## 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-PRIM_RNA_1.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/final_bam/hg38-PRIM_RNA_1.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/qc/markdup/hg38-PRIM_RNA_1.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 14:54:46 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	268	11940288	0	0	164	2650506	2743	0.221984	22763685

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000175	8416771	0	8418738
2.0	1.59211	636812	2612	635142
3.0	1.942437	110448	17	110213
4.0	2.149771	41684	3	41652
5.0	2.272478	22075	2	22064
6.0	2.3451	13160	4	13152
7.0	2.38808	8797	2	8800
8.0	2.413517	6198	0	6189
9.0	2.428572	4530	0	4535
10.0	2.437482	3530	0	3526
11.0	2.442755	2741	1	2737
12.0	2.445875	2153	0	2155
13.0	2.447722	1814	0	1811
14.0	2.448815	1491	1	1495
15.0	2.449462	1255	0	1254
16.0	2.449845	1062	0	1065
17.0	2.450072	925	0	920
18.0	2.450206	788	0	789
19.0	2.450285	668	0	666
20.0	2.450332	612	0	611
21.0	2.45036	516	0	519
22.0	2.450376	460	0	457
23.0	2.450386	465	0	469
24.0	2.450392	421	0	421
25.0	2.450395	387	0	385
26.0	2.450397	358	1	356
27.0	2.450399	303	0	305
28.0	2.450399	270	0	269
29.0	2.4504	255	0	254
30.0	2.4504	253	0	253
31.0	2.4504	244	0	245
32.0	2.4504	233	0	233
33.0	2.4504	209	0	209
34.0	2.4504	185	0	184
35.0	2.4504	161	0	161
36.0	2.4504	185	0	185
37.0	2.4504	156	0	156
38.0	2.4504	125	0	126
39.0	2.4504	128	0	127
40.0	2.4504	144	0	146
41.0	2.4504	122	0	125
42.0	2.4504	149	0	145
43.0	2.4504	124	0	124
44.0	2.4504	111	0	110
45.0	2.4504	88	0	90
46.0	2.4504	114	0	113
47.0	2.4504	109	0	108
48.0	2.4504	108	0	109
49.0	2.4504	86	0	85
50.0	2.4504	65	0	65
51.0	2.4504	83	0	84
52.0	2.4504	91	0	90
53.0	2.4504	72	0	72
54.0	2.4504	68	0	70
55.0	2.4504	65	0	65
56.0	2.4504	65	0	64
57.0	2.4504	55	0	56
58.0	2.4504	62	0	62
59.0	2.4504	62	0	61
60.0	2.4504	61	0	62
61.0	2.4504	66	0	65
62.0	2.4504	63	0	62
63.0	2.4504	56	0	60
64.0	2.4504	60	0	58
65.0	2.4504	54	0	53
66.0	2.4504	60	0	60
67.0	2.4504	55	0	54
68.0	2.4504	43	0	43
69.0	2.4504	52	0	53
70.0	2.4504	41	0	40
71.0	2.4504	41	0	42
72.0	2.4504	46	0	45
73.0	2.4504	40	0	40
74.0	2.4504	28	0	28
75.0	2.4504	34	0	34
76.0	2.4504	36	0	36
77.0	2.4504	35	0	35
78.0	2.4504	47	0	48
79.0	2.4504	39	0	39
80.0	2.4504	26	0	25
81.0	2.4504	31	0	32
82.0	2.4504	33	0	32
83.0	2.4504	26	0	26
84.0	2.4504	37	0	37
85.0	2.4504	29	0	29
86.0	2.4504	37	0	37
87.0	2.4504	32	0	32
88.0	2.4504	29	0	29
89.0	2.4504	32	0	32
90.0	2.4504	20	0	20
91.0	2.4504	22	0	23
92.0	2.4504	28	0	28
93.0	2.4504	35	0	34
94.0	2.4504	19	0	19
95.0	2.4504	23	0	23
96.0	2.4504	24	0	25
97.0	2.4504	21	0	20
98.0	2.4504	21	0	21
99.0	2.4504	16	0	17
100.0	2.4504	19	0	18
101.0	0	29	0	29
102.0	0	19	0	19
103.0	0	15	0	16
104.0	0	22	0	22
105.0	0	26	0	25
106.0	0	22	0	22
107.0	0	18	0	18
108.0	0	18	0	19
109.0	0	18	0	17
110.0	0	25	0	26
111.0	0	18	0	17
112.0	0	16	0	16
113.0	0	13	0	13
114.0	0	18	0	18
115.0	0	16	0	16
116.0	0	15	0	15
117.0	0	12	0	12
118.0	0	18	0	18
119.0	0	22	0	22
120.0	0	18	0	18
121.0	0	9	0	10
122.0	0	17	0	16
123.0	0	20	0	20
124.0	0	16	0	16
125.0	0	14	0	15
126.0	0	16	0	16
127.0	0	15	0	14
128.0	0	14	0	14
129.0	0	3	0	3
130.0	0	10	0	10
131.0	0	12	0	12
132.0	0	8	0	8
133.0	0	19	0	19
134.0	0	10	0	10
135.0	0	9	0	9
136.0	0	11	0	11
137.0	0	11	0	13
138.0	0	11	0	9
139.0	0	10	0	10
140.0	0	15	0	15
141.0	0	17	0	17
142.0	0	12	0	12
143.0	0	11	0	11
144.0	0	9	0	10
145.0	0	14	0	13
146.0	0	9	0	9
147.0	0	9	0	9
148.0	0	9	0	9
149.0	0	12	0	12
150.0	0	10	0	10
151.0	0	10	0	10
152.0	0	12	0	12
153.0	0	6	0	6
154.0	0	10	0	11
155.0	0	7	0	7
156.0	0	8	0	7
157.0	0	11	0	11
158.0	0	10	0	10
159.0	0	6	0	6
160.0	0	15	0	15
161.0	0	15	0	15
162.0	0	7	0	7
163.0	0	8	0	8
164.0	0	9	0	10
165.0	0	13	0	13
166.0	0	12	0	11
167.0	0	6	0	6
168.0	0	10	0	10
169.0	0	10	0	10
170.0	0	8	0	8
171.0	0	5	0	5
172.0	0	8	0	8
173.0	0	7	0	7
174.0	0	10	0	10
175.0	0	6	0	7
176.0	0	7	0	6
177.0	0	8	0	8
178.0	0	5	0	5
179.0	0	0	0	1
180.0	0	9	0	8
181.0	0	6	0	6
182.0	0	3	0	3
183.0	0	6	0	6
184.0	0	6	0	7
185.0	0	7	0	6
186.0	0	6	0	6
187.0	0	4	0	4
188.0	0	6	0	6
189.0	0	8	0	8
190.0	0	7	0	7
191.0	0	7	0	8
192.0	0	5	0	4
193.0	0	5	0	5
194.0	0	6	0	6
195.0	0	9	0	9
196.0	0	5	0	5
197.0	0	9	0	10
198.0	0	11	0	10
199.0	0	4	0	4
200.0	0	4	0	4
201.0	0	2	0	2
202.0	0	6	0	7
203.0	0	6	0	5
204.0	0	6	0	7
205.0	0	6	0	6
206.0	0	5	0	6
207.0	0	6	0	4
208.0	0	3	0	3
209.0	0	3	0	3
210.0	0	4	0	4
211.0	0	2	0	2
212.0	0	5	0	5
213.0	0	7	0	7
214.0	0	4	0	4
215.0	0	9	0	9
216.0	0	2	0	2
217.0	0	6	0	6
218.0	0	1	0	1
219.0	0	2	0	3
220.0	0	6	0	5
221.0	0	7	0	7
222.0	0	2	0	2
223.0	0	1	0	1
224.0	0	5	0	5
225.0	0	5	0	5
226.0	0	5	0	6
227.0	0	7	0	6
228.0	0	7	0	7
229.0	0	3	0	3
230.0	0	5	0	5
231.0	0	2	0	3
232.0	0	2	0	1
233.0	0	3	0	3
234.0	0	2	0	2
235.0	0	3	0	3
236.0	0	3	0	3
237.0	0	7	0	8
238.0	0	4	0	3
239.0	0	2	0	2
240.0	0	6	0	7
241.0	0	6	0	5
242.0	0	4	0	4
243.0	0	1	0	1
244.0	0	5	0	5
245.0	0	7	0	7
246.0	0	2	0	2
247.0	0	4	0	4
248.0	0	7	0	7
249.0	0	5	0	5
250.0	0	6	0	6
251.0	0	6	0	6
252.0	0	4	0	4
253.0	0	4	0	4
254.0	0	4	0	4
255.0	0	6	0	6
256.0	0	3	0	3
257.0	0	3	0	3
258.0	0	2	0	2
259.0	0	4	0	4
260.0	0	2	0	2
261.0	0	2	0	2
262.0	0	3	0	3
263.0	0	5	0	5
264.0	0	5	0	6
265.0	0	8	0	7
266.0	0	7	0	7
267.0	0	3	0	3
268.0	0	2	0	2
269.0	0	5	0	5
270.0	0	4	0	4
271.0	0	2	0	2
272.0	0	4	0	4
273.0	0	2	0	2
274.0	0	2	0	2
275.0	0	4	0	4
276.0	0	5	0	5
277.0	0	3	0	3
278.0	0	2	0	2
279.0	0	5	0	5
280.0	0	5	0	6
281.0	0	1	0	0
282.0	0	3	0	3
283.0	0	2	0	2
284.0	0	3	0	3
285.0	0	3	0	3
286.0	0	3	0	3
287.0	0	3	0	3
288.0	0	6	0	6
289.0	0	1	0	1
291.0	0	4	0	4
292.0	0	1	0	1
293.0	0	4	0	5
294.0	0	1	0	0
295.0	0	2	0	2
296.0	0	2	0	3
297.0	0	3	0	2
298.0	0	4	0	4
299.0	0	2	0	2
300.0	0	1	0	2
301.0	0	3	0	2
302.0	0	2	0	2
304.0	0	2	0	2
305.0	0	2	0	2
306.0	0	3	0	3
307.0	0	2	0	2
308.0	0	5	0	5
309.0	0	5	0	5
311.0	0	2	0	2
312.0	0	1	0	2
313.0	0	4	0	3
314.0	0	1	0	1
315.0	0	1	0	1
316.0	0	1	0	2
317.0	0	3	0	2
318.0	0	1	0	1
319.0	0	2	0	2
320.0	0	4	0	5
321.0	0	3	0	3
322.0	0	3	0	2
323.0	0	3	0	3
324.0	0	1	0	1
325.0	0	1	0	1
327.0	0	1	0	1
328.0	0	2	0	2
329.0	0	1	0	1
332.0	0	3	0	3
333.0	0	3	0	4
334.0	0	3	0	2
335.0	0	3	0	3
338.0	0	5	0	5
339.0	0	2	0	2
340.0	0	2	0	2
341.0	0	3	0	3
343.0	0	4	0	4
344.0	0	2	0	2
345.0	0	4	0	4
347.0	0	2	0	2
348.0	0	2	0	2
349.0	0	2	0	2
350.0	0	4	0	4
351.0	0	4	0	4
352.0	0	2	0	2
353.0	0	3	0	3
354.0	0	3	0	3
355.0	0	4	0	4
357.0	0	3	0	4
358.0	0	1	0	0
359.0	0	5	0	5
360.0	0	1	0	1
361.0	0	1	0	1
363.0	0	1	0	1
364.0	0	1	0	1
365.0	0	1	0	1
367.0	0	2	0	2
368.0	0	2	0	2
369.0	0	3	0	3
370.0	0	2	0	2
371.0	0	1	0	1
373.0	0	1	0	1
374.0	0	2	0	2
375.0	0	1	0	1
376.0	0	1	0	1
377.0	0	1	0	1
378.0	0	2	0	2
379.0	0	2	0	2
380.0	0	2	0	2
382.0	0	1	0	1
383.0	0	2	0	3
384.0	0	3	0	2
385.0	0	1	0	1
387.0	0	1	0	1
388.0	0	3	0	3
392.0	0	1	0	1
393.0	0	2	0	2
395.0	0	1	0	1
396.0	0	1	0	1
398.0	0	1	0	1
399.0	0	1	0	1
400.0	0	1	0	1
401.0	0	2	0	2
403.0	0	2	0	2
404.0	0	6	0	6
405.0	0	5	0	5
408.0	0	2	0	2
409.0	0	1	0	1
410.0	0	0	0	1
411.0	0	4	0	3
412.0	0	1	0	1
413.0	0	1	0	1
414.0	0	2	0	2
415.0	0	1	0	1
416.0	0	3	0	3
417.0	0	2	0	2
418.0	0	3	0	3
419.0	0	1	0	1
420.0	0	1	0	1
421.0	0	1	0	1
422.0	0	1	0	1
423.0	0	3	0	3
425.0	0	1	0	1
426.0	0	1	0	1
427.0	0	2	0	2
430.0	0	1	0	2
431.0	0	3	0	3
432.0	0	2	0	1
433.0	0	1	0	1
434.0	0	3	0	4
435.0	0	2	0	1
436.0	0	2	0	2
437.0	0	1	0	1
438.0	0	1	0	1
439.0	0	1	0	1
440.0	0	2	0	2
441.0	0	1	0	1
443.0	0	1	0	1
444.0	0	1	0	1
445.0	0	1	0	1
449.0	0	3	0	3
452.0	0	1	0	1
453.0	0	2	0	2
455.0	0	1	0	1
457.0	0	2	0	2
458.0	0	1	0	1
459.0	0	1	0	1
461.0	0	1	0	1
462.0	0	1	0	1
463.0	0	1	0	1
464.0	0	2	0	2
469.0	0	1	0	1
470.0	0	2	0	2
472.0	0	1	0	1
473.0	0	1	0	1
475.0	0	1	0	1
476.0	0	1	0	1
477.0	0	3	0	3
478.0	0	0	0	1
479.0	0	1	0	0
480.0	0	2	0	2
482.0	0	2	0	2
483.0	0	2	0	3
484.0	0	2	0	1
485.0	0	1	0	1
486.0	0	1	0	1
488.0	0	1	0	1
492.0	0	2	0	2
495.0	0	1	0	2
496.0	0	2	0	1
498.0	0	1	0	1
499.0	0	1	0	1
500.0	0	2	0	3
501.0	0	1	0	0
502.0	0	2	0	2
503.0	0	1	0	1
504.0	0	1	0	1
507.0	0	2	0	2
508.0	0	2	0	2
512.0	0	2	0	2
514.0	0	1	0	1
515.0	0	2	0	2
516.0	0	1	0	1
518.0	0	3	0	3
519.0	0	1	0	1
522.0	0	2	0	2
531.0	0	1	0	1
533.0	0	1	0	1
534.0	0	1	0	1
535.0	0	1	0	1
537.0	0	1	0	1
538.0	0	2	0	2
540.0	0	2	0	2
541.0	0	1	0	1
544.0	0	1	0	1
546.0	0	1	0	1
547.0	0	1	0	1
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555.0	0	2	0	3
556.0	0	2	0	1
560.0	0	1	0	1
561.0	0	1	0	1
566.0	0	1	0	1
572.0	0	1	0	1
574.0	0	1	0	1
582.0	0	1	0	1
583.0	0	3	0	3
589.0	0	1	0	1
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592.0	0	1	0	0
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600.0	0	2	0	1
603.0	0	1	0	1
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608.0	0	2	0	2
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610.0	0	2	0	1
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624.0	0	1	0	1
627.0	0	2	0	2
631.0	0	1	0	1
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633.0	0	1	0	0
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661.0	0	1	0	1
665.0	0	3	0	3
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681.0	0	1	0	0
684.0	0	2	0	2
689.0	0	0	0	1
690.0	0	1	0	0
693.0	0	1	0	1
695.0	0	0	0	1
696.0	0	2	0	1
697.0	0	1	0	1
698.0	0	1	0	1
702.0	0	1	0	1
705.0	0	1	0	1
711.0	0	1	0	1
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