## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/siebrenf/hendrik/results2/star/hg38-White-Bloodcells-Morsche-MDL2-C-nonstimulated-1-16239.samtools-coordinate-sieved.bam] OUTPUT=/scratch/siebrenf/hendrik/results2/final_bam/hg38-White-Bloodcells-Morsche-MDL2-C-nonstimulated-1-16239.samtools-coordinate.bam METRICS_FILE=/scratch/siebrenf/hendrik/results2/qc/markdup/hg38-White-Bloodcells-Morsche-MDL2-C-nonstimulated-1-16239.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/siebrenf/tmp/gN7y]    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: Wed Nov 04 11:07:40 CET 2020

## 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	114	16956156	0	0	46	2392448	3754	0.141097	54360508

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000189	13088722	0	13091604
2.0	1.732367	1274315	3736	1272058
3.0	2.26835	129565	9	129018
4.0	2.660711	25946	0	25890
5.0	2.947935	11042	0	11032
6.0	3.158194	6384	0	6383
7.0	3.312112	4162	0	4159
8.0	3.424786	2912	0	2908
9.0	3.507268	2156	0	2153
10.0	3.567649	1690	0	1694
11.0	3.611849	1355	0	1354
12.0	3.644206	1108	0	1104
13.0	3.667892	943	0	943
14.0	3.685232	817	0	820
15.0	3.697925	638	0	637
16.0	3.707216	577	0	576
17.0	3.714018	526	0	525
18.0	3.718998	486	0	490
19.0	3.722643	412	0	409
20.0	3.725311	378	0	377
21.0	3.727265	320	0	322
22.0	3.728694	311	0	309
23.0	3.729741	314	0	315
24.0	3.730507	249	0	251
25.0	3.731068	260	0	258
26.0	3.731479	215	0	215
27.0	3.73178	212	0	212
28.0	3.732	197	0	196
29.0	3.732161	182	0	183
30.0	3.732279	187	0	187
31.0	3.732365	176	0	176
32.0	3.732428	177	0	177
33.0	3.732474	137	0	138
34.0	3.732508	150	0	149
35.0	3.732533	148	0	147
36.0	3.732551	120	0	120
37.0	3.732565	117	0	117
38.0	3.732574	128	0	129
39.0	3.732581	111	0	110
40.0	3.732587	99	0	100
41.0	3.73259	109	0	108
42.0	3.732593	90	0	93
43.0	3.732595	90	0	88
44.0	3.732597	79	0	78
45.0	3.732598	89	0	89
46.0	3.732599	68	0	68
47.0	3.732599	71	0	71
48.0	3.7326	68	0	69
49.0	3.7326	82	0	82
50.0	3.7326	62	0	61
51.0	3.7326	70	0	70
52.0	3.7326	71	0	72
53.0	3.732601	68	0	67
54.0	3.732601	58	0	59
55.0	3.732601	59	0	58
56.0	3.732601	48	0	49
57.0	3.732601	41	0	41
58.0	3.732601	60	0	60
59.0	3.732601	43	0	42
60.0	3.732601	49	0	50
61.0	3.732601	45	0	45
62.0	3.732601	55	0	55
63.0	3.732601	54	0	54
64.0	3.732601	49	0	48
65.0	3.732601	51	0	51
66.0	3.732601	34	0	34
67.0	3.732601	40	0	41
68.0	3.732601	42	0	41
69.0	3.732601	34	0	34
70.0	3.732601	30	0	30
71.0	3.732601	47	0	48
72.0	3.732601	36	0	35
73.0	3.732601	31	0	32
74.0	3.732601	40	0	39
75.0	3.732601	32	0	32
76.0	3.732601	24	0	24
77.0	3.732601	42	0	43
78.0	3.732601	30	0	30
79.0	3.732601	30	0	30
80.0	3.732601	36	0	37
81.0	3.732601	26	0	24
82.0	3.732601	24	0	25
83.0	3.732601	28	0	28
84.0	3.732601	29	0	29
85.0	3.732601	30	0	29
86.0	3.732601	19	0	20
87.0	3.732601	27	0	26
88.0	3.732601	30	0	30
89.0	3.732601	18	0	18
90.0	3.732601	24	0	26
91.0	3.732601	20	0	19
92.0	3.732601	27	0	26
93.0	3.732601	23	0	23
94.0	3.732601	20	0	20
95.0	3.732601	20	0	20
96.0	3.732601	22	0	22
97.0	3.732601	18	0	20
98.0	3.732601	20	0	18
99.0	3.732601	28	0	28
100.0	3.732601	17	0	18
101.0	0	7	0	6
102.0	0	20	0	20
103.0	0	13	0	14
104.0	0	18	0	17
105.0	0	16	0	16
106.0	0	18	0	18
107.0	0	13	0	13
108.0	0	14	0	14
109.0	0	13	0	13
110.0	0	12	0	12
111.0	0	11	0	11
112.0	0	20	0	20
113.0	0	11	0	11
114.0	0	7	0	7
115.0	0	8	0	8
116.0	0	10	0	10
117.0	0	11	0	11
118.0	0	14	0	14
119.0	0	13	0	13
120.0	0	6	0	7
121.0	0	8	0	7
122.0	0	10	0	10
123.0	0	16	0	17
124.0	0	12	0	11
125.0	0	9	0	9
126.0	0	11	0	11
127.0	0	9	0	9
128.0	0	8	0	8
129.0	0	18	0	18
130.0	0	11	0	11
131.0	0	11	0	12
132.0	0	8	0	8
133.0	0	6	0	5
134.0	0	10	0	10
135.0	0	9	0	9
136.0	0	12	0	12
137.0	0	8	0	8
138.0	0	12	0	12
139.0	0	4	0	4
140.0	0	9	0	11
141.0	0	11	0	10
142.0	0	8	0	7
143.0	0	8	0	9
144.0	0	5	0	5
145.0	0	7	0	8
146.0	0	12	0	10
147.0	0	4	0	4
148.0	0	6	0	6
149.0	0	7	0	7
150.0	0	5	0	5
151.0	0	8	0	8
152.0	0	9	0	9
153.0	0	10	0	10
154.0	0	7	0	7
155.0	0	5	0	5
156.0	0	7	0	7
157.0	0	11	0	11
158.0	0	10	0	11
159.0	0	7	0	6
160.0	0	5	0	5
161.0	0	5	0	5
162.0	0	5	0	5
163.0	0	9	0	9
164.0	0	6	0	6
165.0	0	7	0	7
166.0	0	3	0	3
167.0	0	8	0	8
168.0	0	2	0	2
169.0	0	5	0	5
170.0	0	7	0	7
171.0	0	10	0	10
172.0	0	9	0	9
173.0	0	7	0	7
174.0	0	3	0	3
175.0	0	5	0	5
176.0	0	4	0	4
177.0	0	6	0	6
178.0	0	4	0	4
179.0	0	7	0	7
180.0	0	5	0	6
181.0	0	8	0	7
182.0	0	2	0	2
183.0	0	2	0	2
184.0	0	5	0	6
185.0	0	9	0	8
186.0	0	4	0	4
187.0	0	3	0	3
188.0	0	5	0	5
189.0	0	4	0	4
190.0	0	7	0	7
191.0	0	8	0	9
192.0	0	4	0	4
193.0	0	5	0	4
194.0	0	5	0	5
195.0	0	4	0	4
196.0	0	3	0	3
197.0	0	1	0	1
198.0	0	3	0	3
199.0	0	3	0	3
200.0	0	4	0	4
201.0	0	1	0	1
202.0	0	7	0	7
203.0	0	2	0	2
204.0	0	3	0	3
205.0	0	3	0	3
206.0	0	1	0	1
207.0	0	4	0	4
208.0	0	4	0	4
210.0	0	5	0	5
211.0	0	2	0	2
212.0	0	3	0	3
213.0	0	1	0	1
214.0	0	5	0	5
215.0	0	4	0	4
216.0	0	5	0	5
217.0	0	3	0	3
218.0	0	3	0	3
220.0	0	2	0	2
221.0	0	4	0	4
222.0	0	5	0	5
223.0	0	3	0	4
224.0	0	5	0	4
225.0	0	4	0	4
226.0	0	2	0	2
227.0	0	2	0	2
229.0	0	2	0	3
230.0	0	5	0	4
231.0	0	4	0	4
232.0	0	4	0	4
233.0	0	4	0	4
234.0	0	1	0	1
235.0	0	5	0	5
236.0	0	1	0	1
237.0	0	1	0	1
238.0	0	1	0	1
239.0	0	4	0	4
240.0	0	2	0	2
242.0	0	1	0	1
243.0	0	2	0	2
244.0	0	3	0	3
245.0	0	2	0	2
246.0	0	4	0	4
247.0	0	3	0	3
248.0	0	2	0	2
249.0	0	3	0	3
250.0	0	1	0	1
251.0	0	1	0	1
252.0	0	3	0	3
253.0	0	3	0	3
254.0	0	2	0	2
255.0	0	2	0	2
256.0	0	3	0	3
257.0	0	1	0	1
258.0	0	4	0	4
259.0	0	1	0	1
260.0	0	2	0	2
261.0	0	1	0	1
262.0	0	4	0	4
263.0	0	2	0	2
264.0	0	1	0	1
265.0	0	1	0	1
267.0	0	1	0	1
269.0	0	5	0	5
270.0	0	2	0	2
272.0	0	2	0	2
273.0	0	2	0	2
274.0	0	1	0	1
276.0	0	1	0	1
277.0	0	4	0	4
278.0	0	4	0	4
279.0	0	2	0	2
280.0	0	0	0	1
281.0	0	1	0	0
282.0	0	1	0	2
283.0	0	4	0	3
285.0	0	3	0	3
286.0	0	1	0	1
287.0	0	1	0	1
288.0	0	2	0	2
289.0	0	2	0	2
291.0	0	2	0	2
293.0	0	1	0	1
294.0	0	2	0	2
295.0	0	3	0	3
297.0	0	2	0	2
298.0	0	1	0	1
299.0	0	4	0	4
300.0	0	1	0	1
301.0	0	2	0	2
302.0	0	1	0	1
304.0	0	2	0	2
305.0	0	3	0	3
306.0	0	1	0	1
307.0	0	1	0	1
308.0	0	1	0	1
313.0	0	1	0	2
314.0	0	2	0	1
315.0	0	2	0	2
316.0	0	0	0	1
317.0	0	4	0	3
319.0	0	1	0	1
321.0	0	2	0	2
322.0	0	4	0	4
323.0	0	2	0	3
324.0	0	1	0	0
326.0	0	3	0	3
327.0	0	1	0	1
329.0	0	1	0	1
331.0	0	1	0	1
333.0	0	1	0	1
334.0	0	1	0	1
335.0	0	2	0	2
337.0	0	1	0	1
339.0	0	1	0	1
340.0	0	2	0	2
342.0	0	4	0	4
343.0	0	1	0	1
345.0	0	1	0	1
346.0	0	1	0	1
348.0	0	1	0	1
349.0	0	1	0	1
350.0	0	2	0	2
352.0	0	1	0	1
354.0	0	2	0	2
355.0	0	1	0	1
359.0	0	3	0	3
361.0	0	2	0	2
362.0	0	1	0	1
364.0	0	1	0	1
372.0	0	1	0	1
374.0	0	1	0	1
376.0	0	1	0	1
378.0	0	1	0	1
380.0	0	1	0	1
386.0	0	1	0	1
388.0	0	2	0	2
389.0	0	2	0	2
390.0	0	2	0	2
391.0	0	1	0	1
392.0	0	1	0	1
393.0	0	1	0	1
394.0	0	1	0	1
396.0	0	1	0	1
398.0	0	1	0	1
399.0	0	1	0	1
403.0	0	2	0	2
404.0	0	1	0	1
410.0	0	1	0	1
413.0	0	1	0	1
416.0	0	2	0	2
418.0	0	2	0	2
421.0	0	1	0	1
423.0	0	1	0	1
424.0	0	1	0	1
426.0	0	1	0	1
427.0	0	1	0	1
428.0	0	1	0	1
429.0	0	2	0	2
430.0	0	1	0	1
431.0	0	1	0	1
432.0	0	1	0	1
433.0	0	1	0	1
434.0	0	1	0	1
436.0	0	1	0	1
438.0	0	2	0	2
441.0	0	1	0	1
442.0	0	1	0	1
443.0	0	1	0	1
450.0	0	1	0	1
451.0	0	1	0	1
454.0	0	1	0	1
456.0	0	2	0	2
463.0	0	1	0	1
470.0	0	2	0	2
471.0	0	1	0	1
472.0	0	1	0	1
476.0	0	3	0	3
477.0	0	2	0	2
482.0	0	2	0	2
486.0	0	1	0	1
490.0	0	1	0	1
493.0	0	1	0	1
497.0	0	1	0	1
499.0	0	1	0	1
508.0	0	1	0	1
511.0	0	1	0	1
512.0	0	1	0	1
517.0	0	2	0	2
539.0	0	1	0	1
542.0	0	1	0	1
546.0	0	1	0	1
547.0	0	1	0	1
553.0	0	2	0	2
559.0	0	1	0	1
566.0	0	0	0	1
567.0	0	1	0	0
582.0	0	0	0	1
584.0	0	1	0	0
591.0	0	1	0	1
597.0	0	1	0	1
600.0	0	1	0	1
608.0	0	1	0	1
610.0	0	1	0	1
614.0	0	0	0	1
615.0	0	1	0	0
619.0	0	1	0	1
625.0	0	0	0	1
626.0	0	1	0	0
630.0	0	0	0	1
631.0	0	1	0	1
632.0	0	1	0	0
650.0	0	0	0	1
651.0	0	1	0	0
657.0	0	1	0	1
660.0	0	1	0	1
677.0	0	1	0	1
693.0	0	0	0	1
694.0	0	1	0	0
717.0	0	1	0	1
721.0	0	1	0	1
731.0	0	0	0	1
732.0	0	1	0	0
735.0	0	1	0	1
755.0	0	1	0	1
769.0	0	1	0	1
782.0	0	1	0	1
842.0	0	1	0	1
862.0	0	1	0	1
867.0	0	1	0	2
868.0	0	1	0	0
878.0	0	1	0	1
931.0	0	1	0	1
979.0	0	1	0	1
1011.0	0	1	0	1
1056.0	0	1	0	1
1172.0	0	1	0	1
1211.0	0	1	0	1
1239.0	0	1	0	1
1252.0	0	1	0	1
1255.0	0	0	0	1
1257.0	0	1	0	0
1421.0	0	0	0	1
1423.0	0	1	0	0
1454.0	0	1	0	1
1631.0	0	1	0	1
2035.0	0	1	0	1
2380.0	0	0	0	1
2381.0	0	1	0	0