## 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_1.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/final_bam/hg38-PKC19_RNA_1.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/RNAseq/results/qc/markdup/hg38-PKC19_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 14:03:15 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	196	14015432	0	0	142	2700701	2479	0.192699	31548866

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000141	10460627	0	10462513
2.0	1.641539	576126	2444	574462
3.0	2.052873	121284	10	121123
4.0	2.316665	50837	1	50801
5.0	2.485836	27662	0	27656
6.0	2.594328	17157	1	17153
7.0	2.663904	11257	0	11251
8.0	2.708524	7846	1	7849
9.0	2.737139	5942	0	5941
10.0	2.75549	4536	0	4526
11.0	2.767259	3604	0	3606
12.0	2.774806	2740	0	2745
13.0	2.779646	2327	0	2326
14.0	2.78275	1923	0	1921
15.0	2.784741	1625	0	1624
16.0	2.786018	1351	0	1347
17.0	2.786836	1211	0	1212
18.0	2.787361	1045	0	1047
19.0	2.787698	873	0	874
20.0	2.787914	809	0	806
21.0	2.788053	741	0	742
22.0	2.788141	631	0	630
23.0	2.788198	589	0	591
24.0	2.788235	536	0	535
25.0	2.788258	457	0	455
26.0	2.788273	414	0	418
27.0	2.788283	394	0	391
28.0	2.788289	352	0	352
29.0	2.788293	327	0	326
30.0	2.788296	318	0	319
31.0	2.788297	282	0	281
32.0	2.788298	280	0	282
33.0	2.788299	255	0	254
34.0	2.788299	243	0	244
35.0	2.7883	219	0	217
36.0	2.7883	190	0	190
37.0	2.7883	180	0	181
38.0	2.7883	173	0	174
39.0	2.7883	184	0	183
40.0	2.7883	169	0	169
41.0	2.7883	142	0	143
42.0	2.7883	167	0	165
43.0	2.7883	142	0	145
44.0	2.7883	131	0	129
45.0	2.7883	122	0	123
46.0	2.7883	132	0	132
47.0	2.7883	117	0	116
48.0	2.7883	106	0	108
49.0	2.7883	98	0	95
50.0	2.7883	111	0	114
51.0	2.7883	114	0	112
52.0	2.7883	92	0	92
53.0	2.7883	94	0	94
54.0	2.7883	98	0	97
55.0	2.7883	85	0	85
56.0	2.7883	74	0	75
57.0	2.7883	65	0	64
58.0	2.7883	73	0	74
59.0	2.7883	80	0	79
60.0	2.7883	63	0	63
61.0	2.7883	77	0	77
62.0	2.7883	62	0	64
63.0	2.7883	73	0	71
64.0	2.7883	59	0	60
65.0	2.7883	53	0	54
66.0	2.7883	63	0	62
67.0	2.7883	53	0	52
68.0	2.7883	39	0	39
69.0	2.7883	60	0	60
70.0	2.7883	63	0	65
71.0	2.7883	56	0	54
72.0	2.7883	44	0	44
73.0	2.7883	31	0	33
74.0	2.7883	45	0	43
75.0	2.7883	41	0	43
76.0	2.7883	50	0	48
77.0	2.7883	44	0	44
78.0	2.7883	39	0	39
79.0	2.7883	37	0	37
80.0	2.7883	47	0	48
81.0	2.7883	38	0	37
82.0	2.7883	33	0	34
83.0	2.7883	29	0	29
84.0	2.7883	37	0	36
85.0	2.7883	30	0	30
86.0	2.7883	30	0	30
87.0	2.7883	35	0	35
88.0	2.7883	44	0	44
89.0	2.7883	32	0	32
90.0	2.7883	27	0	27
91.0	2.7883	31	0	31
92.0	2.7883	31	0	31
93.0	2.7883	24	0	25
94.0	2.7883	29	0	30
95.0	2.7883	37	0	36
96.0	2.7883	32	0	32
97.0	2.7883	26	0	25
98.0	2.7883	32	0	32
99.0	2.7883	39	0	39
100.0	2.7883	22	0	22
101.0	0	21	0	23
102.0	0	32	0	30
103.0	0	18	0	20
104.0	0	21	0	20
105.0	0	21	0	20
106.0	0	21	0	22
107.0	0	21	0	20
108.0	0	21	0	21
109.0	0	23	0	23
110.0	0	10	0	10
111.0	0	15	0	16
112.0	0	23	0	22
113.0	0	22	0	22
114.0	0	22	0	23
115.0	0	21	0	21
116.0	0	19	0	18
117.0	0	11	0	11
118.0	0	23	0	23
119.0	0	22	0	22
120.0	0	18	0	19
121.0	0	16	0	15
122.0	0	16	0	16
123.0	0	13	0	13
124.0	0	16	0	16
125.0	0	23	0	23
126.0	0	13	0	13
127.0	0	16	0	17
128.0	0	15	0	14
129.0	0	19	0	19
130.0	0	12	0	14
131.0	0	14	0	12
132.0	0	15	0	16
133.0	0	12	0	11
134.0	0	12	0	12
135.0	0	11	0	11
136.0	0	13	0	13
137.0	0	12	0	13
138.0	0	15	0	14
139.0	0	13	0	14
140.0	0	12	0	11
141.0	0	14	0	14
142.0	0	10	0	10
143.0	0	13	0	13
144.0	0	15	0	15
145.0	0	11	0	11
146.0	0	8	0	8
147.0	0	11	0	11
148.0	0	13	0	13
149.0	0	11	0	11
150.0	0	7	0	7
151.0	0	3	0	3
152.0	0	13	0	13
153.0	0	5	0	5
154.0	0	14	0	15
155.0	0	12	0	11
156.0	0	8	0	8
157.0	0	6	0	6
158.0	0	12	0	12
159.0	0	9	0	9
160.0	0	12	0	12
161.0	0	9	0	9
162.0	0	17	0	17
163.0	0	11	0	11
164.0	0	9	0	9
165.0	0	13	0	13
166.0	0	11	0	11
167.0	0	7	0	7
168.0	0	14	0	14
169.0	0	4	0	4
170.0	0	8	0	8
171.0	0	12	0	12
172.0	0	3	0	3
173.0	0	8	0	8
174.0	0	7	0	7
175.0	0	8	0	8
176.0	0	8	0	8
177.0	0	9	0	9
178.0	0	10	0	11
179.0	0	9	0	8
180.0	0	6	0	6
181.0	0	11	0	11
182.0	0	6	0	6
183.0	0	12	0	12
184.0	0	6	0	7
185.0	0	6	0	5
186.0	0	6	0	7
187.0	0	6	0	5
188.0	0	11	0	11
189.0	0	7	0	7
190.0	0	8	0	8
191.0	0	6	0	6
192.0	0	6	0	6
193.0	0	9	0	9
194.0	0	7	0	7
195.0	0	2	0	3
196.0	0	8	0	7
197.0	0	8	0	9
198.0	0	8	0	7
199.0	0	6	0	6
200.0	0	7	0	7
201.0	0	10	0	10
202.0	0	5	0	5
203.0	0	3	0	3
204.0	0	8	0	8
205.0	0	7	0	7
206.0	0	5	0	5
207.0	0	7	0	7
208.0	0	5	0	5
209.0	0	8	0	8
210.0	0	7	0	7
211.0	0	5	0	5
212.0	0	4	0	4
213.0	0	9	0	9
214.0	0	4	0	4
215.0	0	5	0	5
216.0	0	4	0	4
217.0	0	1	0	1
218.0	0	12	0	12
219.0	0	3	0	3
220.0	0	10	0	10
221.0	0	4	0	5
222.0	0	12	0	12
223.0	0	7	0	6
224.0	0	3	0	3
225.0	0	3	0	3
226.0	0	4	0	4
227.0	0	3	0	3
228.0	0	3	0	4
229.0	0	7	0	7
230.0	0	4	0	3
231.0	0	2	0	2
232.0	0	4	0	4
233.0	0	4	0	4
234.0	0	3	0	3
235.0	0	4	0	4
236.0	0	4	0	4
237.0	0	5	0	5
238.0	0	4	0	4
239.0	0	4	0	4
240.0	0	4	0	4
241.0	0	4	0	4
242.0	0	4	0	4
243.0	0	2	0	2
244.0	0	4	0	5
245.0	0	6	0	5
246.0	0	3	0	3
247.0	0	2	0	2
248.0	0	3	0	3
249.0	0	3	0	3
251.0	0	4	0	4
252.0	0	7	0	7
253.0	0	7	0	7
254.0	0	5	0	5
255.0	0	2	0	2
256.0	0	4	0	4
257.0	0	2	0	2
259.0	0	3	0	3
260.0	0	3	0	3
262.0	0	3	0	4
263.0	0	8	0	7
264.0	0	1	0	1
265.0	0	2	0	2
266.0	0	4	0	4
267.0	0	3	0	3
268.0	0	3	0	3
269.0	0	6	0	6
270.0	0	2	0	3
271.0	0	4	0	3
272.0	0	1	0	1
273.0	0	6	0	6
274.0	0	2	0	3
275.0	0	6	0	6
276.0	0	4	0	3
277.0	0	2	0	2
278.0	0	2	0	2
279.0	0	6	0	7
280.0	0	2	0	1
281.0	0	4	0	4
282.0	0	1	0	1
283.0	0	2	0	2
284.0	0	2	0	2
285.0	0	6	0	6
286.0	0	3	0	3
287.0	0	1	0	1
288.0	0	4	0	4
289.0	0	2	0	2
290.0	0	3	0	3
291.0	0	3	0	3
295.0	0	4	0	4
296.0	0	4	0	4
297.0	0	1	0	1
298.0	0	4	0	4
299.0	0	2	0	2
300.0	0	5	0	5
301.0	0	3	0	3
302.0	0	3	0	3
303.0	0	2	0	3
304.0	0	5	0	4
305.0	0	5	0	5
306.0	0	2	0	2
307.0	0	3	0	3
308.0	0	4	0	4
309.0	0	3	0	3
311.0	0	3	0	3
312.0	0	3	0	3
313.0	0	2	0	3
314.0	0	3	0	2
315.0	0	3	0	3
316.0	0	5	0	6
317.0	0	5	0	4
318.0	0	3	0	3
319.0	0	3	0	3
320.0	0	3	0	3
321.0	0	1	0	1
322.0	0	4	0	4
325.0	0	1	0	1
326.0	0	2	0	2
327.0	0	3	0	3
328.0	0	2	0	2
329.0	0	8	0	9
330.0	0	2	0	1
331.0	0	2	0	2
332.0	0	3	0	3
333.0	0	3	0	3
334.0	0	3	0	3
335.0	0	2	0	3
336.0	0	3	0	2
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345.0	0	2	0	2
346.0	0	3	0	3
348.0	0	3	0	4
349.0	0	2	0	1
351.0	0	1	0	2
352.0	0	3	0	2
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354.0	0	2	0	2
355.0	0	3	0	3
357.0	0	1	0	2
358.0	0	1	0	0
360.0	0	4	0	4
362.0	0	2	0	2
363.0	0	4	0	4
364.0	0	1	0	2
365.0	0	6	0	5
366.0	0	3	0	3
367.0	0	1	0	1
368.0	0	1	0	2
369.0	0	2	0	1
370.0	0	1	0	1
371.0	0	1	0	1
373.0	0	2	0	2
374.0	0	2	0	2
375.0	0	4	0	4
376.0	0	2	0	2
377.0	0	1	0	1
379.0	0	1	0	1
381.0	0	2	0	2
382.0	0	1	0	1
383.0	0	2	0	2
384.0	0	2	0	2
385.0	0	0	0	1
386.0	0	2	0	1
387.0	0	2	0	2
388.0	0	3	0	3
389.0	0	1	0	1
390.0	0	5	0	5
391.0	0	2	0	2
392.0	0	1	0	1
394.0	0	3	0	3
397.0	0	3	0	3
399.0	0	3	0	3
400.0	0	1	0	1
401.0	0	1	0	1
402.0	0	3	0	4
403.0	0	1	0	1
404.0	0	2	0	1
405.0	0	0	0	1
406.0	0	3	0	2
407.0	0	2	0	2
408.0	0	2	0	2
410.0	0	1	0	1
411.0	0	1	0	1
412.0	0	1	0	1
413.0	0	3	0	3
414.0	0	2	0	2
415.0	0	2	0	2
417.0	0	2	0	2
418.0	0	2	0	2
419.0	0	1	0	1
420.0	0	1	0	1
422.0	0	1	0	1
424.0	0	1	0	1
425.0	0	1	0	1
426.0	0	3	0	3
429.0	0	2	0	2
430.0	0	2	0	2
431.0	0	4	0	4
433.0	0	1	0	1
434.0	0	2	0	2
435.0	0	2	0	2
436.0	0	1	0	1
437.0	0	2	0	2
438.0	0	1	0	1
439.0	0	1	0	1
441.0	0	2	0	2
442.0	0	1	0	1
443.0	0	2	0	2
444.0	0	2	0	2
445.0	0	1	0	1
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450.0	0	1	0	2
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456.0	0	1	0	1
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461.0	0	2	0	2
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467.0	0	1	0	1
472.0	0	1	0	1
473.0	0	2	0	2
474.0	0	1	0	1
475.0	0	2	0	2
478.0	0	1	0	1
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480.0	0	1	0	1
483.0	0	1	0	1
484.0	0	4	0	4
485.0	0	1	0	2
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501.0	0	3	0	3
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685.0	0	1	0	1
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