## 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_3JQ.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/final_bam/hg38-PKC19_RNA_3JQ.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/qc/markdup/hg38-PKC19_RNA_3JQ.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/cBuu]    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: Thu Feb 11 21:45:19 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	83	21931500	0	0	50	7802301	12715	0.355758	22990609

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000347	11993046	0	12000474
2.0	1.385703	1404834	12073	1399128
3.0	1.534151	317884	111	316719
4.0	1.591337	127646	43	127360
5.0	1.613366	69158	11	69054
6.0	1.621853	43158	14	43110
7.0	1.625122	29633	5	29600
8.0	1.626381	21536	2	21532
9.0	1.626866	16228	3	16226
10.0	1.627053	12728	1	12702
11.0	1.627125	10136	2	10134
12.0	1.627153	8285	0	8271
13.0	1.627163	6937	1	6940
14.0	1.627167	5773	1	5767
15.0	1.627169	5121	0	5114
16.0	1.62717	4206	0	4207
17.0	1.62717	3730	1	3740
18.0	1.62717	3274	1	3259
19.0	1.62717	2987	0	2988
20.0	1.62717	2647	0	2639
21.0	1.62717	2305	0	2304
22.0	1.62717	2103	0	2112
23.0	1.62717	1855	1	1848
24.0	1.62717	1708	0	1715
25.0	1.62717	1602	0	1598
26.0	1.62717	1442	0	1445
27.0	1.62717	1315	0	1310
28.0	1.62717	1247	0	1244
29.0	1.62717	1085	0	1080
30.0	1.62717	996	0	997
31.0	1.62717	903	0	906
32.0	1.62717	902	0	898
33.0	1.62717	831	0	831
34.0	1.62717	774	0	779
35.0	1.62717	734	0	730
36.0	1.62717	702	0	697
37.0	1.62717	647	0	652
38.0	1.62717	613	0	609
39.0	1.62717	561	0	562
40.0	1.62717	535	0	539
41.0	1.62717	511	0	511
42.0	1.62717	482	0	485
43.0	1.62717	443	0	434
44.0	1.62717	437	0	444
45.0	1.62717	425	0	413
46.0	1.62717	382	0	390
47.0	1.62717	405	0	404
48.0	1.62717	340	0	338
49.0	1.62717	377	0	382
50.0	1.62717	308	0	308
51.0	1.62717	317	0	311
52.0	1.62717	297	0	297
53.0	1.62717	291	0	295
54.0	1.62717	281	0	276
55.0	1.62717	253	0	259
56.0	1.62717	271	0	265
57.0	1.62717	238	0	240
58.0	1.62717	254	0	252
59.0	1.62717	214	0	213
60.0	1.62717	214	0	218
61.0	1.62717	185	0	181
62.0	1.62717	218	0	219
63.0	1.62717	202	0	202
64.0	1.62717	165	0	163
65.0	1.62717	187	0	188
66.0	1.62717	195	0	197
67.0	1.62717	167	0	170
68.0	1.62717	170	0	165
69.0	1.62717	146	0	144
70.0	1.62717	127	0	130
71.0	1.62717	151	0	148
72.0	1.62717	122	0	122
73.0	1.62717	145	0	147
74.0	1.62717	116	0	120
75.0	1.62717	140	0	137
76.0	1.62717	109	0	111
77.0	1.62717	121	0	117
78.0	1.62717	114	0	117
79.0	1.62717	119	0	116
80.0	1.62717	106	0	111
81.0	1.62717	108	0	105
82.0	1.62717	120	0	119
83.0	1.62717	88	0	91
84.0	1.62717	89	0	87
85.0	1.62717	86	0	83
86.0	1.62717	73	0	74
87.0	1.62717	101	0	103
88.0	1.62717	100	0	96
89.0	1.62717	80	0	84
90.0	1.62717	97	0	96
91.0	1.62717	71	0	71
92.0	1.62717	74	0	71
93.0	1.62717	78	0	80
94.0	1.62717	70	0	73
95.0	1.62717	74	0	71
96.0	1.62717	68	0	67
97.0	1.62717	61	0	61
98.0	1.62717	75	0	78
99.0	1.62717	81	0	78
100.0	1.62717	65	0	67
101.0	0	79	0	83
102.0	0	54	0	48
103.0	0	54	0	54
104.0	0	57	0	57
105.0	0	52	0	51
106.0	0	59	0	61
107.0	0	57	0	57
108.0	0	58	0	56
109.0	0	56	0	57
110.0	0	46	0	50
111.0	0	56	0	53
112.0	0	50	0	49
113.0	0	54	0	55
114.0	0	44	0	43
115.0	0	41	0	44
116.0	0	50	0	46
117.0	0	52	0	53
118.0	0	47	0	50
119.0	0	38	0	35
120.0	0	48	0	46
121.0	0	46	0	46
122.0	0	37	0	40
123.0	0	54	0	53
124.0	0	49	0	50
125.0	0	46	0	45
126.0	0	50	0	49
127.0	0	26	0	26
128.0	0	33	0	35
129.0	0	55	0	56
130.0	0	38	0	37
131.0	0	34	0	31
132.0	0	39	0	42
133.0	0	37	0	36
134.0	0	33	0	34
135.0	0	41	0	41
136.0	0	31	0	30
137.0	0	25	0	24
138.0	0	26	0	26
139.0	0	34	0	34
140.0	0	26	0	28
141.0	0	24	0	23
142.0	0	20	0	21
143.0	0	31	0	30
144.0	0	23	0	23
145.0	0	25	0	25
146.0	0	31	0	31
147.0	0	23	0	23
148.0	0	28	0	26
149.0	0	30	0	31
150.0	0	25	0	24
151.0	0	16	0	19
152.0	0	36	0	36
153.0	0	28	0	27
154.0	0	28	0	30
155.0	0	26	0	23
156.0	0	18	0	17
157.0	0	23	0	24
158.0	0	18	0	20
159.0	0	30	0	27
160.0	0	26	0	26
161.0	0	16	0	16
162.0	0	23	0	26
163.0	0	22	0	23
164.0	0	18	0	16
165.0	0	19	0	17
166.0	0	25	0	26
167.0	0	19	0	18
168.0	0	23	0	24
169.0	0	16	0	17
170.0	0	25	0	23
171.0	0	24	0	25
172.0	0	20	0	19
173.0	0	15	0	16
174.0	0	18	0	17
175.0	0	18	0	20
176.0	0	19	0	19
177.0	0	28	0	26
178.0	0	15	0	16
179.0	0	15	0	14
180.0	0	17	0	18
181.0	0	18	0	20
182.0	0	20	0	18
183.0	0	17	0	19
184.0	0	23	0	23
185.0	0	24	0	24
186.0	0	20	0	21
187.0	0	17	0	13
188.0	0	15	0	16
189.0	0	17	0	16
190.0	0	10	0	12
191.0	0	16	0	15
192.0	0	17	0	16
193.0	0	16	0	17
194.0	0	15	0	15
195.0	0	19	0	18
196.0	0	16	0	17
197.0	0	16	0	16
198.0	0	9	0	9
199.0	0	21	0	22
200.0	0	12	0	12
201.0	0	15	0	14
202.0	0	14	0	14
203.0	0	21	0	20
204.0	0	12	0	12
205.0	0	11	0	12
206.0	0	9	0	9
207.0	0	11	0	11
208.0	0	6	0	6
209.0	0	11	0	12
210.0	0	11	0	11
211.0	0	11	0	12
212.0	0	9	0	8
213.0	0	11	0	10
214.0	0	17	0	16
215.0	0	17	0	17
216.0	0	9	0	10
217.0	0	5	0	4
218.0	0	17	0	17
219.0	0	11	0	11
220.0	0	12	0	15
221.0	0	14	0	12
222.0	0	8	0	8
223.0	0	12	0	11
224.0	0	14	0	16
225.0	0	10	0	9
226.0	0	6	0	7
227.0	0	11	0	10
228.0	0	8	0	7
229.0	0	2	0	5
230.0	0	18	0	17
231.0	0	10	0	8
232.0	0	17	0	18
233.0	0	6	0	7
234.0	0	9	0	10
235.0	0	13	0	11
236.0	0	3	0	2
237.0	0	12	0	12
238.0	0	5	0	5
239.0	0	9	0	10
240.0	0	8	0	7
241.0	0	9	0	9
242.0	0	6	0	6
243.0	0	9	0	11
244.0	0	9	0	8
245.0	0	9	0	10
246.0	0	9	0	9
247.0	0	9	0	9
248.0	0	8	0	8
249.0	0	15	0	13
250.0	0	4	0	5
251.0	0	6	0	6
252.0	0	10	0	10
253.0	0	7	0	7
254.0	0	7	0	7
255.0	0	6	0	6
256.0	0	12	0	11
257.0	0	8	0	9
258.0	0	6	0	5
259.0	0	7	0	8
260.0	0	14	0	14
261.0	0	10	0	10
262.0	0	11	0	10
263.0	0	5	0	6
264.0	0	6	0	7
265.0	0	10	0	9
266.0	0	5	0	4
267.0	0	4	0	4
268.0	0	7	0	7
269.0	0	9	0	9
270.0	0	3	0	3
271.0	0	9	0	11
272.0	0	7	0	6
273.0	0	8	0	7
274.0	0	6	0	6
275.0	0	7	0	8
276.0	0	7	0	6
277.0	0	4	0	7
278.0	0	6	0	5
279.0	0	11	0	11
280.0	0	9	0	8
281.0	0	6	0	5
282.0	0	6	0	6
283.0	0	4	0	5
284.0	0	8	0	9
285.0	0	3	0	3
286.0	0	13	0	12
287.0	0	6	0	5
288.0	0	6	0	7
289.0	0	6	0	6
290.0	0	3	0	4
291.0	0	8	0	6
292.0	0	7	0	8
293.0	0	7	0	8
294.0	0	7	0	5
295.0	0	6	0	7
296.0	0	7	0	7
297.0	0	7	0	7
298.0	0	11	0	11
299.0	0	6	0	5
300.0	0	2	0	4
301.0	0	9	0	7
302.0	0	2	0	2
303.0	0	5	0	5
304.0	0	4	0	5
305.0	0	5	0	4
306.0	0	2	0	5
307.0	0	7	0	5
308.0	0	4	0	8
309.0	0	13	0	8
310.0	0	6	0	6
311.0	0	4	0	4
312.0	0	7	0	7
313.0	0	3	0	3
314.0	0	4	0	4
315.0	0	3	0	4
316.0	0	4	0	4
317.0	0	4	0	4
318.0	0	6	0	5
319.0	0	4	0	6
320.0	0	13	0	12
321.0	0	7	0	7
322.0	0	3	0	3
323.0	0	3	0	2
324.0	0	8	0	8
325.0	0	6	0	6
326.0	0	4	0	4
327.0	0	3	0	3
328.0	0	7	0	8
329.0	0	7	0	6
330.0	0	8	0	8
331.0	0	1	0	2
332.0	0	13	0	13
333.0	0	4	0	3
334.0	0	4	0	5
335.0	0	3	0	3
336.0	0	5	0	4
337.0	0	7	0	8
338.0	0	2	0	2
339.0	0	1	0	1
340.0	0	6	0	5
341.0	0	4	0	4
342.0	0	2	0	2
343.0	0	6	0	6
344.0	0	3	0	4
345.0	0	5	0	4
346.0	0	1	0	1
347.0	0	4	0	4
348.0	0	2	0	2
349.0	0	3	0	3
350.0	0	4	0	6
351.0	0	9	0	9
352.0	0	5	0	3
353.0	0	6	0	6
354.0	0	3	0	3
355.0	0	4	0	4
356.0	0	5	0	5
357.0	0	5	0	7
358.0	0	4	0	2
359.0	0	2	0	4
360.0	0	5	0	3
361.0	0	2	0	2
362.0	0	5	0	5
363.0	0	3	0	5
364.0	0	6	0	5
365.0	0	7	0	6
366.0	0	2	0	2
367.0	0	1	0	1
368.0	0	2	0	3
369.0	0	5	0	6
370.0	0	5	0	5
371.0	0	6	0	4
372.0	0	2	0	2
373.0	0	5	0	5
374.0	0	1	0	2
375.0	0	9	0	9
376.0	0	4	0	5
377.0	0	3	0	3
378.0	0	3	0	3
379.0	0	6	0	4
380.0	0	4	0	6
381.0	0	3	0	3
382.0	0	4	0	2
383.0	0	5	0	5
384.0	0	2	0	2
385.0	0	4	0	4
386.0	0	5	0	5
387.0	0	1	0	1
388.0	0	2	0	5
389.0	0	5	0	3
390.0	0	4	0	3
392.0	0	3	0	4
393.0	0	5	0	6
394.0	0	5	0	3
395.0	0	7	0	7
396.0	0	3	0	4
397.0	0	1	0	0
398.0	0	1	0	1
399.0	0	2	0	3
400.0	0	7	0	6
401.0	0	3	0	4
402.0	0	2	0	1
403.0	0	2	0	2
404.0	0	1	0	1
405.0	0	1	0	1
407.0	0	3	0	3
408.0	0	2	0	4
409.0	0	8	0	6
410.0	0	3	0	4
411.0	0	4	0	5
412.0	0	2	0	0
413.0	0	1	0	4
414.0	0	6	0	3
415.0	0	2	0	2
416.0	0	3	0	4
417.0	0	8	0	8
418.0	0	3	0	3
419.0	0	2	0	2
420.0	0	2	0	1
421.0	0	3	0	5
422.0	0	6	0	4
423.0	0	3	0	3
424.0	0	3	0	3
425.0	0	7	0	8
426.0	0	3	0	2
427.0	0	5	0	5
428.0	0	6	0	7
429.0	0	2	0	2
430.0	0	2	0	1
431.0	0	3	0	3
432.0	0	4	0	4
433.0	0	1	0	1
434.0	0	4	0	4
435.0	0	2	0	2
436.0	0	2	0	3
437.0	0	1	0	2
438.0	0	4	0	3
439.0	0	4	0	3
440.0	0	4	0	4
441.0	0	2	0	2
442.0	0	5	0	6
443.0	0	1	0	0
444.0	0	3	0	4
445.0	0	2	0	3
446.0	0	1	0	0
447.0	0	5	0	6
448.0	0	6	0	5
449.0	0	5	0	4
450.0	0	1	0	1
451.0	0	1	0	1
452.0	0	2	0	2
453.0	0	2	0	2
454.0	0	0	0	1
455.0	0	3	0	2
456.0	0	4	0	4
457.0	0	1	0	1
458.0	0	2	0	2
459.0	0	2	0	2
460.0	0	5	0	5
461.0	0	1	0	2
462.0	0	1	0	0
463.0	0	2	0	2
464.0	0	2	0	2
465.0	0	4	0	5
466.0	0	1	0	1
467.0	0	1	0	1
468.0	0	1	0	1
469.0	0	7	0	6
470.0	0	2	0	2
471.0	0	2	0	2
472.0	0	1	0	1
473.0	0	2	0	3
474.0	0	4	0	3
475.0	0	3	0	4
476.0	0	3	0	3
477.0	0	4	0	4
478.0	0	5	0	8
479.0	0	5	0	1
480.0	0	0	0	1
481.0	0	1	0	1
482.0	0	4	0	5
483.0	0	4	0	2
484.0	0	1	0	1
485.0	0	6	0	6
489.0	0	3	0	3
490.0	0	3	0	4
491.0	0	3	0	2
492.0	0	1	0	2
493.0	0	2	0	2
494.0	0	3	0	2
495.0	0	2	0	2
497.0	0	1	0	1
498.0	0	6	0	7
499.0	0	5	0	5
500.0	0	3	0	2
501.0	0	2	0	2
502.0	0	1	0	1
503.0	0	1	0	1
504.0	0	4	0	4
505.0	0	1	0	1
506.0	0	3	0	4
507.0	0	4	0	3
508.0	0	1	0	3
509.0	0	2	0	2
510.0	0	2	0	0
511.0	0	0	0	1
512.0	0	3	0	2
513.0	0	1	0	1
514.0	0	1	0	2
515.0	0	2	0	1
516.0	0	4	0	5
517.0	0	1	0	0
518.0	0	4	0	4
519.0	0	4	0	4
520.0	0	2	0	2
522.0	0	1	0	1
523.0	0	1	0	1
524.0	0	1	0	1
526.0	0	2	0	2
527.0	0	1	0	1
528.0	0	2	0	2
529.0	0	2	0	2
530.0	0	3	0	3
532.0	0	1	0	1
533.0	0	1	0	1
534.0	0	2	0	2
535.0	0	4	0	4
536.0	0	0	0	1
537.0	0	2	0	1
540.0	0	3	0	3
541.0	0	1	0	1
542.0	0	2	0	2
543.0	0	1	0	2
544.0	0	2	0	3
545.0	0	1	0	0
546.0	0	3	0	3
547.0	0	2	0	2
548.0	0	2	0	1
549.0	0	2	0	2
550.0	0	1	0	1
551.0	0	1	0	2
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1913.0	0	1	0	2
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1924.0	0	1	0	1
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