## 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_RU1uM_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uM_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_RU1uM_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 03:41:58 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	402	17516842	15624999	0	335	2776591	0	0.158518	49246957

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	13623699	13623699
2.0	1.700687	785828	785828
3.0	2.191649	143837	143837
4.0	2.53566	59969	59969
5.0	2.776704	32983	32983
6.0	2.945601	20677	20677
7.0	3.063944	14273	14273
8.0	3.146866	9840	9840
9.0	3.204969	7301	7301
10.0	3.24568	5811	5811
11.0	3.274206	4531	4531
12.0	3.294194	3585	3585
13.0	3.308199	2961	2961
14.0	3.318012	2503	2503
15.0	3.324888	2057	2057
16.0	3.329706	1784	1784
17.0	3.333082	1545	1545
18.0	3.335448	1370	1370
19.0	3.337105	1192	1192
20.0	3.338266	965	965
21.0	3.33908	905	905
22.0	3.33965	796	796
23.0	3.34005	757	757
24.0	3.34033	638	638
25.0	3.340526	601	601
26.0	3.340663	523	523
27.0	3.34076	485	485
28.0	3.340827	436	436
29.0	3.340874	406	406
30.0	3.340907	406	406
31.0	3.340931	372	372
32.0	3.340947	337	337
33.0	3.340958	292	292
34.0	3.340966	300	300
35.0	3.340972	261	261
36.0	3.340976	254	254
37.0	3.340979	228	228
38.0	3.34098	229	229
39.0	3.340982	203	203
40.0	3.340983	197	197
41.0	3.340983	158	158
42.0	3.340984	172	172
43.0	3.340984	154	154
44.0	3.340984	125	125
45.0	3.340985	140	140
46.0	3.340985	127	127
47.0	3.340985	114	114
48.0	3.340985	105	105
49.0	3.340985	140	140
50.0	3.340985	90	90
51.0	3.340985	93	93
52.0	3.340985	102	102
53.0	3.340985	93	93
54.0	3.340985	90	90
55.0	3.340985	95	95
56.0	3.340985	86	86
57.0	3.340985	77	77
58.0	3.340985	72	72
59.0	3.340985	58	58
60.0	3.340985	72	72
61.0	3.340985	70	70
62.0	3.340985	54	54
63.0	3.340985	57	57
64.0	3.340985	58	58
65.0	3.340985	61	61
66.0	3.340985	52	52
67.0	3.340985	46	46
68.0	3.340985	45	45
69.0	3.340985	54	54
70.0	3.340985	36	36
71.0	3.340985	47	47
72.0	3.340985	40	40
73.0	3.340985	41	41
74.0	3.340985	37	37
75.0	3.340985	33	33
76.0	3.340985	41	41
77.0	3.340985	32	32
78.0	3.340985	44	44
79.0	3.340985	44	44
80.0	3.340985	34	34
81.0	3.340985	31	31
82.0	3.340985	26	26
83.0	3.340985	24	24
84.0	3.340985	34	34
85.0	3.340985	37	37
86.0	3.340985	21	21
87.0	3.340985	28	28
88.0	3.340985	31	31
89.0	3.340985	29	29
90.0	3.340985	27	27
91.0	3.340985	22	22
92.0	3.340985	27	27
93.0	3.340985	28	28
94.0	3.340985	27	27
95.0	3.340985	31	31
96.0	3.340985	26	26
97.0	3.340985	15	15
98.0	3.340985	25	25
99.0	3.340985	22	22
100.0	3.340985	16	16
101.0	0	17	17
102.0	0	14	14
103.0	0	21	21
104.0	0	18	18
105.0	0	23	23
106.0	0	18	18
107.0	0	13	13
108.0	0	15	15
109.0	0	18	18
110.0	0	20	20
111.0	0	16	16
112.0	0	18	18
113.0	0	18	18
114.0	0	15	15
115.0	0	14	14
116.0	0	12	12
117.0	0	14	14
118.0	0	14	14
119.0	0	14	14
120.0	0	9	9
121.0	0	19	19
122.0	0	13	13
123.0	0	8	8
124.0	0	11	11
125.0	0	8	8
126.0	0	11	11
127.0	0	8	8
128.0	0	11	11
129.0	0	6	6
130.0	0	12	12
131.0	0	9	9
132.0	0	9	9
133.0	0	10	10
134.0	0	12	12
135.0	0	19	19
136.0	0	10	10
137.0	0	2	2
138.0	0	23	23
139.0	0	17	17
140.0	0	11	11
141.0	0	14	14
142.0	0	6	6
143.0	0	10	10
144.0	0	12	12
145.0	0	12	12
146.0	0	7	7
147.0	0	8	8
148.0	0	8	8
149.0	0	6	6
150.0	0	4	4
151.0	0	8	8
152.0	0	11	11
153.0	0	5	5
154.0	0	11	11
155.0	0	3	3
156.0	0	5	5
157.0	0	4	4
158.0	0	12	12
159.0	0	5	5
161.0	0	3	3
162.0	0	4	4
163.0	0	5	5
164.0	0	7	7
165.0	0	5	5
166.0	0	5	5
167.0	0	7	7
168.0	0	4	4
169.0	0	8	8
170.0	0	5	5
171.0	0	6	6
172.0	0	7	7
173.0	0	2	2
174.0	0	5	5
175.0	0	7	7
176.0	0	7	7
177.0	0	4	4
178.0	0	3	3
179.0	0	3	3
180.0	0	3	3
181.0	0	4	4
182.0	0	2	2
183.0	0	6	6
184.0	0	4	4
185.0	0	6	6
187.0	0	4	4
188.0	0	2	2
189.0	0	7	7
190.0	0	6	6
191.0	0	5	5
192.0	0	3	3
193.0	0	8	8
194.0	0	4	4
195.0	0	5	5
196.0	0	7	7
197.0	0	5	5
198.0	0	5	5
199.0	0	4	4
200.0	0	10	10
202.0	0	6	6
203.0	0	5	5
204.0	0	3	3
205.0	0	7	7
206.0	0	4	4
207.0	0	4	4
209.0	0	1	1
210.0	0	5	5
211.0	0	6	6
212.0	0	1	1
214.0	0	8	8
216.0	0	4	4
217.0	0	2	2
218.0	0	1	1
219.0	0	4	4
220.0	0	2	2
221.0	0	4	4
223.0	0	3	3
224.0	0	4	4
225.0	0	3	3
226.0	0	2	2
227.0	0	4	4
228.0	0	5	5
229.0	0	2	2
230.0	0	1	1
231.0	0	4	4
232.0	0	1	1
233.0	0	1	1
234.0	0	5	5
235.0	0	2	2
236.0	0	2	2
237.0	0	5	5
238.0	0	3	3
239.0	0	4	4
240.0	0	4	4
241.0	0	3	3
242.0	0	1	1
243.0	0	3	3
244.0	0	2	2
245.0	0	2	2
246.0	0	2	2
247.0	0	1	1
248.0	0	2	2
249.0	0	1	1
250.0	0	3	3
251.0	0	2	2
252.0	0	2	2
253.0	0	3	3
254.0	0	1	1
256.0	0	1	1
257.0	0	3	3
258.0	0	2	2
260.0	0	2	2
263.0	0	2	2
264.0	0	3	3
265.0	0	2	2
267.0	0	2	2
269.0	0	1	1
271.0	0	1	1
272.0	0	2	2
274.0	0	2	2
275.0	0	2	2
276.0	0	2	2
277.0	0	3	3
279.0	0	1	1
280.0	0	1	1
283.0	0	2	2
284.0	0	3	3
286.0	0	2	2
287.0	0	4	4
288.0	0	3	3
289.0	0	1	1
290.0	0	2	2
291.0	0	2	2
292.0	0	1	1
294.0	0	1	1
295.0	0	2	2
296.0	0	2	2
297.0	0	1	1
298.0	0	2	2
299.0	0	1	1
300.0	0	2	2
301.0	0	2	2
304.0	0	1	1
305.0	0	1	1
306.0	0	2	2
307.0	0	2	2
308.0	0	2	2
309.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	2	2
313.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	2	2
318.0	0	1	1
319.0	0	1	1
320.0	0	1	1
323.0	0	1	1
324.0	0	1	1
325.0	0	1	1
328.0	0	4	4
329.0	0	3	3
330.0	0	2	2
331.0	0	2	2
332.0	0	2	2
333.0	0	1	1
334.0	0	1	1
336.0	0	1	1
339.0	0	1	1
340.0	0	1	1
341.0	0	1	1
342.0	0	1	1
346.0	0	1	1
349.0	0	1	1
351.0	0	1	1
354.0	0	3	3
355.0	0	1	1
358.0	0	2	2
362.0	0	1	1
364.0	0	1	1
365.0	0	1	1
370.0	0	1	1
371.0	0	2	2
372.0	0	2	2
375.0	0	1	1
378.0	0	1	1
379.0	0	1	1
380.0	0	2	2
381.0	0	2	2
385.0	0	1	1
386.0	0	1	1
387.0	0	1	1
389.0	0	2	2
391.0	0	2	2
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
403.0	0	1	1
408.0	0	1	1
409.0	0	1	1
414.0	0	1	1
419.0	0	1	1
421.0	0	2	2
424.0	0	1	1
425.0	0	2	2
432.0	0	3	3
434.0	0	1	1
435.0	0	1	1
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
448.0	0	1	1
449.0	0	1	1
453.0	0	1	1
465.0	0	3	3
468.0	0	1	1
470.0	0	2	2
471.0	0	1	1
475.0	0	2	2
476.0	0	1	1
478.0	0	1	1
485.0	0	1	1
506.0	0	1	1
509.0	0	1	1
515.0	0	1	1
518.0	0	1	1
520.0	0	1	1
526.0	0	1	1
527.0	0	1	1
530.0	0	1	1
534.0	0	1	1
535.0	0	1	1
540.0	0	2	2
543.0	0	1	1
554.0	0	1	1
557.0	0	1	1
574.0	0	1	1
579.0	0	2	2
581.0	0	1	1
589.0	0	1	1
593.0	0	1	1
597.0	0	1	1
602.0	0	1	1
607.0	0	1	1
612.0	0	1	1
613.0	0	1	1
620.0	0	1	1
621.0	0	1	1
636.0	0	1	1
638.0	0	1	1
648.0	0	1	1
656.0	0	1	1
682.0	0	1	1
691.0	0	1	1
695.0	0	1	1
704.0	0	1	1
707.0	0	1	1
712.0	0	1	1
713.0	0	1	1
718.0	0	1	1
736.0	0	1	1
759.0	0	1	1
786.0	0	1	1
792.0	0	1	1
795.0	0	1	1
796.0	0	1	1
826.0	0	1	1
862.0	0	1	1
877.0	0	1	1
911.0	0	1	1
916.0	0	1	1
940.0	0	1	1
971.0	0	1	1
985.0	0	1	1
998.0	0	1	1
1073.0	0	1	1
1130.0	0	1	1
1137.0	0	1	1
1207.0	0	1	1
1209.0	0	1	1
1245.0	0	1	1
1312.0	0	2	2
1325.0	0	1	1
1334.0	0	1	1
1403.0	0	1	1
1423.0	0	1	1
1445.0	0	1	1
1470.0	0	1	1
1506.0	0	1	1
1670.0	0	1	1
1713.0	0	1	1
2353.0	0	1	1
2990.0	0	1	1