## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_supernatant_DMSO_3.samtools-coordinate.metrics.txt TMP_DIR=[/scratch/slrinzema/tmp]    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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Oct 06 01:06:06 CEST 2023

## 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	818	22259537	16109203	0	723	3369160	0	0.151372	65908869

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	17560669	17560669
2.0	1.713386	934930	934930
3.0	2.222307	170765	170765
4.0	2.585363	71441	71441
5.0	2.844363	39503	39503
6.0	3.02913	24936	24936
7.0	3.16094	16677	16677
8.0	3.254972	12134	12134
9.0	3.322053	8843	8843
10.0	3.369907	6890	6890
11.0	3.404046	5465	5465
12.0	3.4284	4260	4260
13.0	3.445774	3454	3454
14.0	3.458168	3006	3006
15.0	3.46701	2587	2587
16.0	3.473318	2093	2093
17.0	3.477818	1920	1920
18.0	3.481028	1617	1617
19.0	3.483318	1414	1414
20.0	3.484952	1233	1233
21.0	3.486117	1050	1050
22.0	3.486949	960	960
23.0	3.487542	911	911
24.0	3.487965	784	784
25.0	3.488267	726	726
26.0	3.488482	626	626
27.0	3.488636	615	615
28.0	3.488745	545	545
29.0	3.488824	520	520
30.0	3.488879	438	438
31.0	3.488919	437	437
32.0	3.488948	438	438
33.0	3.488968	356	356
34.0	3.488982	331	331
35.0	3.488993	287	287
36.0	3.489	302	302
37.0	3.489005	284	284
38.0	3.489009	256	256
39.0	3.489012	233	233
40.0	3.489013	223	223
41.0	3.489015	213	213
42.0	3.489016	217	217
43.0	3.489016	176	176
44.0	3.489017	181	181
45.0	3.489017	170	170
46.0	3.489018	155	155
47.0	3.489018	153	153
48.0	3.489018	142	142
49.0	3.489018	131	131
50.0	3.489018	144	144
51.0	3.489018	108	108
52.0	3.489018	125	125
53.0	3.489018	117	117
54.0	3.489018	108	108
55.0	3.489018	115	115
56.0	3.489018	103	103
57.0	3.489018	93	93
58.0	3.489018	94	94
59.0	3.489018	92	92
60.0	3.489018	89	89
61.0	3.489018	83	83
62.0	3.489018	79	79
63.0	3.489018	64	64
64.0	3.489018	79	79
65.0	3.489018	73	73
66.0	3.489018	67	67
67.0	3.489018	62	62
68.0	3.489018	57	57
69.0	3.489018	60	60
70.0	3.489018	61	61
71.0	3.489018	61	61
72.0	3.489018	48	48
73.0	3.489018	54	54
74.0	3.489018	34	34
75.0	3.489018	42	42
76.0	3.489018	48	48
77.0	3.489018	49	49
78.0	3.489018	44	44
79.0	3.489018	33	33
80.0	3.489018	46	46
81.0	3.489018	38	38
82.0	3.489018	33	33
83.0	3.489018	36	36
84.0	3.489018	45	45
85.0	3.489018	52	52
86.0	3.489018	35	35
87.0	3.489018	36	36
88.0	3.489018	33	33
89.0	3.489018	36	36
90.0	3.489018	19	19
91.0	3.489018	33	33
92.0	3.489018	30	30
93.0	3.489018	30	30
94.0	3.489018	22	22
95.0	3.489018	21	21
96.0	3.489018	32	32
97.0	3.489018	21	21
98.0	3.489018	23	23
99.0	3.489018	22	22
100.0	3.489018	27	27
101.0	0	29	29
102.0	0	28	28
103.0	0	11	11
104.0	0	30	30
105.0	0	22	22
106.0	0	23	23
107.0	0	18	18
108.0	0	29	29
109.0	0	22	22
110.0	0	23	23
111.0	0	17	17
112.0	0	14	14
113.0	0	23	23
114.0	0	25	25
115.0	0	25	25
116.0	0	11	11
117.0	0	26	26
118.0	0	20	20
119.0	0	13	13
120.0	0	20	20
121.0	0	18	18
122.0	0	10	10
123.0	0	10	10
124.0	0	21	21
125.0	0	16	16
126.0	0	21	21
127.0	0	17	17
128.0	0	13	13
129.0	0	19	19
130.0	0	14	14
131.0	0	9	9
132.0	0	11	11
133.0	0	17	17
134.0	0	10	10
135.0	0	11	11
136.0	0	7	7
137.0	0	13	13
138.0	0	14	14
139.0	0	12	12
140.0	0	8	8
141.0	0	14	14
142.0	0	12	12
143.0	0	11	11
144.0	0	12	12
145.0	0	7	7
146.0	0	12	12
147.0	0	12	12
148.0	0	13	13
149.0	0	14	14
150.0	0	12	12
151.0	0	8	8
152.0	0	8	8
153.0	0	6	6
154.0	0	8	8
155.0	0	9	9
156.0	0	9	9
157.0	0	6	6
158.0	0	7	7
159.0	0	2	2
160.0	0	9	9
161.0	0	15	15
162.0	0	6	6
163.0	0	7	7
164.0	0	9	9
165.0	0	3	3
166.0	0	11	11
167.0	0	9	9
168.0	0	13	13
169.0	0	3	3
170.0	0	8	8
171.0	0	8	8
172.0	0	5	5
173.0	0	9	9
174.0	0	6	6
175.0	0	4	4
176.0	0	11	11
177.0	0	7	7
178.0	0	4	4
179.0	0	8	8
180.0	0	6	6
181.0	0	6	6
182.0	0	4	4
183.0	0	6	6
184.0	0	7	7
185.0	0	5	5
186.0	0	8	8
187.0	0	4	4
188.0	0	10	10
189.0	0	3	3
190.0	0	5	5
191.0	0	3	3
192.0	0	7	7
193.0	0	7	7
194.0	0	2	2
195.0	0	6	6
196.0	0	4	4
197.0	0	1	1
198.0	0	5	5
199.0	0	4	4
200.0	0	6	6
201.0	0	9	9
202.0	0	7	7
203.0	0	4	4
204.0	0	8	8
205.0	0	3	3
206.0	0	5	5
207.0	0	6	6
208.0	0	2	2
209.0	0	5	5
210.0	0	5	5
211.0	0	7	7
212.0	0	7	7
213.0	0	3	3
214.0	0	3	3
215.0	0	3	3
216.0	0	4	4
217.0	0	4	4
218.0	0	6	6
219.0	0	1	1
220.0	0	4	4
221.0	0	2	2
222.0	0	2	2
223.0	0	2	2
224.0	0	4	4
225.0	0	4	4
226.0	0	1	1
227.0	0	4	4
228.0	0	2	2
229.0	0	5	5
230.0	0	2	2
231.0	0	2	2
232.0	0	2	2
233.0	0	3	3
234.0	0	1	1
235.0	0	6	6
236.0	0	4	4
237.0	0	4	4
238.0	0	5	5
239.0	0	4	4
240.0	0	1	1
241.0	0	3	3
242.0	0	3	3
243.0	0	5	5
244.0	0	3	3
245.0	0	5	5
246.0	0	1	1
247.0	0	3	3
249.0	0	2	2
250.0	0	4	4
251.0	0	1	1
252.0	0	3	3
253.0	0	1	1
254.0	0	4	4
255.0	0	3	3
256.0	0	7	7
257.0	0	3	3
258.0	0	3	3
259.0	0	1	1
260.0	0	2	2
261.0	0	5	5
262.0	0	4	4
263.0	0	2	2
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	3	3
268.0	0	1	1
269.0	0	1	1
270.0	0	6	6
271.0	0	5	5
272.0	0	1	1
273.0	0	5	5
274.0	0	3	3
275.0	0	6	6
276.0	0	2	2
277.0	0	1	1
279.0	0	2	2
280.0	0	1	1
281.0	0	5	5
282.0	0	3	3
285.0	0	2	2
286.0	0	2	2
287.0	0	1	1
289.0	0	5	5
290.0	0	1	1
292.0	0	1	1
293.0	0	5	5
294.0	0	3	3
295.0	0	1	1
296.0	0	4	4
298.0	0	1	1
299.0	0	1	1
301.0	0	2	2
302.0	0	3	3
303.0	0	6	6
305.0	0	1	1
307.0	0	2	2
308.0	0	2	2
309.0	0	3	3
310.0	0	2	2
311.0	0	3	3
312.0	0	2	2
316.0	0	1	1
317.0	0	1	1
318.0	0	1	1
319.0	0	3	3
320.0	0	1	1
321.0	0	1	1
323.0	0	3	3
324.0	0	4	4
325.0	0	3	3
326.0	0	1	1
328.0	0	2	2
329.0	0	1	1
331.0	0	3	3
332.0	0	3	3
333.0	0	3	3
334.0	0	3	3
335.0	0	3	3
336.0	0	1	1
337.0	0	1	1
338.0	0	2	2
339.0	0	2	2
343.0	0	1	1
344.0	0	1	1
346.0	0	1	1
351.0	0	1	1
352.0	0	3	3
353.0	0	1	1
354.0	0	2	2
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
360.0	0	3	3
361.0	0	1	1
363.0	0	2	2
365.0	0	1	1
367.0	0	2	2
368.0	0	1	1
369.0	0	1	1
370.0	0	2	2
371.0	0	1	1
372.0	0	2	2
373.0	0	1	1
374.0	0	2	2
375.0	0	5	5
376.0	0	1	1
377.0	0	1	1
379.0	0	2	2
381.0	0	1	1
382.0	0	3	3
383.0	0	1	1
384.0	0	2	2
387.0	0	1	1
389.0	0	2	2
391.0	0	1	1
392.0	0	2	2
393.0	0	2	2
394.0	0	3	3
395.0	0	1	1
397.0	0	4	4
399.0	0	1	1
401.0	0	1	1
402.0	0	2	2
407.0	0	2	2
408.0	0	2	2
411.0	0	1	1
412.0	0	2	2
421.0	0	1	1
423.0	0	1	1
424.0	0	1	1
425.0	0	2	2
427.0	0	1	1
431.0	0	2	2
434.0	0	1	1
436.0	0	1	1
437.0	0	1	1
440.0	0	1	1
446.0	0	1	1
447.0	0	1	1
450.0	0	1	1
453.0	0	1	1
455.0	0	1	1
458.0	0	3	3
459.0	0	1	1
461.0	0	1	1
465.0	0	1	1
466.0	0	1	1
467.0	0	2	2
468.0	0	2	2
469.0	0	2	2
472.0	0	2	2
476.0	0	2	2
478.0	0	1	1
479.0	0	1	1
480.0	0	1	1
481.0	0	2	2
486.0	0	1	1
490.0	0	1	1
491.0	0	1	1
496.0	0	1	1
502.0	0	1	1
507.0	0	1	1
509.0	0	2	2
515.0	0	1	1
518.0	0	2	2
521.0	0	2	2
525.0	0	1	1
528.0	0	1	1
532.0	0	1	1
547.0	0	3	3
560.0	0	1	1
562.0	0	2	2
563.0	0	1	1
565.0	0	1	1
566.0	0	1	1
567.0	0	1	1
578.0	0	1	1
579.0	0	1	1
584.0	0	1	1
594.0	0	1	1
595.0	0	1	1
603.0	0	1	1
607.0	0	1	1
608.0	0	1	1
617.0	0	1	1
620.0	0	1	1
622.0	0	1	1
626.0	0	3	3
630.0	0	1	1
633.0	0	1	1
644.0	0	1	1
651.0	0	2	2
655.0	0	1	1
668.0	0	1	1
672.0	0	1	1
738.0	0	2	2
742.0	0	2	2
753.0	0	1	1
787.0	0	1	1
788.0	0	2	2
789.0	0	1	1
805.0	0	1	1
811.0	0	1	1
814.0	0	1	1
822.0	0	1	1
831.0	0	1	1
837.0	0	1	1
858.0	0	1	1
887.0	0	1	1
894.0	0	1	1
919.0	0	1	1
940.0	0	1	1
941.0	0	1	1
968.0	0	1	1
979.0	0	1	1
1011.0	0	1	1
1019.0	0	1	1
1049.0	0	1	1
1085.0	0	1	1
1090.0	0	1	1
1128.0	0	1	1
1145.0	0	1	1
1159.0	0	1	1
1189.0	0	1	1
1196.0	0	1	1
1199.0	0	1	1
1215.0	0	1	1
1228.0	0	1	1
1231.0	0	1	1
1258.0	0	1	1
1280.0	0	1	1
1449.0	0	1	1
1525.0	0	1	1
1636.0	0	1	1
1753.0	0	1	1
1756.0	0	1	1
2045.0	0	1	1
2779.0	0	1	1
3268.0	0	1	1
4345.0	0	1	1