## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_2.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-DMSO_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 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: Tue Oct 11 13:30:14 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	1934	45423088	43239224	0	1809	14614799	0	0.321761	54456248

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	23313164	23313164
2.0	1.434256	5344722	5344722
3.0	1.622834	1289620	1289620
4.0	1.704726	371701	371701
5.0	1.740288	148823	148823
6.0	1.755731	79841	79841
7.0	1.762437	51152	51152
8.0	1.765349	35951	35951
9.0	1.766614	26186	26186
10.0	1.767163	20273	20273
11.0	1.767401	16172	16172
12.0	1.767505	12715	12715
13.0	1.76755	10418	10418
14.0	1.767569	8694	8694
15.0	1.767578	7455	7455
16.0	1.767581	6313	6313
17.0	1.767583	5460	5460
18.0	1.767584	4664	4664
19.0	1.767584	4118	4118
20.0	1.767584	3667	3667
21.0	1.767584	3209	3209
22.0	1.767584	2864	2864
23.0	1.767584	2598	2598
24.0	1.767584	2212	2212
25.0	1.767584	2054	2054
26.0	1.767584	1854	1854
27.0	1.767584	1679	1679
28.0	1.767584	1550	1550
29.0	1.767584	1479	1479
30.0	1.767584	1380	1380
31.0	1.767584	1240	1240
32.0	1.767584	1147	1147
33.0	1.767584	1081	1081
34.0	1.767584	991	991
35.0	1.767584	878	878
36.0	1.767584	788	788
37.0	1.767584	764	764
38.0	1.767584	695	695
39.0	1.767584	704	704
40.0	1.767584	669	669
41.0	1.767584	658	658
42.0	1.767584	612	612
43.0	1.767584	556	556
44.0	1.767584	526	526
45.0	1.767584	509	509
46.0	1.767584	459	459
47.0	1.767584	416	416
48.0	1.767584	390	390
49.0	1.767584	408	408
50.0	1.767584	419	419
51.0	1.767584	407	407
52.0	1.767584	355	355
53.0	1.767584	333	333
54.0	1.767584	312	312
55.0	1.767584	280	280
56.0	1.767584	278	278
57.0	1.767584	279	279
58.0	1.767584	245	245
59.0	1.767584	246	246
60.0	1.767584	225	225
61.0	1.767584	223	223
62.0	1.767584	218	218
63.0	1.767584	211	211
64.0	1.767584	222	222
65.0	1.767584	221	221
66.0	1.767584	203	203
67.0	1.767584	157	157
68.0	1.767584	185	185
69.0	1.767584	189	189
70.0	1.767584	167	167
71.0	1.767584	161	161
72.0	1.767584	144	144
73.0	1.767584	152	152
74.0	1.767584	144	144
75.0	1.767584	117	117
76.0	1.767584	162	162
77.0	1.767584	129	129
78.0	1.767584	113	113
79.0	1.767584	128	128
80.0	1.767584	104	104
81.0	1.767584	116	116
82.0	1.767584	114	114
83.0	1.767584	108	108
84.0	1.767584	90	90
85.0	1.767584	98	98
86.0	1.767584	100	100
87.0	1.767584	92	92
88.0	1.767584	98	98
89.0	1.767584	84	84
90.0	1.767584	78	78
91.0	1.767584	78	78
92.0	1.767584	81	81
93.0	1.767584	91	91
94.0	1.767584	89	89
95.0	1.767584	70	70
96.0	1.767584	75	75
97.0	1.767584	76	76
98.0	1.767584	72	72
99.0	1.767584	73	73
100.0	1.767584	72	72
101.0	0	77	77
102.0	0	51	51
103.0	0	55	55
104.0	0	68	68
105.0	0	53	53
106.0	0	65	65
107.0	0	56	56
108.0	0	43	43
109.0	0	60	60
110.0	0	51	51
111.0	0	51	51
112.0	0	53	53
113.0	0	49	49
114.0	0	44	44
115.0	0	54	54
116.0	0	44	44
117.0	0	45	45
118.0	0	38	38
119.0	0	39	39
120.0	0	40	40
121.0	0	40	40
122.0	0	39	39
123.0	0	37	37
124.0	0	37	37
125.0	0	43	43
126.0	0	46	46
127.0	0	34	34
128.0	0	31	31
129.0	0	36	36
130.0	0	30	30
131.0	0	24	24
132.0	0	37	37
133.0	0	36	36
134.0	0	37	37
135.0	0	30	30
136.0	0	29	29
137.0	0	33	33
138.0	0	33	33
139.0	0	28	28
140.0	0	26	26
141.0	0	23	23
142.0	0	33	33
143.0	0	33	33
144.0	0	20	20
145.0	0	31	31
146.0	0	23	23
147.0	0	22	22
148.0	0	22	22
149.0	0	25	25
150.0	0	24	24
151.0	0	22	22
152.0	0	24	24
153.0	0	33	33
154.0	0	22	22
155.0	0	25	25
156.0	0	20	20
157.0	0	16	16
158.0	0	20	20
159.0	0	14	14
160.0	0	21	21
161.0	0	18	18
162.0	0	33	33
163.0	0	14	14
164.0	0	18	18
165.0	0	16	16
166.0	0	20	20
167.0	0	17	17
168.0	0	19	19
169.0	0	22	22
170.0	0	19	19
171.0	0	25	25
172.0	0	20	20
173.0	0	21	21
174.0	0	22	22
175.0	0	23	23
176.0	0	13	13
177.0	0	20	20
178.0	0	11	11
179.0	0	12	12
180.0	0	20	20
181.0	0	13	13
182.0	0	27	27
183.0	0	13	13
184.0	0	16	16
185.0	0	21	21
186.0	0	11	11
187.0	0	15	15
188.0	0	17	17
189.0	0	10	10
190.0	0	11	11
191.0	0	12	12
192.0	0	9	9
193.0	0	17	17
194.0	0	7	7
195.0	0	11	11
196.0	0	7	7
197.0	0	14	14
198.0	0	19	19
199.0	0	11	11
200.0	0	9	9
201.0	0	16	16
202.0	0	19	19
203.0	0	18	18
204.0	0	9	9
205.0	0	11	11
206.0	0	10	10
207.0	0	10	10
208.0	0	9	9
209.0	0	18	18
210.0	0	12	12
211.0	0	7	7
212.0	0	12	12
213.0	0	8	8
214.0	0	6	6
215.0	0	10	10
216.0	0	14	14
217.0	0	5	5
218.0	0	13	13
219.0	0	8	8
220.0	0	7	7
221.0	0	9	9
222.0	0	8	8
223.0	0	12	12
224.0	0	9	9
225.0	0	16	16
226.0	0	14	14
227.0	0	8	8
228.0	0	5	5
229.0	0	6	6
230.0	0	7	7
231.0	0	9	9
232.0	0	9	9
233.0	0	8	8
234.0	0	8	8
235.0	0	5	5
236.0	0	8	8
237.0	0	8	8
238.0	0	8	8
239.0	0	5	5
240.0	0	6	6
241.0	0	3	3
242.0	0	13	13
243.0	0	5	5
244.0	0	11	11
245.0	0	4	4
246.0	0	5	5
247.0	0	10	10
248.0	0	6	6
249.0	0	5	5
250.0	0	3	3
251.0	0	10	10
252.0	0	4	4
253.0	0	10	10
254.0	0	3	3
255.0	0	6	6
256.0	0	5	5
257.0	0	6	6
258.0	0	6	6
259.0	0	8	8
260.0	0	10	10
261.0	0	10	10
262.0	0	11	11
263.0	0	6	6
264.0	0	5	5
265.0	0	11	11
266.0	0	5	5
267.0	0	3	3
268.0	0	3	3
269.0	0	2	2
270.0	0	13	13
271.0	0	8	8
272.0	0	7	7
273.0	0	6	6
274.0	0	7	7
275.0	0	2	2
276.0	0	4	4
277.0	0	5	5
278.0	0	3	3
279.0	0	4	4
280.0	0	3	3
281.0	0	2	2
282.0	0	3	3
283.0	0	5	5
284.0	0	6	6
285.0	0	3	3
286.0	0	3	3
287.0	0	5	5
288.0	0	5	5
289.0	0	3	3
290.0	0	7	7
291.0	0	5	5
292.0	0	2	2
293.0	0	5	5
294.0	0	6	6
296.0	0	4	4
297.0	0	4	4
298.0	0	4	4
299.0	0	4	4
300.0	0	1	1
301.0	0	5	5
302.0	0	7	7
303.0	0	5	5
304.0	0	3	3
306.0	0	4	4
307.0	0	5	5
308.0	0	3	3
309.0	0	1	1
310.0	0	4	4
311.0	0	1	1
312.0	0	5	5
313.0	0	4	4
314.0	0	6	6
315.0	0	4	4
316.0	0	4	4
317.0	0	3	3
318.0	0	1	1
319.0	0	2	2
320.0	0	7	7
321.0	0	4	4
322.0	0	6	6
323.0	0	3	3
324.0	0	4	4
325.0	0	1	1
326.0	0	3	3
327.0	0	2	2
328.0	0	2	2
329.0	0	2	2
331.0	0	3	3
332.0	0	3	3
333.0	0	4	4
334.0	0	1	1
335.0	0	1	1
336.0	0	4	4
337.0	0	4	4
338.0	0	3	3
339.0	0	2	2
340.0	0	3	3
341.0	0	5	5
343.0	0	4	4
344.0	0	8	8
345.0	0	6	6
346.0	0	2	2
347.0	0	5	5
348.0	0	2	2
349.0	0	4	4
350.0	0	1	1
351.0	0	6	6
352.0	0	4	4
353.0	0	1	1
354.0	0	1	1
355.0	0	3	3
356.0	0	1	1
357.0	0	3	3
358.0	0	5	5
359.0	0	3	3
360.0	0	2	2
361.0	0	2	2
362.0	0	5	5
363.0	0	4	4
364.0	0	3	3
365.0	0	3	3
366.0	0	1	1
367.0	0	2	2
368.0	0	2	2
369.0	0	1	1
370.0	0	5	5
371.0	0	2	2
372.0	0	3	3
373.0	0	5	5
374.0	0	2	2
376.0	0	8	8
377.0	0	1	1
378.0	0	3	3
379.0	0	5	5
380.0	0	1	1
381.0	0	2	2
382.0	0	1	1
383.0	0	1	1
384.0	0	6	6
385.0	0	2	2
386.0	0	1	1
388.0	0	3	3
389.0	0	1	1
390.0	0	2	2
391.0	0	4	4
393.0	0	1	1
394.0	0	6	6
396.0	0	1	1
397.0	0	1	1
399.0	0	2	2
401.0	0	3	3
402.0	0	1	1
403.0	0	1	1
404.0	0	3	3
405.0	0	4	4
406.0	0	3	3
407.0	0	1	1
408.0	0	2	2
409.0	0	2	2
410.0	0	1	1
411.0	0	3	3
412.0	0	2	2
413.0	0	1	1
414.0	0	1	1
415.0	0	5	5
417.0	0	4	4
420.0	0	1	1
423.0	0	2	2
424.0	0	2	2
425.0	0	2	2
426.0	0	3	3
427.0	0	1	1
428.0	0	3	3
429.0	0	2	2
430.0	0	1	1
431.0	0	2	2
432.0	0	2	2
433.0	0	1	1
434.0	0	2	2
435.0	0	2	2
436.0	0	1	1
437.0	0	4	4
438.0	0	2	2
439.0	0	1	1
440.0	0	2	2
441.0	0	2	2
442.0	0	2	2
443.0	0	5	5
444.0	0	1	1
445.0	0	2	2
446.0	0	3	3
447.0	0	2	2
448.0	0	1	1
449.0	0	1	1
450.0	0	2	2
451.0	0	1	1
452.0	0	2	2
453.0	0	3	3
454.0	0	1	1
455.0	0	2	2
456.0	0	2	2
458.0	0	1	1
459.0	0	2	2
460.0	0	2	2
461.0	0	1	1
463.0	0	4	4
464.0	0	2	2
465.0	0	2	2
466.0	0	2	2
467.0	0	3	3
468.0	0	1	1
469.0	0	1	1
470.0	0	5	5
471.0	0	1	1
473.0	0	1	1
475.0	0	1	1
476.0	0	1	1
477.0	0	2	2
478.0	0	1	1
479.0	0	3	3
480.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
486.0	0	2	2
489.0	0	1	1
493.0	0	1	1
494.0	0	1	1
495.0	0	4	4
496.0	0	3	3
497.0	0	2	2
498.0	0	1	1
502.0	0	2	2
503.0	0	1	1
504.0	0	2	2
505.0	0	1	1
507.0	0	2	2
508.0	0	3	3
510.0	0	2	2
511.0	0	1	1
513.0	0	3	3
514.0	0	1	1
515.0	0	2	2
516.0	0	2	2
517.0	0	1	1
518.0	0	1	1
519.0	0	1	1
520.0	0	2	2
521.0	0	1	1
522.0	0	1	1
523.0	0	1	1
524.0	0	3	3
526.0	0	2	2
527.0	0	2	2
531.0	0	1	1
532.0	0	2	2
535.0	0	1	1
537.0	0	1	1
538.0	0	3	3
540.0	0	1	1
541.0	0	1	1
542.0	0	3	3
545.0	0	1	1
548.0	0	1	1
549.0	0	3	3
550.0	0	1	1
555.0	0	2	2
556.0	0	1	1
558.0	0	1	1
560.0	0	1	1
561.0	0	1	1
562.0	0	2	2
564.0	0	3	3
565.0	0	1	1
566.0	0	3	3
567.0	0	1	1
568.0	0	1	1
573.0	0	1	1
574.0	0	1	1
575.0	0	1	1
576.0	0	1	1
577.0	0	1	1
580.0	0	1	1
582.0	0	2	2
584.0	0	2	2
585.0	0	1	1
586.0	0	1	1
588.0	0	2	2
590.0	0	1	1
591.0	0	1	1
592.0	0	1	1
593.0	0	1	1
595.0	0	1	1
597.0	0	2	2
599.0	0	1	1
601.0	0	1	1
602.0	0	1	1
603.0	0	1	1
605.0	0	1	1
606.0	0	2	2
608.0	0	1	1
614.0	0	1	1
615.0	0	1	1
617.0	0	4	4
622.0	0	3	3
623.0	0	2	2
626.0	0	1	1
629.0	0	1	1
630.0	0	1	1
631.0	0	1	1
633.0	0	2	2
634.0	0	1	1
636.0	0	3	3
638.0	0	2	2
639.0	0	2	2
640.0	0	1	1
641.0	0	2	2
642.0	0	1	1
647.0	0	2	2
649.0	0	1	1
650.0	0	1	1
653.0	0	1	1
662.0	0	1	1
665.0	0	1	1
666.0	0	1	1
671.0	0	1	1
675.0	0	1	1
677.0	0	2	2
678.0	0	1	1
681.0	0	1	1
683.0	0	1	1
684.0	0	1	1
685.0	0	1	1
690.0	0	1	1
693.0	0	1	1
694.0	0	1	1
697.0	0	1	1
698.0	0	1	1
701.0	0	1	1
702.0	0	2	2
703.0	0	1	1
707.0	0	1	1
713.0	0	1	1
714.0	0	1	1
715.0	0	1	1
717.0	0	1	1
720.0	0	1	1
722.0	0	1	1
724.0	0	1	1
725.0	0	1	1
728.0	0	1	1
731.0	0	1	1
736.0	0	1	1
741.0	0	3	3
743.0	0	1	1
744.0	0	1	1
745.0	0	1	1
746.0	0	1	1
748.0	0	1	1
749.0	0	1	1
752.0	0	2	2
755.0	0	2	2
757.0	0	1	1
760.0	0	1	1
765.0	0	1	1
766.0	0	1	1
767.0	0	1	1
773.0	0	3	3
777.0	0	1	1
779.0	0	1	1
783.0	0	1	1
785.0	0	1	1
798.0	0	1	1
799.0	0	1	1
801.0	0	1	1
802.0	0	2	2
806.0	0	1	1
810.0	0	1	1
813.0	0	1	1
817.0	0	1	1
818.0	0	1	1
821.0	0	2	2
822.0	0	1	1
823.0	0	2	2
826.0	0	1	1
830.0	0	1	1
837.0	0	1	1
847.0	0	1	1
849.0	0	1	1
850.0	0	1	1
855.0	0	1	1
856.0	0	1	1
861.0	0	1	1
881.0	0	2	2
885.0	0	1	1
892.0	0	1	1
894.0	0	1	1
897.0	0	1	1
903.0	0	1	1
908.0	0	2	2
921.0	0	1	1
940.0	0	1	1
947.0	0	1	1
948.0	0	1	1
956.0	0	1	1
965.0	0	1	1
975.0	0	1	1
979.0	0	1	1
980.0	0	1	1
985.0	0	1	1
997.0	0	1	1
1002.0	0	1	1
1010.0	0	1	1
1031.0	0	1	1
1032.0	0	1	1
1034.0	0	1	1
1049.0	0	1	1
1066.0	0	1	1
1069.0	0	1	1
1076.0	0	1	1
1092.0	0	1	1
1110.0	0	1	1
1119.0	0	1	1
1135.0	0	1	1
1137.0	0	1	1
1142.0	0	1	1
1147.0	0	1	1
1156.0	0	1	1
1158.0	0	2	2
1168.0	0	1	1
1196.0	0	1	1
1205.0	0	1	1
1216.0	0	1	1
1234.0	0	1	1
1264.0	0	1	1
1265.0	0	1	1
1322.0	0	1	1
1323.0	0	1	1
1345.0	0	1	1
1356.0	0	1	1
1372.0	0	1	1
1410.0	0	1	1
1441.0	0	1	1
1458.0	0	1	1
1477.0	0	1	1
1498.0	0	1	1
1502.0	0	1	1
1523.0	0	1	1
1524.0	0	1	1
1555.0	0	1	1
1559.0	0	1	1
1573.0	0	1	1
1677.0	0	1	1
1692.0	0	1	1
1696.0	0	1	1
1715.0	0	1	1
1724.0	0	1	1
1781.0	0	1	1
1788.0	0	1	1
1838.0	0	1	1
1867.0	0	1	1
1889.0	0	1	1
1895.0	0	1	1
1922.0	0	1	1
1949.0	0	1	1
2024.0	0	1	1
2070.0	0	1	1
2079.0	0	1	1
2101.0	0	1	1
2261.0	0	1	1
2301.0	0	1	1
2343.0	0	1	1
2415.0	0	1	1
2432.0	0	1	1
2475.0	0	1	1
2527.0	0	1	1
2666.0	0	1	1
2680.0	0	1	1
2895.0	0	1	1
3261.0	0	1	1
3568.0	0	1	1
5011.0	0	1	1
6396.0	0	1	1
6952.0	0	1	1