## 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-D10_supernatant_TA_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D10_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-D10_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 01:26:02 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	3717	35810165	56797089	0	3609	20062065	0	0.560255	18358433

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6950891	6950891
2.0	1.142187	4428228	4428228
3.0	1.162404	2355343	2355343
4.0	1.165279	1079322	1079322
5.0	1.165688	452232	452232
6.0	1.165746	185883	185883
7.0	1.165754	82251	82251
8.0	1.165755	42717	42717
9.0	1.165755	26931	26931
10.0	1.165755	18914	18914
11.0	1.165755	14562	14562
12.0	1.165755	11604	11604
13.0	1.165755	9736	9736
14.0	1.165755	8031	8031
15.0	1.165755	6785	6785
16.0	1.165755	6113	6113
17.0	1.165755	5156	5156
18.0	1.165755	4627	4627
19.0	1.165755	4098	4098
20.0	1.165755	3685	3685
21.0	1.165755	3291	3291
22.0	1.165755	2924	2924
23.0	1.165755	2577	2577
24.0	1.165755	2395	2395
25.0	1.165755	2076	2076
26.0	1.165755	1924	1924
27.0	1.165755	1861	1861
28.0	1.165755	1670	1670
29.0	1.165755	1536	1536
30.0	1.165755	1449	1449
31.0	1.165755	1390	1390
32.0	1.165755	1242	1242
33.0	1.165755	1107	1107
34.0	1.165755	1031	1031
35.0	1.165755	979	979
36.0	1.165755	920	920
37.0	1.165755	827	827
38.0	1.165755	839	839
39.0	1.165755	754	754
40.0	1.165755	719	719
41.0	1.165755	686	686
42.0	1.165755	616	616
43.0	1.165755	583	583
44.0	1.165755	568	568
45.0	1.165755	563	563
46.0	1.165755	519	519
47.0	1.165755	514	514
48.0	1.165755	461	461
49.0	1.165755	453	453
50.0	1.165755	450	450
51.0	1.165755	419	419
52.0	1.165755	392	392
53.0	1.165755	381	381
54.0	1.165755	369	369
55.0	1.165755	354	354
56.0	1.165755	319	319
57.0	1.165755	296	296
58.0	1.165755	257	257
59.0	1.165755	304	304
60.0	1.165755	290	290
61.0	1.165755	275	275
62.0	1.165755	246	246
63.0	1.165755	236	236
64.0	1.165755	257	257
65.0	1.165755	228	228
66.0	1.165755	227	227
67.0	1.165755	198	198
68.0	1.165755	188	188
69.0	1.165755	173	173
70.0	1.165755	181	181
71.0	1.165755	186	186
72.0	1.165755	169	169
73.0	1.165755	171	171
74.0	1.165755	156	156
75.0	1.165755	167	167
76.0	1.165755	143	143
77.0	1.165755	131	131
78.0	1.165755	155	155
79.0	1.165755	126	126
80.0	1.165755	143	143
81.0	1.165755	154	154
82.0	1.165755	116	116
83.0	1.165755	112	112
84.0	1.165755	124	124
85.0	1.165755	121	121
86.0	1.165755	103	103
87.0	1.165755	107	107
88.0	1.165755	115	115
89.0	1.165755	104	104
90.0	1.165755	113	113
91.0	1.165755	84	84
92.0	1.165755	94	94
93.0	1.165755	103	103
94.0	1.165755	100	100
95.0	1.165755	89	89
96.0	1.165755	91	91
97.0	1.165755	100	100
98.0	1.165755	63	63
99.0	1.165755	85	85
100.0	1.165755	87	87
101.0	0	83	83
102.0	0	88	88
103.0	0	60	60
104.0	0	77	77
105.0	0	78	78
106.0	0	65	65
107.0	0	60	60
108.0	0	62	62
109.0	0	67	67
110.0	0	70	70
111.0	0	50	50
112.0	0	58	58
113.0	0	57	57
114.0	0	62	62
115.0	0	64	64
116.0	0	54	54
117.0	0	32	32
118.0	0	57	57
119.0	0	51	51
120.0	0	52	52
121.0	0	36	36
122.0	0	42	42
123.0	0	43	43
124.0	0	36	36
125.0	0	45	45
126.0	0	30	30
127.0	0	47	47
128.0	0	40	40
129.0	0	29	29
130.0	0	49	49
131.0	0	36	36
132.0	0	41	41
133.0	0	35	35
134.0	0	33	33
135.0	0	34	34
136.0	0	36	36
137.0	0	40	40
138.0	0	35	35
139.0	0	31	31
140.0	0	20	20
141.0	0	27	27
142.0	0	29	29
143.0	0	26	26
144.0	0	29	29
145.0	0	27	27
146.0	0	36	36
147.0	0	27	27
148.0	0	34	34
149.0	0	27	27
150.0	0	29	29
151.0	0	30	30
152.0	0	33	33
153.0	0	35	35
154.0	0	31	31
155.0	0	22	22
156.0	0	21	21
157.0	0	25	25
158.0	0	31	31
159.0	0	28	28
160.0	0	29	29
161.0	0	18	18
162.0	0	26	26
163.0	0	17	17
164.0	0	17	17
165.0	0	20	20
166.0	0	14	14
167.0	0	17	17
168.0	0	23	23
169.0	0	29	29
170.0	0	16	16
171.0	0	21	21
172.0	0	19	19
173.0	0	13	13
174.0	0	20	20
175.0	0	18	18
176.0	0	11	11
177.0	0	24	24
178.0	0	24	24
179.0	0	18	18
180.0	0	27	27
181.0	0	22	22
182.0	0	20	20
183.0	0	16	16
184.0	0	18	18
185.0	0	10	10
186.0	0	20	20
187.0	0	13	13
188.0	0	15	15
189.0	0	23	23
190.0	0	15	15
191.0	0	16	16
192.0	0	11	11
193.0	0	21	21
194.0	0	11	11
195.0	0	12	12
196.0	0	20	20
197.0	0	20	20
198.0	0	16	16
199.0	0	19	19
200.0	0	14	14
201.0	0	14	14
202.0	0	19	19
203.0	0	20	20
204.0	0	16	16
205.0	0	15	15
206.0	0	21	21
207.0	0	12	12
208.0	0	6	6
209.0	0	10	10
210.0	0	16	16
211.0	0	12	12
212.0	0	7	7
213.0	0	7	7
214.0	0	12	12
215.0	0	11	11
216.0	0	8	8
217.0	0	10	10
218.0	0	10	10
219.0	0	14	14
220.0	0	6	6
221.0	0	6	6
222.0	0	9	9
223.0	0	13	13
224.0	0	9	9
225.0	0	15	15
226.0	0	4	4
227.0	0	13	13
228.0	0	10	10
229.0	0	9	9
230.0	0	13	13
231.0	0	10	10
232.0	0	9	9
233.0	0	11	11
234.0	0	10	10
235.0	0	10	10
236.0	0	10	10
237.0	0	5	5
238.0	0	11	11
239.0	0	7	7
240.0	0	8	8
241.0	0	8	8
242.0	0	10	10
243.0	0	11	11
244.0	0	10	10
245.0	0	9	9
246.0	0	9	9
247.0	0	4	4
248.0	0	5	5
249.0	0	7	7
250.0	0	6	6
251.0	0	8	8
252.0	0	4	4
253.0	0	7	7
254.0	0	1	1
255.0	0	8	8
256.0	0	5	5
257.0	0	16	16
258.0	0	7	7
259.0	0	8	8
260.0	0	10	10
261.0	0	2	2
262.0	0	5	5
263.0	0	7	7
264.0	0	6	6
265.0	0	6	6
266.0	0	6	6
267.0	0	6	6
268.0	0	6	6
269.0	0	9	9
270.0	0	5	5
271.0	0	7	7
272.0	0	9	9
273.0	0	6	6
274.0	0	5	5
275.0	0	7	7
276.0	0	5	5
277.0	0	9	9
278.0	0	1	1
279.0	0	8	8
280.0	0	5	5
281.0	0	6	6
282.0	0	1	1
283.0	0	4	4
284.0	0	8	8
285.0	0	4	4
286.0	0	3	3
287.0	0	7	7
288.0	0	4	4
289.0	0	6	6
290.0	0	8	8
291.0	0	4	4
292.0	0	2	2
293.0	0	5	5
294.0	0	4	4
295.0	0	4	4
296.0	0	7	7
297.0	0	3	3
298.0	0	3	3
299.0	0	6	6
300.0	0	7	7
301.0	0	5	5
302.0	0	6	6
303.0	0	7	7
304.0	0	8	8
305.0	0	2	2
306.0	0	5	5
307.0	0	4	4
308.0	0	8	8
309.0	0	3	3
310.0	0	4	4
311.0	0	7	7
312.0	0	6	6
313.0	0	4	4
314.0	0	7	7
315.0	0	5	5
316.0	0	6	6
317.0	0	3	3
318.0	0	1	1
319.0	0	5	5
320.0	0	4	4
321.0	0	1	1
322.0	0	4	4
323.0	0	2	2
324.0	0	2	2
325.0	0	6	6
326.0	0	3	3
327.0	0	3	3
328.0	0	4	4
329.0	0	1	1
330.0	0	2	2
331.0	0	5	5
332.0	0	2	2
333.0	0	3	3
334.0	0	4	4
335.0	0	3	3
336.0	0	3	3
337.0	0	4	4
338.0	0	5	5
339.0	0	2	2
340.0	0	4	4
341.0	0	3	3
342.0	0	2	2
343.0	0	2	2
344.0	0	4	4
345.0	0	2	2
346.0	0	2	2
347.0	0	5	5
348.0	0	5	5
349.0	0	2	2
351.0	0	4	4
352.0	0	4	4
353.0	0	4	4
354.0	0	2	2
355.0	0	3	3
356.0	0	1	1
357.0	0	5	5
358.0	0	2	2
359.0	0	2	2
361.0	0	2	2
362.0	0	5	5
363.0	0	6	6
364.0	0	3	3
365.0	0	3	3
366.0	0	3	3
367.0	0	6	6
368.0	0	5	5
370.0	0	2	2
371.0	0	3	3
372.0	0	4	4
373.0	0	1	1
374.0	0	2	2
375.0	0	1	1
376.0	0	5	5
377.0	0	6	6
378.0	0	5	5
379.0	0	3	3
380.0	0	1	1
381.0	0	1	1
382.0	0	4	4
383.0	0	2	2
384.0	0	3	3
385.0	0	2	2
386.0	0	1	1
388.0	0	1	1
390.0	0	3	3
391.0	0	2	2
392.0	0	1	1
393.0	0	2	2
394.0	0	1	1
395.0	0	5	5
396.0	0	2	2
397.0	0	1	1
398.0	0	8	8
399.0	0	3	3
400.0	0	4	4
402.0	0	1	1
403.0	0	2	2
405.0	0	2	2
406.0	0	4	4
407.0	0	2	2
408.0	0	2	2
409.0	0	6	6
410.0	0	2	2
411.0	0	3	3
412.0	0	3	3
413.0	0	2	2
414.0	0	6	6
415.0	0	4	4
416.0	0	3	3
417.0	0	5	5
418.0	0	3	3
419.0	0	1	1
420.0	0	4	4
421.0	0	1	1
422.0	0	2	2
424.0	0	1	1
425.0	0	1	1
427.0	0	1	1
428.0	0	1	1
429.0	0	3	3
430.0	0	3	3
432.0	0	2	2
434.0	0	3	3
435.0	0	4	4
436.0	0	3	3
437.0	0	1	1
438.0	0	3	3
439.0	0	1	1
440.0	0	3	3
441.0	0	1	1
442.0	0	1	1
443.0	0	2	2
444.0	0	1	1
445.0	0	2	2
446.0	0	1	1
447.0	0	1	1
448.0	0	2	2
449.0	0	2	2
450.0	0	2	2
452.0	0	4	4
453.0	0	5	5
454.0	0	1	1
458.0	0	2	2
459.0	0	2	2
460.0	0	3	3
461.0	0	2	2
463.0	0	2	2
464.0	0	3	3
465.0	0	2	2
466.0	0	1	1
467.0	0	2	2
468.0	0	2	2
469.0	0	1	1
471.0	0	2	2
472.0	0	2	2
473.0	0	1	1
476.0	0	4	4
477.0	0	2	2
478.0	0	1	1
480.0	0	1	1
482.0	0	1	1
483.0	0	2	2
486.0	0	4	4
487.0	0	1	1
488.0	0	1	1
490.0	0	1	1
492.0	0	3	3
493.0	0	2	2
494.0	0	1	1
496.0	0	2	2
497.0	0	2	2
499.0	0	1	1
500.0	0	1	1
502.0	0	4	4
504.0	0	1	1
506.0	0	1	1
508.0	0	3	3
509.0	0	1	1
510.0	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	3	3
517.0	0	3	3
518.0	0	2	2
521.0	0	1	1
523.0	0	4	4
524.0	0	3	3
525.0	0	2	2
526.0	0	3	3
527.0	0	2	2
528.0	0	1	1
530.0	0	2	2
532.0	0	1	1
533.0	0	1	1
535.0	0	1	1
541.0	0	1	1
542.0	0	1	1
543.0	0	1	1
544.0	0	2	2
545.0	0	3	3
547.0	0	2	2
548.0	0	1	1
549.0	0	2	2
550.0	0	1	1
551.0	0	1	1
552.0	0	1	1
553.0	0	1	1
554.0	0	1	1
557.0	0	1	1
558.0	0	1	1
559.0	0	1	1
561.0	0	2	2
562.0	0	1	1
563.0	0	3	3
566.0	0	1	1
567.0	0	1	1
568.0	0	1	1
571.0	0	1	1
574.0	0	3	3
575.0	0	1	1
576.0	0	1	1
578.0	0	1	1
580.0	0	1	1
584.0	0	1	1
586.0	0	1	1
587.0	0	2	2
588.0	0	1	1
593.0	0	1	1
596.0	0	1	1
597.0	0	2	2
599.0	0	1	1
600.0	0	2	2
604.0	0	1	1
610.0	0	2	2
611.0	0	1	1
612.0	0	2	2
617.0	0	1	1
618.0	0	1	1
621.0	0	2	2
626.0	0	1	1
628.0	0	1	1
629.0	0	5	5
633.0	0	3	3
637.0	0	1	1
638.0	0	1	1
639.0	0	1	1
640.0	0	1	1
641.0	0	2	2
643.0	0	2	2
645.0	0	2	2
646.0	0	2	2
654.0	0	2	2
658.0	0	1	1
659.0	0	1	1
662.0	0	1	1
664.0	0	1	1
665.0	0	2	2
669.0	0	1	1
670.0	0	1	1
671.0	0	1	1
678.0	0	1	1
681.0	0	2	2
682.0	0	1	1
683.0	0	1	1
684.0	0	2	2
690.0	0	1	1
693.0	0	1	1
694.0	0	1	1
699.0	0	1	1
702.0	0	1	1
703.0	0	1	1
704.0	0	1	1
706.0	0	1	1
708.0	0	1	1
709.0	0	2	2
710.0	0	1	1
718.0	0	2	2
719.0	0	2	2
722.0	0	3	3
723.0	0	1	1
729.0	0	1	1
730.0	0	1	1
733.0	0	1	1
738.0	0	1	1
739.0	0	1	1
740.0	0	1	1
745.0	0	2	2
747.0	0	1	1
751.0	0	1	1
763.0	0	1	1
764.0	0	2	2
771.0	0	1	1
772.0	0	1	1
778.0	0	1	1
784.0	0	1	1
786.0	0	1	1
788.0	0	1	1
793.0	0	1	1
794.0	0	1	1
800.0	0	1	1
806.0	0	1	1
813.0	0	1	1
814.0	0	1	1
817.0	0	2	2
822.0	0	2	2
835.0	0	1	1
836.0	0	1	1
844.0	0	1	1
851.0	0	1	1
865.0	0	1	1
869.0	0	1	1
872.0	0	1	1
877.0	0	1	1
879.0	0	1	1
883.0	0	1	1
885.0	0	1	1
893.0	0	1	1
895.0	0	1	1
902.0	0	1	1
903.0	0	1	1
906.0	0	1	1
908.0	0	1	1
912.0	0	1	1
931.0	0	1	1
954.0	0	1	1
965.0	0	1	1
970.0	0	1	1
982.0	0	1	1
988.0	0	1	1
1000.0	0	2	2
1008.0	0	1	1
1015.0	0	1	1
1016.0	0	1	1
1019.0	0	1	1
1063.0	0	1	1
1072.0	0	1	1
1154.0	0	1	1
1156.0	0	1	1
1157.0	0	1	1
1170.0	0	1	1
1201.0	0	1	1
1214.0	0	1	1
1221.0	0	3	3
1232.0	0	1	1
1266.0	0	1	1
1316.0	0	1	1
1340.0	0	1	1
1348.0	0	1	1
1353.0	0	1	1
1379.0	0	1	1
1395.0	0	1	1
1399.0	0	1	1
1411.0	0	1	1
1482.0	0	1	1
1503.0	0	2	2
1521.0	0	1	1
1593.0	0	1	1
1627.0	0	1	1
1718.0	0	1	1
1747.0	0	1	1
1783.0	0	1	1
1921.0	0	1	1
1992.0	0	1	1
1995.0	0	1	1
2018.0	0	1	1
2108.0	0	1	1
2381.0	0	1	1
2530.0	0	1	1
2579.0	0	1	1
2597.0	0	1	1
2611.0	0	1	1
2669.0	0	1	1
2847.0	0	1	1
2913.0	0	1	1
3066.0	0	1	1
3163.0	0	1	1
3255.0	0	1	1
3259.0	0	1	1
3985.0	0	1	1
4450.0	0	1	1
4546.0	0	1	1