## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_TA_1uM.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/star/GRCh37-HSC_D12_TA_1uM.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/projects/colin_2022/results/qc/markdup/GRCh37-HSC_D12_TA_1uM.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: Wed Sep 14 15:46:47 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	2856	54713711	20599725	0	2669	11288507	0	0.206339	113649332

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	39638272	39638272
2.0	1.617902	2526419	2526419
3.0	1.999704	519471	519471
4.0	2.235621	222155	222155
5.0	2.381394	125123	125123
6.0	2.471468	79388	79388
7.0	2.527124	55382	55382
8.0	2.561515	39880	39880
9.0	2.582765	30346	30346
10.0	2.595895	23633	23633
11.0	2.604008	18988	18988
12.0	2.609021	15636	15636
13.0	2.612119	12983	12983
14.0	2.614033	10727	10727
15.0	2.615216	9350	9350
16.0	2.615947	8018	8018
17.0	2.616398	6788	6788
18.0	2.616677	5961	5961
19.0	2.61685	5253	5253
20.0	2.616956	4790	4790
21.0	2.617022	4360	4360
22.0	2.617063	3922	3922
23.0	2.617088	3376	3376
24.0	2.617103	3160	3160
25.0	2.617113	2835	2835
26.0	2.617119	2527	2527
27.0	2.617122	2363	2363
28.0	2.617125	2106	2106
29.0	2.617126	2033	2033
30.0	2.617127	1828	1828
31.0	2.617127	1718	1718
32.0	2.617128	1545	1545
33.0	2.617128	1461	1461
34.0	2.617128	1351	1351
35.0	2.617128	1273	1273
36.0	2.617128	1168	1168
37.0	2.617128	1105	1105
38.0	2.617128	1051	1051
39.0	2.617128	971	971
40.0	2.617128	971	971
41.0	2.617128	926	926
42.0	2.617128	838	838
43.0	2.617128	793	793
44.0	2.617128	743	743
45.0	2.617128	697	697
46.0	2.617128	637	637
47.0	2.617128	673	673
48.0	2.617128	629	629
49.0	2.617128	577	577
50.0	2.617128	530	530
51.0	2.617128	522	522
52.0	2.617128	506	506
53.0	2.617128	491	491
54.0	2.617128	438	438
55.0	2.617128	440	440
56.0	2.617128	444	444
57.0	2.617128	402	402
58.0	2.617128	385	385
59.0	2.617128	352	352
60.0	2.617128	370	370
61.0	2.617128	332	332
62.0	2.617128	276	276
63.0	2.617128	330	330
64.0	2.617128	302	302
65.0	2.617128	326	326
66.0	2.617128	284	284
67.0	2.617128	290	290
68.0	2.617128	274	274
69.0	2.617128	257	257
70.0	2.617128	249	249
71.0	2.617128	239	239
72.0	2.617128	206	206
73.0	2.617128	216	216
74.0	2.617128	217	217
75.0	2.617128	183	183
76.0	2.617128	205	205
77.0	2.617128	183	183
78.0	2.617128	175	175
79.0	2.617128	163	163
80.0	2.617128	183	183
81.0	2.617128	163	163
82.0	2.617128	176	176
83.0	2.617128	166	166
84.0	2.617128	156	156
85.0	2.617128	167	167
86.0	2.617128	145	145
87.0	2.617128	140	140
88.0	2.617128	138	138
89.0	2.617128	134	134
90.0	2.617128	155	155
91.0	2.617128	129	129
92.0	2.617128	114	114
93.0	2.617128	115	115
94.0	2.617128	113	113
95.0	2.617128	122	122
96.0	2.617128	95	95
97.0	2.617128	120	120
98.0	2.617128	114	114
99.0	2.617128	113	113
100.0	2.617128	121	121
101.0	0	108	108
102.0	0	83	83
103.0	0	90	90
104.0	0	100	100
105.0	0	92	92
106.0	0	83	83
107.0	0	91	91
108.0	0	95	95
109.0	0	68	68
110.0	0	74	74
111.0	0	91	91
112.0	0	59	59
113.0	0	70	70
114.0	0	90	90
115.0	0	78	78
116.0	0	74	74
117.0	0	58	58
118.0	0	63	63
119.0	0	55	55
120.0	0	53	53
121.0	0	83	83
122.0	0	55	55
123.0	0	50	50
124.0	0	57	57
125.0	0	56	56
126.0	0	72	72
127.0	0	60	60
128.0	0	60	60
129.0	0	55	55
130.0	0	48	48
131.0	0	54	54
132.0	0	53	53
133.0	0	39	39
134.0	0	47	47
135.0	0	51	51
136.0	0	49	49
137.0	0	47	47
138.0	0	52	52
139.0	0	42	42
140.0	0	47	47
141.0	0	40	40
142.0	0	37	37
143.0	0	36	36
144.0	0	41	41
145.0	0	48	48
146.0	0	39	39
147.0	0	39	39
148.0	0	33	33
149.0	0	34	34
150.0	0	37	37
151.0	0	35	35
152.0	0	38	38
153.0	0	45	45
154.0	0	26	26
155.0	0	32	32
156.0	0	39	39
157.0	0	34	34
158.0	0	40	40
159.0	0	29	29
160.0	0	26	26
161.0	0	26	26
162.0	0	23	23
163.0	0	35	35
164.0	0	31	31
165.0	0	29	29
166.0	0	28	28
167.0	0	31	31
168.0	0	24	24
169.0	0	29	29
170.0	0	27	27
171.0	0	33	33
172.0	0	21	21
173.0	0	23	23
174.0	0	26	26
175.0	0	24	24
176.0	0	27	27
177.0	0	30	30
178.0	0	23	23
179.0	0	20	20
180.0	0	19	19
181.0	0	32	32
182.0	0	19	19
183.0	0	24	24
184.0	0	18	18
185.0	0	19	19
186.0	0	25	25
187.0	0	19	19
188.0	0	20	20
189.0	0	22	22
190.0	0	19	19
191.0	0	20	20
192.0	0	25	25
193.0	0	19	19
194.0	0	19	19
195.0	0	23	23
196.0	0	13	13
197.0	0	9	9
198.0	0	18	18
199.0	0	17	17
200.0	0	17	17
201.0	0	18	18
202.0	0	20	20
203.0	0	16	16
204.0	0	9	9
205.0	0	17	17
206.0	0	19	19
207.0	0	16	16
208.0	0	18	18
209.0	0	18	18
210.0	0	14	14
211.0	0	19	19
212.0	0	15	15
213.0	0	14	14
214.0	0	5	5
215.0	0	12	12
216.0	0	14	14
217.0	0	16	16
218.0	0	13	13
219.0	0	17	17
220.0	0	18	18
221.0	0	15	15
222.0	0	14	14
223.0	0	12	12
224.0	0	10	10
225.0	0	10	10
226.0	0	16	16
227.0	0	9	9
228.0	0	21	21
229.0	0	9	9
230.0	0	21	21
231.0	0	12	12
232.0	0	13	13
233.0	0	16	16
234.0	0	12	12
235.0	0	18	18
236.0	0	10	10
237.0	0	9	9
238.0	0	17	17
239.0	0	7	7
240.0	0	9	9
241.0	0	8	8
242.0	0	9	9
243.0	0	8	8
244.0	0	13	13
245.0	0	10	10
246.0	0	14	14
247.0	0	8	8
248.0	0	13	13
249.0	0	14	14
250.0	0	12	12
251.0	0	10	10
252.0	0	6	6
253.0	0	7	7
254.0	0	12	12
255.0	0	7	7
256.0	0	10	10
257.0	0	8	8
258.0	0	6	6
259.0	0	14	14
260.0	0	11	11
261.0	0	8	8
262.0	0	8	8
263.0	0	7	7
264.0	0	11	11
265.0	0	7	7
266.0	0	8	8
267.0	0	5	5
268.0	0	8	8
269.0	0	10	10
270.0	0	6	6
271.0	0	10	10
272.0	0	9	9
273.0	0	7	7
274.0	0	9	9
275.0	0	6	6
276.0	0	11	11
277.0	0	9	9
278.0	0	11	11
279.0	0	10	10
280.0	0	4	4
281.0	0	9	9
282.0	0	4	4
283.0	0	15	15
284.0	0	5	5
285.0	0	7	7
286.0	0	7	7
287.0	0	3	3
288.0	0	7	7
289.0	0	4	4
290.0	0	6	6
291.0	0	7	7
292.0	0	7	7
293.0	0	4	4
294.0	0	7	7
295.0	0	6	6
296.0	0	5	5
297.0	0	9	9
298.0	0	8	8
299.0	0	9	9
300.0	0	8	8
301.0	0	4	4
302.0	0	6	6
303.0	0	7	7
304.0	0	4	4
305.0	0	8	8
306.0	0	9	9
307.0	0	6	6
308.0	0	3	3
309.0	0	7	7
310.0	0	6	6
311.0	0	12	12
312.0	0	6	6
313.0	0	11	11
314.0	0	6	6
315.0	0	8	8
316.0	0	7	7
317.0	0	5	5
318.0	0	4	4
319.0	0	4	4
320.0	0	5	5
321.0	0	4	4
322.0	0	8	8
323.0	0	9	9
324.0	0	3	3
325.0	0	3	3
326.0	0	5	5
327.0	0	4	4
328.0	0	3	3
329.0	0	3	3
330.0	0	7	7
331.0	0	8	8
332.0	0	3	3
333.0	0	9	9
334.0	0	2	2
335.0	0	4	4
336.0	0	5	5
337.0	0	5	5
338.0	0	4	4
339.0	0	6	6
340.0	0	5	5
341.0	0	7	7
342.0	0	5	5
343.0	0	4	4
344.0	0	7	7
345.0	0	3	3
346.0	0	6	6
347.0	0	3	3
348.0	0	4	4
349.0	0	4	4
350.0	0	6	6
351.0	0	3	3
352.0	0	6	6
353.0	0	5	5
354.0	0	2	2
355.0	0	6	6
356.0	0	3	3
357.0	0	5	5
359.0	0	3	3
360.0	0	4	4
361.0	0	4	4
362.0	0	2	2
363.0	0	4	4
364.0	0	4	4
365.0	0	8	8
366.0	0	6	6
367.0	0	4	4
368.0	0	4	4
369.0	0	4	4
370.0	0	5	5
371.0	0	4	4
372.0	0	6	6
373.0	0	4	4
374.0	0	4	4
375.0	0	3	3
376.0	0	5	5
377.0	0	2	2
378.0	0	4	4
379.0	0	4	4
380.0	0	1	1
382.0	0	2	2
383.0	0	7	7
384.0	0	4	4
385.0	0	4	4
386.0	0	2	2
387.0	0	3	3
388.0	0	4	4
390.0	0	3	3
391.0	0	2	2
392.0	0	3	3
393.0	0	2	2
394.0	0	5	5
395.0	0	3	3
396.0	0	3	3
397.0	0	4	4
398.0	0	2	2
399.0	0	3	3
400.0	0	4	4
401.0	0	3	3
402.0	0	2	2
403.0	0	1	1
404.0	0	4	4
405.0	0	2	2
406.0	0	4	4
407.0	0	4	4
408.0	0	8	8
409.0	0	2	2
410.0	0	2	2
411.0	0	4	4
412.0	0	5	5
413.0	0	7	7
414.0	0	5	5
415.0	0	2	2
416.0	0	2	2
417.0	0	2	2
418.0	0	2	2
419.0	0	5	5
420.0	0	1	1
421.0	0	3	3
422.0	0	1	1
423.0	0	5	5
424.0	0	2	2
426.0	0	2	2
427.0	0	4	4
428.0	0	3	3
429.0	0	3	3
430.0	0	2	2
431.0	0	2	2
432.0	0	2	2
433.0	0	1	1
434.0	0	3	3
435.0	0	3	3
436.0	0	1	1
437.0	0	3	3
438.0	0	1	1
439.0	0	4	4
440.0	0	4	4
441.0	0	1	1
442.0	0	3	3
443.0	0	1	1
444.0	0	2	2
445.0	0	3	3
446.0	0	1	1
447.0	0	3	3
448.0	0	5	5
449.0	0	2	2
450.0	0	1	1
451.0	0	2	2
452.0	0	3	3
453.0	0	1	1
454.0	0	1	1
455.0	0	6	6
456.0	0	6	6
457.0	0	1	1
458.0	0	2	2
459.0	0	2	2
460.0	0	4	4
461.0	0	1	1
462.0	0	3	3
463.0	0	2	2
464.0	0	3	3
465.0	0	5	5
466.0	0	1	1
468.0	0	5	5
469.0	0	1	1
470.0	0	1	1
472.0	0	1	1
474.0	0	2	2
475.0	0	2	2
476.0	0	1	1
477.0	0	1	1
479.0	0	2	2
480.0	0	3	3
481.0	0	3	3
482.0	0	4	4
483.0	0	2	2
484.0	0	2	2
485.0	0	1	1
486.0	0	2	2
487.0	0	3	3
488.0	0	1	1
489.0	0	4	4
490.0	0	2	2
491.0	0	2	2
494.0	0	3	3
495.0	0	1	1
496.0	0	1	1
497.0	0	2	2
498.0	0	2	2
500.0	0	2	2
501.0	0	4	4
503.0	0	2	2
504.0	0	1	1
506.0	0	1	1
507.0	0	1	1
508.0	0	1	1
509.0	0	3	3
510.0	0	2	2
511.0	0	2	2
512.0	0	3	3
513.0	0	2	2
514.0	0	1	1
515.0	0	1	1
516.0	0	2	2
517.0	0	1	1
518.0	0	3	3
519.0	0	1	1
520.0	0	3	3
521.0	0	1	1
522.0	0	1	1
524.0	0	3	3
525.0	0	2	2
526.0	0	3	3
527.0	0	1	1
528.0	0	1	1
529.0	0	3	3
530.0	0	1	1
531.0	0	2	2
532.0	0	1	1
534.0	0	3	3
535.0	0	4	4
537.0	0	1	1
538.0	0	1	1
539.0	0	1	1
540.0	0	1	1
541.0	0	1	1
542.0	0	1	1
543.0	0	3	3
544.0	0	1	1
545.0	0	2	2
547.0	0	2	2
549.0	0	3	3
550.0	0	2	2
551.0	0	3	3
552.0	0	2	2
553.0	0	2	2
554.0	0	1	1
556.0	0	1	1
557.0	0	3	3
559.0	0	1	1
560.0	0	2	2
562.0	0	1	1
563.0	0	1	1
566.0	0	2	2
567.0	0	1	1
568.0	0	1	1
570.0	0	2	2
572.0	0	1	1
573.0	0	2	2
574.0	0	1	1
576.0	0	2	2
577.0	0	3	3
578.0	0	3	3
579.0	0	1	1
580.0	0	1	1
582.0	0	2	2
583.0	0	2	2
584.0	0	1	1
586.0	0	1	1
587.0	0	1	1
589.0	0	2	2
590.0	0	1	1
591.0	0	4	4
592.0	0	1	1
595.0	0	1	1
597.0	0	1	1
601.0	0	2	2
603.0	0	2	2
604.0	0	1	1
607.0	0	2	2
608.0	0	1	1
609.0	0	1	1
610.0	0	1	1
611.0	0	1	1
612.0	0	1	1
613.0	0	1	1
615.0	0	1	1
619.0	0	1	1
620.0	0	1	1
621.0	0	1	1
622.0	0	3	3
623.0	0	1	1
625.0	0	1	1
626.0	0	1	1
627.0	0	1	1
628.0	0	1	1
630.0	0	2	2
631.0	0	2	2
632.0	0	1	1
633.0	0	2	2
635.0	0	3	3
636.0	0	2	2
637.0	0	1	1
638.0	0	2	2
640.0	0	1	1
642.0	0	1	1
643.0	0	1	1
644.0	0	2	2
645.0	0	1	1
647.0	0	1	1
648.0	0	1	1
649.0	0	1	1
652.0	0	1	1
653.0	0	1	1
654.0	0	2	2
655.0	0	1	1
656.0	0	1	1
659.0	0	1	1
661.0	0	2	2
664.0	0	1	1
666.0	0	1	1
669.0	0	1	1
671.0	0	2	2
672.0	0	3	3
678.0	0	3	3
681.0	0	2	2
684.0	0	1	1
686.0	0	1	1
689.0	0	1	1
690.0	0	1	1
694.0	0	1	1
695.0	0	2	2
696.0	0	1	1
698.0	0	1	1
700.0	0	1	1
701.0	0	1	1
703.0	0	2	2
705.0	0	2	2
707.0	0	1	1
708.0	0	2	2
710.0	0	1	1
711.0	0	2	2
712.0	0	2	2
715.0	0	1	1
717.0	0	1	1
719.0	0	1	1
720.0	0	1	1
721.0	0	1	1
723.0	0	1	1
725.0	0	1	1
726.0	0	2	2
727.0	0	1	1
728.0	0	1	1
729.0	0	1	1
730.0	0	1	1
731.0	0	1	1
733.0	0	1	1
734.0	0	4	4
735.0	0	1	1
738.0	0	1	1
739.0	0	1	1
743.0	0	1	1
744.0	0	1	1
745.0	0	1	1
752.0	0	1	1
753.0	0	1	1
754.0	0	1	1
756.0	0	1	1
757.0	0	1	1
758.0	0	2	2
760.0	0	1	1
761.0	0	1	1
764.0	0	1	1
766.0	0	1	1
768.0	0	2	2
772.0	0	4	4
773.0	0	1	1
776.0	0	1	1
777.0	0	2	2
780.0	0	2	2
781.0	0	1	1
782.0	0	1	1
783.0	0	1	1
785.0	0	1	1
786.0	0	1	1
798.0	0	1	1
802.0	0	1	1
803.0	0	1	1
804.0	0	1	1
809.0	0	2	2
811.0	0	2	2
813.0	0	2	2
821.0	0	1	1
822.0	0	1	1
823.0	0	1	1
825.0	0	1	1
833.0	0	1	1
836.0	0	1	1
837.0	0	1	1
839.0	0	1	1
843.0	0	1	1
845.0	0	1	1
851.0	0	2	2
852.0	0	1	1
853.0	0	1	1
855.0	0	1	1
856.0	0	1	1
857.0	0	1	1
861.0	0	1	1
862.0	0	1	1
863.0	0	1	1
865.0	0	1	1
870.0	0	2	2
878.0	0	1	1
885.0	0	1	1
886.0	0	1	1
887.0	0	1	1
894.0	0	1	1
896.0	0	1	1
902.0	0	1	1
908.0	0	1	1
921.0	0	2	2
922.0	0	1	1
924.0	0	1	1
926.0	0	1	1
937.0	0	1	1
938.0	0	2	2
945.0	0	1	1
947.0	0	1	1
949.0	0	1	1
953.0	0	1	1
955.0	0	1	1
960.0	0	1	1
961.0	0	1	1
963.0	0	1	1
977.0	0	1	1
981.0	0	2	2
988.0	0	1	1
991.0	0	1	1
993.0	0	1	1
997.0	0	1	1
999.0	0	1	1
1004.0	0	1	1
1006.0	0	1	1
1021.0	0	1	1
1022.0	0	1	1
1023.0	0	1	1
1024.0	0	1	1
1035.0	0	1	1
1042.0	0	1	1
1043.0	0	2	2
1045.0	0	1	1
1046.0	0	1	1
1048.0	0	1	1
1049.0	0	1	1
1055.0	0	1	1
1060.0	0	1	1
1061.0	0	1	1
1062.0	0	1	1
1063.0	0	1	1
1065.0	0	2	2
1070.0	0	1	1
1071.0	0	1	1
1076.0	0	1	1
1078.0	0	1	1
1082.0	0	1	1
1084.0	0	1	1
1098.0	0	1	1
1110.0	0	1	1
1113.0	0	1	1
1118.0	0	1	1
1121.0	0	1	1
1123.0	0	1	1
1129.0	0	1	1
1136.0	0	1	1
1148.0	0	1	1
1154.0	0	1	1
1157.0	0	1	1
1161.0	0	1	1
1174.0	0	1	1
1178.0	0	2	2
1184.0	0	1	1
1193.0	0	2	2
1198.0	0	1	1
1200.0	0	1	1
1202.0	0	1	1
1205.0	0	1	1
1208.0	0	1	1
1218.0	0	1	1
1227.0	0	1	1
1230.0	0	1	1
1261.0	0	1	1
1272.0	0	1	1
1277.0	0	1	1
1321.0	0	1	1
1347.0	0	1	1
1349.0	0	1	1
1353.0	0	1	1
1359.0	0	1	1
1361.0	0	1	1
1385.0	0	1	1
1412.0	0	1	1
1414.0	0	1	1
1417.0	0	1	1
1421.0	0	1	1
1454.0	0	1	1
1462.0	0	1	1
1479.0	0	1	1
1487.0	0	1	1
1510.0	0	1	1
1536.0	0	1	1
1547.0	0	1	1
1550.0	0	1	1
1551.0	0	1	1
1555.0	0	1	1
1569.0	0	1	1
1677.0	0	1	1
1784.0	0	1	1
1817.0	0	1	1
1823.0	0	1	1
1866.0	0	1	1
1874.0	0	1	1
1877.0	0	1	1
1903.0	0	1	1
1959.0	0	1	1
1985.0	0	1	1
1995.0	0	1	1
2004.0	0	1	1
2074.0	0	1	1
2124.0	0	1	1
2144.0	0	1	1
2152.0	0	1	1
2153.0	0	1	1
2168.0	0	1	1
2181.0	0	1	1
2195.0	0	1	1
2234.0	0	1	1
2241.0	0	1	1
2254.0	0	1	1
2338.0	0	1	1
2349.0	0	1	1
2427.0	0	1	1
2454.0	0	1	1
2472.0	0	1	1
2537.0	0	1	1
2548.0	0	1	1
2608.0	0	1	1
2642.0	0	1	1
2651.0	0	1	1
2661.0	0	1	1
3068.0	0	1	1
3353.0	0	1	1
3529.0	0	1	1
3566.0	0	1	1
3591.0	0	1	1
3798.0	0	1	1
3946.0	0	1	1
4001.0	0	1	1
5216.0	0	1	1
5444.0	0	1	1
5758.0	0	1	1
9097.0	0	1	1
10236.0	0	1	1