## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/star/hg38-PKC19_RNA_2.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/final_bam/hg38-PKC19_RNA_2.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/qc/markdup/hg38-PKC19_RNA_2.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/aa5P]    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 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: Fri Feb 12 13:35:56 CET 2021

## 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	241	14049278	0	0	177	3260517	2998	0.232082	25393837

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00016	9873991	0	9876152
2.0	1.575326	599041	2871	597138
3.0	1.90609	132390	20	132201
4.0	2.096304	56933	8	56917
5.0	2.205691	31715	3	31690
6.0	2.268597	19826	3	19821
7.0	2.304772	13489	1	13486
8.0	2.325576	9568	3	9561
9.0	2.33754	7113	0	7106
10.0	2.34442	5573	1	5574
11.0	2.348376	4337	0	4334
12.0	2.350651	3564	0	3566
13.0	2.35196	2902	0	2904
14.0	2.352712	2385	0	2383
15.0	2.353145	2054	0	2053
16.0	2.353394	1715	0	1715
17.0	2.353537	1489	0	1486
18.0	2.353619	1324	0	1327
19.0	2.353667	1066	0	1063
20.0	2.353694	1015	0	1015
21.0	2.353709	873	0	875
22.0	2.353718	812	0	812
23.0	2.353724	700	0	697
24.0	2.353727	641	0	641
25.0	2.353728	572	0	573
26.0	2.353729	509	0	509
27.0	2.35373	512	0	512
28.0	2.35373	472	0	471
29.0	2.35373	394	0	395
30.0	2.35373	348	0	347
31.0	2.353731	357	0	358
32.0	2.353731	325	0	326
33.0	2.353731	319	0	318
34.0	2.353731	264	0	263
35.0	2.353731	239	0	238
36.0	2.353731	242	0	242
37.0	2.353731	225	0	226
38.0	2.353731	214	0	214
39.0	2.353731	229	0	228
40.0	2.353731	185	0	186
41.0	2.353731	202	0	202
42.0	2.353731	170	0	169
43.0	2.353731	161	0	161
44.0	2.353731	139	0	140
45.0	2.353731	145	0	144
46.0	2.353731	146	0	146
47.0	2.353731	144	0	144
48.0	2.353731	122	0	124
49.0	2.353731	128	0	127
50.0	2.353731	125	0	126
51.0	2.353731	105	0	104
52.0	2.353731	118	0	117
53.0	2.353731	120	0	121
54.0	2.353731	102	0	102
55.0	2.353731	109	0	108
56.0	2.353731	86	0	86
57.0	2.353731	90	0	90
58.0	2.353731	89	0	91
59.0	2.353731	91	0	90
60.0	2.353731	80	0	79
61.0	2.353731	85	0	86
62.0	2.353731	77	0	78
63.0	2.353731	82	0	80
64.0	2.353731	68	0	68
65.0	2.353731	76	0	77
66.0	2.353731	66	0	65
67.0	2.353731	64	0	64
68.0	2.353731	63	0	66
69.0	2.353731	69	0	68
70.0	2.353731	62	0	63
71.0	2.353731	59	0	56
72.0	2.353731	51	0	53
73.0	2.353731	40	0	38
74.0	2.353731	57	0	57
75.0	2.353731	46	0	47
76.0	2.353731	60	0	60
77.0	2.353731	52	0	51
78.0	2.353731	52	0	52
79.0	2.353731	41	0	42
80.0	2.353731	42	0	42
81.0	2.353731	51	0	50
82.0	2.353731	49	0	49
83.0	2.353731	41	0	41
84.0	2.353731	39	0	40
85.0	2.353731	33	0	33
86.0	2.353731	45	0	45
87.0	2.353731	33	0	32
88.0	2.353731	34	0	35
89.0	2.353731	35	0	34
90.0	2.353731	39	0	39
91.0	2.353731	44	0	44
92.0	2.353731	35	0	35
93.0	2.353731	31	0	31
94.0	2.353731	34	0	35
95.0	2.353731	29	0	28
96.0	2.353731	26	0	26
97.0	2.353731	35	0	36
98.0	2.353731	30	0	29
99.0	2.353731	38	0	39
100.0	2.353731	28	0	28
101.0	0	25	0	25
102.0	0	29	0	28
103.0	0	23	0	23
104.0	0	25	0	25
105.0	0	25	0	26
106.0	0	22	0	21
107.0	0	27	0	27
108.0	0	24	0	24
109.0	0	26	0	26
110.0	0	19	0	19
111.0	0	34	0	34
112.0	0	19	0	21
113.0	0	23	0	22
114.0	0	27	0	26
115.0	0	26	0	26
116.0	0	26	0	27
117.0	0	28	0	27
118.0	0	28	0	29
119.0	0	25	0	24
120.0	0	27	0	27
121.0	0	17	0	17
122.0	0	15	0	15
123.0	0	22	0	24
124.0	0	17	0	15
125.0	0	16	0	17
126.0	0	16	0	15
127.0	0	13	0	13
128.0	0	17	0	17
129.0	0	18	0	18
130.0	0	17	0	17
131.0	0	17	0	17
132.0	0	17	0	18
133.0	0	16	0	15
134.0	0	10	0	10
135.0	0	13	0	14
136.0	0	18	0	17
137.0	0	12	0	12
138.0	0	17	0	17
139.0	0	11	0	11
140.0	0	18	0	18
141.0	0	13	0	13
142.0	0	18	0	18
143.0	0	14	0	14
144.0	0	13	0	13
145.0	0	13	0	13
146.0	0	11	0	11
147.0	0	11	0	11
148.0	0	17	0	17
149.0	0	13	0	13
150.0	0	19	0	20
151.0	0	12	0	11
152.0	0	12	0	12
153.0	0	8	0	8
154.0	0	10	0	10
155.0	0	15	0	15
156.0	0	9	0	10
157.0	0	13	0	12
158.0	0	22	0	22
159.0	0	17	0	17
160.0	0	9	0	9
161.0	0	10	0	10
162.0	0	9	0	9
163.0	0	12	0	14
164.0	0	13	0	11
165.0	0	11	0	12
166.0	0	6	0	6
167.0	0	13	0	13
168.0	0	16	0	15
169.0	0	15	0	16
170.0	0	9	0	8
171.0	0	7	0	7
172.0	0	4	0	4
173.0	0	12	0	12
174.0	0	8	0	10
175.0	0	9	0	7
176.0	0	12	0	14
177.0	0	10	0	8
178.0	0	10	0	10
179.0	0	6	0	6
180.0	0	6	0	6
181.0	0	7	0	7
182.0	0	13	0	13
183.0	0	8	0	9
184.0	0	15	0	15
185.0	0	11	0	11
186.0	0	13	0	12
187.0	0	7	0	7
188.0	0	9	0	9
189.0	0	6	0	7
190.0	0	7	0	6
191.0	0	7	0	8
192.0	0	10	0	9
193.0	0	10	0	10
194.0	0	5	0	6
195.0	0	8	0	7
196.0	0	5	0	5
197.0	0	5	0	5
198.0	0	11	0	11
199.0	0	7	0	7
200.0	0	5	0	5
201.0	0	6	0	6
202.0	0	9	0	9
203.0	0	8	0	9
204.0	0	9	0	8
205.0	0	7	0	7
206.0	0	4	0	4
207.0	0	6	0	6
208.0	0	9	0	9
209.0	0	8	0	8
210.0	0	8	0	8
211.0	0	4	0	4
212.0	0	10	0	10
213.0	0	6	0	6
214.0	0	5	0	5
215.0	0	8	0	8
216.0	0	8	0	8
217.0	0	3	0	3
218.0	0	4	0	4
219.0	0	6	0	7
220.0	0	7	0	6
221.0	0	5	0	5
222.0	0	7	0	7
223.0	0	6	0	6
224.0	0	2	0	2
225.0	0	9	0	9
226.0	0	8	0	8
227.0	0	5	0	5
228.0	0	7	0	7
229.0	0	2	0	2
230.0	0	4	0	4
231.0	0	5	0	5
232.0	0	4	0	4
233.0	0	2	0	2
234.0	0	3	0	3
235.0	0	4	0	6
236.0	0	10	0	8
237.0	0	6	0	6
238.0	0	6	0	6
239.0	0	6	0	7
240.0	0	7	0	6
241.0	0	11	0	11
242.0	0	5	0	5
243.0	0	2	0	2
244.0	0	2	0	2
245.0	0	4	0	4
246.0	0	6	0	6
247.0	0	5	0	5
248.0	0	5	0	5
249.0	0	4	0	4
250.0	0	1	0	1
251.0	0	2	0	2
252.0	0	4	0	4
253.0	0	8	0	8
254.0	0	1	0	1
255.0	0	3	0	3
256.0	0	8	0	8
257.0	0	3	0	3
258.0	0	5	0	5
259.0	0	11	0	12
260.0	0	7	0	7
261.0	0	6	0	5
262.0	0	1	0	2
263.0	0	5	0	4
264.0	0	4	0	5
265.0	0	5	0	4
266.0	0	6	0	6
267.0	0	4	0	4
268.0	0	4	0	5
269.0	0	3	0	3
270.0	0	3	0	2
271.0	0	6	0	6
272.0	0	5	0	5
273.0	0	8	0	8
274.0	0	3	0	3
275.0	0	5	0	5
276.0	0	1	0	2
277.0	0	6	0	5
278.0	0	4	0	4
279.0	0	4	0	4
280.0	0	4	0	4
281.0	0	8	0	9
282.0	0	5	0	4
283.0	0	3	0	3
284.0	0	5	0	5
285.0	0	3	0	3
286.0	0	4	0	4
287.0	0	3	0	3
288.0	0	3	0	3
289.0	0	5	0	5
290.0	0	0	0	2
291.0	0	5	0	3
292.0	0	2	0	2
293.0	0	8	0	8
294.0	0	3	0	3
295.0	0	5	0	5
296.0	0	2	0	2
297.0	0	2	0	2
298.0	0	3	0	4
299.0	0	5	0	4
300.0	0	5	0	6
301.0	0	5	0	4
302.0	0	2	0	2
304.0	0	5	0	5
305.0	0	2	0	2
306.0	0	3	0	3
307.0	0	4	0	4
308.0	0	4	0	4
309.0	0	3	0	3
310.0	0	6	0	6
311.0	0	4	0	5
312.0	0	4	0	3
313.0	0	0	0	1
314.0	0	5	0	5
315.0	0	5	0	4
316.0	0	4	0	4
317.0	0	3	0	4
318.0	0	4	0	3
319.0	0	1	0	1
320.0	0	2	0	2
322.0	0	4	0	4
323.0	0	1	0	1
324.0	0	2	0	2
325.0	0	1	0	1
326.0	0	4	0	4
327.0	0	3	0	4
328.0	0	5	0	4
329.0	0	8	0	8
331.0	0	1	0	1
332.0	0	4	0	4
333.0	0	5	0	5
334.0	0	2	0	2
335.0	0	3	0	4
336.0	0	2	0	1
337.0	0	4	0	4
338.0	0	4	0	4
339.0	0	2	0	3
340.0	0	3	0	2
342.0	0	2	0	2
343.0	0	2	0	2
344.0	0	3	0	3
345.0	0	1	0	1
346.0	0	2	0	2
348.0	0	6	0	6
349.0	0	1	0	2
350.0	0	4	0	3
351.0	0	2	0	2
352.0	0	2	0	2
353.0	0	3	0	3
355.0	0	1	0	2
356.0	0	2	0	1
358.0	0	1	0	1
359.0	0	1	0	1
361.0	0	4	0	4
362.0	0	7	0	7
363.0	0	4	0	4
364.0	0	3	0	3
365.0	0	3	0	3
366.0	0	1	0	1
367.0	0	1	0	1
368.0	0	3	0	3
370.0	0	3	0	3
371.0	0	2	0	3
372.0	0	5	0	4
373.0	0	5	0	5
374.0	0	2	0	2
376.0	0	3	0	5
377.0	0	4	0	2
378.0	0	2	0	2
379.0	0	1	0	1
380.0	0	4	0	4
381.0	0	3	0	3
383.0	0	2	0	2
385.0	0	3	0	3
386.0	0	1	0	1
387.0	0	1	0	1
389.0	0	3	0	3
390.0	0	2	0	2
391.0	0	4	0	4
392.0	0	3	0	3
393.0	0	1	0	2
394.0	0	2	0	1
396.0	0	1	0	1
397.0	0	1	0	1
398.0	0	5	0	5
399.0	0	1	0	2
400.0	0	2	0	1
401.0	0	1	0	1
404.0	0	1	0	1
406.0	0	1	0	1
407.0	0	1	0	1
408.0	0	1	0	1
409.0	0	1	0	1
410.0	0	1	0	1
411.0	0	2	0	2
412.0	0	3	0	3
413.0	0	1	0	1
414.0	0	2	0	2
415.0	0	1	0	1
416.0	0	1	0	1
417.0	0	2	0	2
418.0	0	1	0	1
419.0	0	1	0	1
421.0	0	3	0	4
422.0	0	4	0	3
423.0	0	4	0	4
425.0	0	3	0	3
427.0	0	2	0	2
428.0	0	4	0	4
429.0	0	2	0	2
430.0	0	4	0	5
431.0	0	1	0	0
432.0	0	3	0	3
433.0	0	1	0	1
434.0	0	3	0	3
435.0	0	1	0	1
436.0	0	2	0	2
437.0	0	1	0	1
438.0	0	5	0	5
439.0	0	2	0	2
440.0	0	4	0	5
441.0	0	2	0	1
442.0	0	2	0	2
443.0	0	3	0	3
444.0	0	2	0	2
446.0	0	1	0	1
447.0	0	2	0	2
448.0	0	2	0	2
449.0	0	1	0	2
450.0	0	2	0	1
451.0	0	3	0	3
452.0	0	1	0	1
453.0	0	2	0	2
454.0	0	2	0	2
455.0	0	2	0	2
456.0	0	4	0	4
458.0	0	1	0	1
459.0	0	3	0	3
461.0	0	3	0	3
462.0	0	2	0	2
463.0	0	1	0	1
464.0	0	1	0	1
465.0	0	1	0	1
467.0	0	1	0	1
468.0	0	0	0	1
469.0	0	1	0	1
470.0	0	3	0	2
471.0	0	2	0	2
473.0	0	1	0	1
474.0	0	2	0	2
475.0	0	0	0	1
476.0	0	2	0	1
477.0	0	1	0	1
478.0	0	1	0	1
479.0	0	1	0	1
482.0	0	1	0	1
483.0	0	1	0	1
484.0	0	1	0	1
487.0	0	1	0	1
489.0	0	1	0	1
490.0	0	1	0	1
493.0	0	1	0	1
494.0	0	1	0	1
495.0	0	1	0	2
496.0	0	1	0	0
497.0	0	2	0	2
500.0	0	4	0	4
501.0	0	1	0	1
502.0	0	2	0	2
503.0	0	2	0	2
504.0	0	2	0	2
505.0	0	1	0	1
506.0	0	1	0	1
507.0	0	1	0	1
510.0	0	2	0	2
512.0	0	1	0	1
513.0	0	3	0	3
514.0	0	3	0	3
516.0	0	2	0	2
518.0	0	0	0	1
520.0	0	4	0	4
521.0	0	2	0	1
522.0	0	1	0	1
523.0	0	2	0	3
524.0	0	3	0	2
525.0	0	1	0	2
526.0	0	1	0	1
527.0	0	1	0	0
530.0	0	1	0	1
531.0	0	1	0	1
534.0	0	0	0	1
535.0	0	2	0	1
539.0	0	2	0	3
540.0	0	1	0	0
543.0	0	1	0	2
544.0	0	2	0	1
545.0	0	2	0	2
548.0	0	1	0	1
550.0	0	2	0	2
553.0	0	0	0	1
554.0	0	3	0	2
555.0	0	1	0	1
557.0	0	1	0	1
558.0	0	1	0	1
559.0	0	1	0	1
561.0	0	1	0	1
562.0	0	1	0	1
564.0	0	1	0	1
566.0	0	1	0	1
567.0	0	1	0	1
569.0	0	1	0	1
571.0	0	2	0	2
572.0	0	2	0	2
573.0	0	0	0	1
574.0	0	2	0	1
575.0	0	1	0	1
576.0	0	1	0	1
577.0	0	2	0	2
578.0	0	0	0	1
579.0	0	2	0	1
581.0	0	1	0	1
583.0	0	1	0	1
584.0	0	2	0	2
585.0	0	1	0	1
586.0	0	1	0	1
588.0	0	1	0	1
589.0	0	2	0	2
590.0	0	0	0	1
591.0	0	2	0	1
593.0	0	1	0	1
595.0	0	1	0	1
596.0	0	1	0	1
597.0	0	0	0	1
598.0	0	2	0	1
601.0	0	1	0	1
602.0	0	2	0	2
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