	2	2
359.0	0	2	2
360.0	0	3	3
361.0	0	1	1
363.0	0	2	2
364.0	0	2	2
365.0	0	1	1
366.0	0	1	1
367.0	0	1	1
368.0	0	5	5
369.0	0	1	1
370.0	0	1	1
371.0	0	2	2
372.0	0	1	1
373.0	0	1	1
375.0	0	2	2
377.0	0	4	4
384.0	0	1	1
385.0	0	2	2
386.0	0	2	2
387.0	0	3	3
388.0	0	1	1
389.0	0	2	2
390.0	0	1	1
391.0	0	1	1
392.0	0	2	2
393.0	0	2	2
394.0	0	1	1
395.0	0	1	1
396.0	0	1	1
398.0	0	2	2
399.0	0	2	2
403.0	0	1	1
405.0	0	1	1
406.0	0	1	1
407.0	0	2	2
408.0	0	1	1
409.0	0	1	1
410.0	0	2	2
411.0	0	1	1
412.0	0	2	2
413.0	0	1	1
415.0	0	2	2
417.0	0	2	2
418.0	0	1	1
419.0	0	2	2
421.0	0	2	2
422.0	0	1	1
423.0	0	2	2
424.0	0	1	1
425.0	0	1	1
427.0	0	1	1
429.0	0	3	3
430.0	0	1	1
431.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	2	2
438.0	0	1	1
439.0	0	1	1
440.0	0	1	1
442.0	0	1	1
444.0	0	3	3
446.0	0	1	1
450.0	0	2	2
451.0	0	2	2
452.0	0	1	1
453.0	0	1	1
454.0	0	1	1
457.0	0	3	3
459.0	0	1	1
461.0	0	2	2
462.0	0	2	2
463.0	0	1	1
464.0	0	2	2
465.0	0	1	1
474.0	0	2	2
477.0	0	3	3
478.0	0	2	2
480.0	0	3	3
481.0	0	1	1
482.0	0	1	1
483.0	0	1	1
485.0	0	2	2
487.0	0	2	2
490.0	0	2	2
491.0	0	1	1
492.0	0	1	1
497.0	0	2	2
499.0	0	1	1
502.0	0	1	1
504.0	0	2	2
505.0	0	1	1
507.0	0	1	1
509.0	0	1	1
511.0	0	1	1
513.0	0	2	2
516.0	0	1	1
517.0	0	2	2
520.0	0	3	3
524.0	0	1	1
526.0	0	2	2
527.0	0	2	2
534.0	0	1	1
543.0	0	1	1
546.0	0	1	1
552.0	0	1	1
555.0	0	1	1
557.0	0	2	2
558.0	0	1	1
561.0	0	2	2
563.0	0	1	1
565.0	0	1	1
566.0	0	1	1
572.0	0	1	1
574.0	0	1	1
579.0	0	1	1
588.0	0	1	1
592.0	0	1	1
593.0	0	1	1
594.0	0	2	2
601.0	0	1	1
610.0	0	1	1
615.0	0	1	1
618.0	0	1	1
621.0	0	1	1
644.0	0	2	2
645.0	0	2	2
659.0	0	1	1
662.0	0	1	1
663.0	0	1	1
664.0	0	1	1
666.0	0	1	1
668.0	0	1	1
682.0	0	1	1
685.0	0	1	1
688.0	0	2	2
689.0	0	1	1
691.0	0	1	1
699.0	0	1	1
703.0	0	1	1
709.0	0	1	1
711.0	0	1	1
716.0	0	1	1
720.0	0	1	1
726.0	0	1	1
728.0	0	1	1
731.0	0	1	1
735.0	0	1	1
741.0	0	1	1
774.0	0	1	1
786.0	0	1	1
790.0	0	1	1
791.0	0	1	1
795.0	0	1	1
808.0	0	1	1
814.0	0	1	1
824.0	0	1	1
826.0	0	1	1
827.0	0	1	1
831.0	0	1	1
853.0	0	1	1
866.0	0	1	1
876.0	0	1	1
881.0	0	1	1
893.0	0	1	1
897.0	0	1	1
899.0	0	1	1
925.0	0	1	1
948.0	0	1	1
961.0	0	1	1
1007.0	0	1	1
1042.0	0	2	2
1080.0	0	1	1
1120.0	0	1	1
1128.0	0	1	1
1158.0	0	1	1
1167.0	0	1	1
1180.0	0	1	1
1228.0	0	1	1
1281.0	0	1	1
1310.0	0	1	1
1351.0	0	1	1
1422.0	0	1	1
1440.0	0	1	1
1446.0	0	1	1
1473.0	0	1	1
1579.0	0	1	1
1593.0	0	1	1
1642.0	0	1	1
1646.0	0	1	1
1658.0	0	1	1
1683.0	0	1	1
1732.0	0	1	1
1736.0	0	1	1
1821.0	0	1	1
1827.0	0	1	1
1869.0	0	1	1
1890.0	0	1	1
1892.0	0	1	1
1903.0	0	1	1
1910.0	0	1	1
2034.0	0	1	1
2129.0	0	1	1
2140.0	0	1	1
2292.0	0	1	1
4110.0	0	1	1
6030.0	0	1	1