## 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_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_supernatant_TA_3.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_3.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 01:30:11 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	534	27530519	17745248	0	458	4632747	0	0.168283	72341026

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20984217	20984217
2.0	1.683475	1435800	1435800
3.0	2.150612	219473	219473
4.0	2.469889	82551	82551
5.0	2.688106	44245	44245
6.0	2.837252	27829	27829
7.0	2.93919	18794	18794
8.0	3.008862	13750	13750
9.0	3.056481	10127	10127
10.0	3.089027	7851	7851
11.0	3.111271	6107	6107
12.0	3.126475	5144	5144
13.0	3.136866	4211	4211
14.0	3.143968	3507	3507
15.0	3.148823	2931	2931
16.0	3.15214	2427	2427
17.0	3.154408	2225	2225
18.0	3.155958	1983	1983
19.0	3.157017	1666	1666
20.0	3.157741	1460	1460
21.0	3.158236	1323	1323
22.0	3.158574	1197	1197
23.0	3.158805	1050	1050
24.0	3.158963	977	977
25.0	3.159071	883	883
26.0	3.159145	737	737
27.0	3.159195	736	736
28.0	3.15923	709	709
29.0	3.159253	629	629
30.0	3.159269	544	544
31.0	3.15928	521	521
32.0	3.159288	482	482
33.0	3.159293	444	444
34.0	3.159297	406	406
35.0	3.159299	395	395
36.0	3.159301	382	382
37.0	3.159302	361	361
38.0	3.159302	339	339
39.0	3.159303	299	299
40.0	3.159303	295	295
41.0	3.159304	270	270
42.0	3.159304	256	256
43.0	3.159304	257	257
44.0	3.159304	233	233
45.0	3.159304	218	218
46.0	3.159304	179	179
47.0	3.159304	191	191
48.0	3.159304	200	200
49.0	3.159304	184	184
50.0	3.159304	176	176
51.0	3.159304	146	146
52.0	3.159304	165	165
53.0	3.159304	132	132
54.0	3.159304	124	124
55.0	3.159304	129	129
56.0	3.159304	121	121
57.0	3.159304	129	129
58.0	3.159304	143	143
59.0	3.159304	110	110
60.0	3.159304	123	123
61.0	3.159304	97	97
62.0	3.159304	104	104
63.0	3.159304	122	122
64.0	3.159304	103	103
65.0	3.159304	95	95
66.0	3.159304	93	93
67.0	3.159304	81	81
68.0	3.159304	86	86
69.0	3.159304	93	93
70.0	3.159304	72	72
71.0	3.159304	82	82
72.0	3.159304	59	59
73.0	3.159304	80	80
74.0	3.159304	67	67
75.0	3.159304	91	91
76.0	3.159304	59	59
77.0	3.159304	50	50
78.0	3.159304	66	66
79.0	3.159304	60	60
80.0	3.159304	70	70
81.0	3.159304	45	45
82.0	3.159304	49	49
83.0	3.159304	46	46
84.0	3.159304	43	43
85.0	3.159304	57	57
86.0	3.159304	40	40
87.0	3.159304	42	42
88.0	3.159304	38	38
89.0	3.159304	42	42
90.0	3.159304	48	48
91.0	3.159304	40	40
92.0	3.159304	30	30
93.0	3.159304	40	40
94.0	3.159304	39	39
95.0	3.159304	32	32
96.0	3.159304	31	31
97.0	3.159304	34	34
98.0	3.159304	41	41
99.0	3.159304	39	39
100.0	3.159304	35	35
101.0	0	38	38
102.0	0	29	29
103.0	0	26	26
104.0	0	42	42
105.0	0	21	21
106.0	0	42	42
107.0	0	25	25
108.0	0	28	28
109.0	0	41	41
110.0	0	28	28
111.0	0	29	29
112.0	0	25	25
113.0	0	36	36
114.0	0	23	23
115.0	0	21	21
116.0	0	17	17
117.0	0	34	34
118.0	0	29	29
119.0	0	19	19
120.0	0	27	27
121.0	0	21	21
122.0	0	27	27
123.0	0	18	18
124.0	0	23	23
125.0	0	18	18
126.0	0	18	18
127.0	0	19	19
128.0	0	25	25
129.0	0	21	21
130.0	0	12	12
131.0	0	25	25
132.0	0	29	29
133.0	0	21	21
134.0	0	19	19
135.0	0	16	16
136.0	0	15	15
137.0	0	19	19
138.0	0	18	18
139.0	0	20	20
140.0	0	14	14
141.0	0	16	16
142.0	0	22	22
143.0	0	11	11
144.0	0	20	20
145.0	0	16	16
146.0	0	14	14
147.0	0	9	9
148.0	0	14	14
149.0	0	13	13
150.0	0	18	18
151.0	0	14	14
152.0	0	16	16
153.0	0	9	9
154.0	0	11	11
155.0	0	8	8
156.0	0	21	21
157.0	0	16	16
158.0	0	13	13
159.0	0	14	14
160.0	0	16	16
161.0	0	16	16
162.0	0	13	13
163.0	0	17	17
164.0	0	16	16
165.0	0	10	10
166.0	0	17	17
167.0	0	9	9
168.0	0	8	8
169.0	0	10	10
170.0	0	11	11
171.0	0	10	10
172.0	0	9	9
173.0	0	14	14
174.0	0	10	10
175.0	0	9	9
176.0	0	10	10
177.0	0	14	14
178.0	0	13	13
179.0	0	8	8
180.0	0	9	9
181.0	0	11	11
182.0	0	7	7
183.0	0	7	7
184.0	0	9	9
185.0	0	6	6
186.0	0	7	7
187.0	0	11	11
188.0	0	11	11
189.0	0	9	9
190.0	0	8	8
191.0	0	6	6
192.0	0	17	17
193.0	0	12	12
194.0	0	9	9
195.0	0	11	11
196.0	0	5	5
197.0	0	4	4
198.0	0	4	4
199.0	0	8	8
200.0	0	8	8
201.0	0	14	14
202.0	0	12	12
203.0	0	6	6
204.0	0	9	9
205.0	0	11	11
206.0	0	9	9
207.0	0	5	5
208.0	0	10	10
209.0	0	5	5
210.0	0	8	8
211.0	0	6	6
212.0	0	7	7
213.0	0	2	2
214.0	0	5	5
215.0	0	4	4
216.0	0	10	10
217.0	0	5	5
218.0	0	8	8
219.0	0	6	6
220.0	0	5	5
221.0	0	4	4
222.0	0	6	6
223.0	0	3	3
224.0	0	5	5
225.0	0	11	11
226.0	0	7	7
227.0	0	6	6
228.0	0	9	9
229.0	0	8	8
230.0	0	5	5
231.0	0	10	10
232.0	0	7	7
233.0	0	4	4
234.0	0	6	6
235.0	0	6	6
236.0	0	2	2
237.0	0	4	4
238.0	0	5	5
239.0	0	5	5
240.0	0	6	6
241.0	0	5	5
242.0	0	8	8
243.0	0	10	10
244.0	0	3	3
245.0	0	4	4
246.0	0	4	4
247.0	0	4	4
248.0	0	5	5
249.0	0	3	3
250.0	0	6	6
251.0	0	5	5
252.0	0	8	8
253.0	0	5	5
254.0	0	9	9
255.0	0	6	6
256.0	0	6	6
257.0	0	6	6
258.0	0	4	4
259.0	0	4	4
260.0	0	5	5
261.0	0	6	6
262.0	0	7	7
263.0	0	3	3
264.0	0	4	4
265.0	0	2	2
266.0	0	1	1
268.0	0	7	7
269.0	0	7	7
270.0	0	3	3
271.0	0	3	3
272.0	0	3	3
273.0	0	7	7
274.0	0	5	5
275.0	0	5	5
276.0	0	8	8
277.0	0	4	4
278.0	0	1	1
279.0	0	6	6
280.0	0	2	2
281.0	0	4	4
282.0	0	4	4
283.0	0	6	6
284.0	0	3	3
285.0	0	4	4
286.0	0	2	2
287.0	0	4	4
288.0	0	3	3
289.0	0	3	3
290.0	0	3	3
291.0	0	3	3
292.0	0	3	3
293.0	0	1	1
294.0	0	4	4
295.0	0	6	6
296.0	0	4	4
297.0	0	4	4
298.0	0	2	2
299.0	0	6	6
300.0	0	3	3
301.0	0	7	7
302.0	0	5	5
303.0	0	4	4
304.0	0	4	4
305.0	0	5	5
306.0	0	5	5
307.0	0	2	2
308.0	0	2	2
309.0	0	5	5
310.0	0	1	1
311.0	0	5	5
312.0	0	1	1
313.0	0	3	3
314.0	0	4	4
315.0	0	3	3
316.0	0	1	1
317.0	0	4	4
318.0	0	3	3
319.0	0	5	5
321.0	0	5	5
322.0	0	3	3
323.0	0	3	3
324.0	0	3	3
325.0	0	1	1
327.0	0	6	6
328.0	0	1	1
329.0	0	4	4
330.0	0	4	4
331.0	0	1	1
332.0	0	4	4
333.0	0	3	3
334.0	0	4	4
336.0	0	2	2
337.0	0	4	4
338.0	0	2	2
339.0	0	3	3
340.0	0	2	2
341.0	0	2	2
342.0	0	1	1
343.0	0	4	4
344.0	0	1	1
345.0	0	1	1
346.0	0	1	1
347.0	0	4	4
348.0	0	3	3
349.0	0	5	5
350.0	0	3	3
351.0	0	3	3
353.0	0	1	1
354.0	0	3	3
355.0	0	2	2
356.0	0	3	3
357.0	0	3	3
358.0	0	3	3
359.0	0	3	3
360.0	0	3	3
362.0	0	4	4
363.0	0	4	4
364.0	0	8	8
365.0	0	1	1
366.0	0	2	2
367.0	0	1	1
368.0	0	1	1
369.0	0	2	2
370.0	0	4	4
371.0	0	3	3
372.0	0	3	3
373.0	0	2	2
374.0	0	2	2
375.0	0	2	2
376.0	0	2	2
377.0	0	1	1
379.0	0	2	2
380.0	0	2	2
381.0	0	2	2
382.0	0	1	1
384.0	0	5	5
385.0	0	3	3
386.0	0	1	1
387.0	0	3	3
388.0	0	3	3
390.0	0	1	1
391.0	0	2	2
392.0	0	2	2
393.0	0	2	2
394.0	0	3	3
395.0	0	2	2
396.0	0	3	3
397.0	0	4	4
398.0	0	2	2
399.0	0	2	2
400.0	0	1	1
401.0	0	3	3
404.0	0	3	3
405.0	0	1	1
406.0	0	3	3
407.0	0	4	4
408.0	0	2	2
410.0	0	4	4
411.0	0	2	2
413.0	0	2	2
414.0	0	3	3
415.0	0	2	2
416.0	0	2	2
417.0	0	2	2
418.0	0	3	3
419.0	0	1	1
420.0	0	1	1
421.0	0	1	1
422.0	0	2	2
423.0	0	2	2
424.0	0	1	1
426.0	0	1	1
427.0	0	1	1
428.0	0	1	1
429.0	0	1	1
430.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	3	3
435.0	0	2	2
437.0	0	2	2
438.0	0	1	1
439.0	0	1	1
441.0	0	3	3
442.0	0	3	3
444.0	0	1	1
445.0	0	3	3
446.0	0	3	3
447.0	0	2	2
448.0	0	1	1
451.0	0	2	2
452.0	0	1	1
453.0	0	2	2
454.0	0	1	1
455.0	0	3	3
457.0	0	3	3
459.0	0	1	1
460.0	0	2	2
462.0	0	2	2
463.0	0	3	3
464.0	0	2	2
465.0	0	2	2
468.0	0	3	3
469.0	0	2	2
471.0	0	2	2
472.0	0	2	2
475.0	0	2	2
476.0	0	1	1
477.0	0	1	1
478.0	0	4	4
480.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
486.0	0	2	2
491.0	0	4	4
492.0	0	1	1
494.0	0	2	2
498.0	0	1	1
502.0	0	1	1
503.0	0	1	1
505.0	0	3	3
506.0	0	1	1
511.0	0	1	1
512.0	0	1	1
513.0	0	1	1
514.0	0	2	2
515.0	0	1	1
516.0	0	1	1
518.0	0	2	2
524.0	0	1	1
526.0	0	1	1
527.0	0	2	2
529.0	0	2	2
530.0	0	1	1
533.0	0	1	1
534.0	0	2	2
536.0	0	1	1
537.0	0	2	2
542.0	0	2	2
543.0	0	1	1
545.0	0	1	1
546.0	0	3	3
547.0	0	1	1
549.0	0	2	2
554.0	0	1	1
555.0	0	1	1
557.0	0	1	1
559.0	0	2	2
560.0	0	1	1
561.0	0	1	1
562.0	0	2	2
563.0	0	2	2
564.0	0	1	1
565.0	0	2	2
566.0	0	1	1
567.0	0	1	1
569.0	0	1	1
570.0	0	2	2
571.0	0	1	1
572.0	0	2	2
573.0	0	1	1
574.0	0	1	1
575.0	0	1	1
576.0	0	1	1
577.0	0	2	2
580.0	0	2	2
583.0	0	1	1
584.0	0	1	1
586.0	0	1	1
590.0	0	1	1
591.0	0	2	2
593.0	0	1	1
594.0	0	1	1
595.0	0	1	1
600.0	0	2	2
601.0	0	1	1
602.0	0	1	1
603.0	0	1	1
605.0	0	1	1
612.0	0	1	1
613.0	0	1	1
617.0	0	1	1
622.0	0	1	1
624.0	0	1	1
625.0	0	2	2
628.0	0	2	2
630.0	0	1	1
631.0	0	2	2
632.0	0	1	1
634.0	0	3	3
640.0	0	2	2
648.0	0	1	1
655.0	0	1	1
659.0	0	1	1
661.0	0	1	1
662.0	0	1	1
666.0	0	1	1
668.0	0	1	1
675.0	0	1	1
676.0	0	1	1
677.0	0	1	1
681.0	0	1	1
691.0	0	3	3
692.0	0	2	2
696.0	0	1	1
697.0	0	1	1
699.0	0	1	1
704.0	0	3	3
713.0	0	1	1
719.0	0	1	1
721.0	0	1	1
724.0	0	1	1
728.0	0	1	1
732.0	0	1	1
735.0	0	1	1
738.0	0	1	1
753.0	0	1	1
755.0	0	1	1
758.0	0	2	2
759.0	0	1	1
766.0	0	1	1
770.0	0	1	1
771.0	0	2	2
773.0	0	1	1
774.0	0	1	1
777.0	0	1	1
789.0	0	2	2
790.0	0	1	1
793.0	0	1	1
795.0	0	1	1
796.0	0	1	1
797.0	0	1	1
798.0	0	2	2
800.0	0	1	1
801.0	0	1	1
811.0	0	1	1
812.0	0	1	1
813.0	0	2	2
815.0	0	1	1
827.0	0	1	1
832.0	0	1	1
834.0	0	1	1
839.0	0	1	1
847.0	0	1	1
851.0	0	2	2
859.0	0	1	1
860.0	0	1	1
876.0	0	1	1
877.0	0	1	1
880.0	0	1	1
885.0	0	1	1
886.0	0	1	1
889.0	0	1	1
891.0	0	1	1
902.0	0	1	1
905.0	0	1	1
907.0	0	1	1
914.0	0	1	1
916.0	0	1	1
918.0	0	1	1
922.0	0	1	1
925.0	0	1	1
929.0	0	1	1
932.0	0	2	2
945.0	0	2	2
955.0	0	1	1
960.0	0	1	1
963.0	0	1	1
975.0	0	1	1
1006.0	0	1	1
1008.0	0	1	1
1014.0	0	1	1
1019.0	0	1	1
1021.0	0	1	1
1056.0	0	1	1
1066.0	0	1	1
1080.0	0	1	1
1100.0	0	1	1
1104.0	0	1	1
1113.0	0	1	1
1125.0	0	1	1
1145.0	0	1	1
1156.0	0	1	1
1189.0	0	1	1
1201.0	0	1	1
1202.0	0	1	1
1221.0	0	1	1
1240.0	0	1	1
1290.0	0	1	1
1295.0	0	1	1
1298.0	0	1	1
1359.0	0	1	1
1417.0	0	1	1
1453.0	0	1	1
1493.0	0	1	1
1499.0	0	1	1
1512.0	0	1	1
1554.0	0	1	1
1634.0	0	1	1
1677.0	0	1	1
1734.0	0	1	1
1746.0	0	1	1
1878.0	0	1	1
1887.0	0	1	1
2180.0	0	1	1
2235.0	0	1	1
2246.0	0	1	1
2281.0	0	1	1
2304.0	0	1	1
2386.0	0	1	1
2468.0	0	1	1
2490.0	0	1	1
2557.0	0	1	1
2764.0	0	1	1
2921.0	0	1	1
3453.0	0	1	1
3478.0	0	1	1
3509.0	0	1	1
4130.0	0	1	1