## 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_RU1uMTA1uM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA1uM_1.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_RU1uMTA1uM_1.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 03:10:53 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	602	19898603	17051388	0	492	2928131	0	0.147163	60802424

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	15638553	15638553
2.0	1.720892	965760	965760
3.0	2.240576	165405	165405
4.0	2.615212	66384	66384
5.0	2.885284	36346	36346
6.0	3.079977	22541	22541
7.0	3.220329	14957	14957
8.0	3.321508	10749	10749
9.0	3.394447	8072	8072
10.0	3.447028	6150	6150
11.0	3.484933	4782	4782
12.0	3.512259	3874	3874
13.0	3.531958	3118	3118
14.0	3.546158	2584	2584
15.0	3.556395	2214	2214
16.0	3.563775	1861	1861
17.0	3.569095	1560	1560
18.0	3.572931	1351	1351
19.0	3.575695	1163	1163
20.0	3.577689	946	946
21.0	3.579125	908	908
22.0	3.580161	758	758
23.0	3.580908	673	673
24.0	3.581446	656	656
25.0	3.581834	564	564
26.0	3.582114	506	506
27.0	3.582315	448	448
28.0	3.582461	449	449
29.0	3.582566	412	412
30.0	3.582641	346	346
31.0	3.582696	335	335
32.0	3.582735	301	301
33.0	3.582763	294	294
34.0	3.582784	257	257
35.0	3.582798	240	240
36.0	3.582809	210	210
37.0	3.582817	176	176
38.0	3.582822	200	200
39.0	3.582826	187	187
40.0	3.582829	154	154
41.0	3.582831	144	144
42.0	3.582833	150	150
43.0	3.582834	117	117
44.0	3.582834	127	127
45.0	3.582835	166	166
46.0	3.582835	124	124
47.0	3.582836	121	121
48.0	3.582836	85	85
49.0	3.582836	107	107
50.0	3.582836	91	91
51.0	3.582836	93	93
52.0	3.582836	82	82
53.0	3.582836	74	74
54.0	3.582836	82	82
55.0	3.582836	62	62
56.0	3.582836	59	59
57.0	3.582836	59	59
58.0	3.582836	66	66
59.0	3.582836	63	63
60.0	3.582836	77	77
61.0	3.582836	52	52
62.0	3.582836	70	70
63.0	3.582836	49	49
64.0	3.582836	46	46
65.0	3.582836	57	57
66.0	3.582836	38	38
67.0	3.582836	44	44
68.0	3.582836	33	33
69.0	3.582836	41	41
70.0	3.582836	34	34
71.0	3.582836	47	47
72.0	3.582836	41	41
73.0	3.582836	34	34
74.0	3.582836	36	36
75.0	3.582836	26	26
76.0	3.582836	26	26
77.0	3.582836	28	28
78.0	3.582836	22	22
79.0	3.582836	21	21
80.0	3.582836	29	29
81.0	3.582836	31	31
82.0	3.582836	15	15
83.0	3.582836	28	28
84.0	3.582836	27	27
85.0	3.582836	27	27
86.0	3.582836	20	20
87.0	3.582836	22	22
88.0	3.582836	25	25
89.0	3.582836	22	22
90.0	3.582836	15	15
91.0	3.582836	21	21
92.0	3.582836	19	19
93.0	3.582836	25	25
94.0	3.582836	20	20
95.0	3.582836	11	11
96.0	3.582836	20	20
97.0	3.582836	23	23
98.0	3.582836	20	20
99.0	3.582836	14	14
100.0	3.582836	17	17
101.0	0	16	16
102.0	0	13	13
103.0	0	16	16
104.0	0	8	8
105.0	0	12	12
106.0	0	13	13
107.0	0	17	17
108.0	0	9	9
109.0	0	8	8
110.0	0	12	12
111.0	0	13	13
112.0	0	10	10
113.0	0	7	7
114.0	0	12	12
115.0	0	17	17
116.0	0	9	9
117.0	0	9	9
118.0	0	6	6
119.0	0	12	12
120.0	0	3	3
121.0	0	10	10
122.0	0	14	14
123.0	0	17	17
124.0	0	5	5
125.0	0	10	10
126.0	0	6	6
127.0	0	10	10
128.0	0	7	7
129.0	0	10	10
130.0	0	13	13
131.0	0	5	5
132.0	0	11	11
133.0	0	7	7
134.0	0	4	4
135.0	0	4	4
136.0	0	4	4
137.0	0	4	4
138.0	0	4	4
139.0	0	12	12
140.0	0	5	5
141.0	0	8	8
142.0	0	3	3
143.0	0	8	8
144.0	0	8	8
145.0	0	7	7
146.0	0	2	2
147.0	0	9	9
148.0	0	5	5
149.0	0	3	3
150.0	0	9	9
151.0	0	9	9
152.0	0	6	6
153.0	0	4	4
154.0	0	6	6
155.0	0	8	8
156.0	0	4	4
157.0	0	2	2
158.0	0	5	5
159.0	0	4	4
160.0	0	3	3
161.0	0	1	1
162.0	0	8	8
163.0	0	3	3
164.0	0	5	5
165.0	0	6	6
166.0	0	1	1
167.0	0	8	8
168.0	0	8	8
169.0	0	3	3
170.0	0	3	3
171.0	0	2	2
172.0	0	2	2
173.0	0	4	4
174.0	0	3	3
175.0	0	4	4
176.0	0	2	2
177.0	0	3	3
178.0	0	3	3
179.0	0	2	2
180.0	0	5	5
181.0	0	3	3
182.0	0	1	1
183.0	0	4	4
184.0	0	2	2
185.0	0	1	1
186.0	0	3	3
188.0	0	3	3
189.0	0	6	6
190.0	0	6	6
191.0	0	2	2
192.0	0	5	5
193.0	0	7	7
194.0	0	4	4
195.0	0	9	9
196.0	0	1	1
197.0	0	3	3
198.0	0	2	2
199.0	0	1	1
200.0	0	3	3
202.0	0	2	2
203.0	0	1	1
204.0	0	2	2
205.0	0	4	4
206.0	0	1	1
207.0	0	4	4
208.0	0	2	2
210.0	0	3	3
211.0	0	3	3
213.0	0	1	1
214.0	0	2	2
215.0	0	3	3
217.0	0	2	2
218.0	0	1	1
219.0	0	3	3
220.0	0	3	3
221.0	0	2	2
222.0	0	2	2
223.0	0	1	1
224.0	0	1	1
225.0	0	1	1
226.0	0	4	4
227.0	0	3	3
228.0	0	3	3
231.0	0	1	1
232.0	0	3	3
234.0	0	1	1
236.0	0	2	2
237.0	0	2	2
238.0	0	1	1
240.0	0	2	2
241.0	0	3	3
243.0	0	3	3
244.0	0	1	1
245.0	0	1	1
246.0	0	1	1
247.0	0	2	2
249.0	0	1	1
250.0	0	2	2
251.0	0	2	2
252.0	0	1	1
255.0	0	3	3
256.0	0	5	5
257.0	0	1	1
258.0	0	1	1
259.0	0	4	4
260.0	0	2	2
261.0	0	2	2
262.0	0	3	3
263.0	0	2	2
265.0	0	2	2
266.0	0	1	1
267.0	0	1	1
269.0	0	1	1
271.0	0	1	1
272.0	0	2	2
273.0	0	1	1
274.0	0	2	2
276.0	0	1	1
277.0	0	1	1
278.0	0	3	3
279.0	0	1	1
282.0	0	2	2
283.0	0	1	1
284.0	0	4	4
287.0	0	1	1
289.0	0	2	2
294.0	0	1	1
295.0	0	1	1
298.0	0	2	2
301.0	0	2	2
302.0	0	1	1
303.0	0	1	1
305.0	0	1	1
308.0	0	1	1
311.0	0	2	2
314.0	0	2	2
317.0	0	1	1
319.0	0	1	1
320.0	0	1	1
321.0	0	1	1
324.0	0	2	2
325.0	0	1	1
328.0	0	1	1
329.0	0	3	3
335.0	0	2	2
336.0	0	1	1
343.0	0	1	1
345.0	0	1	1
346.0	0	1	1
352.0	0	1	1
353.0	0	1	1
359.0	0	1	1
360.0	0	2	2
361.0	0	1	1
362.0	0	1	1
365.0	0	1	1
366.0	0	2	2
368.0	0	1	1
371.0	0	1	1
372.0	0	1	1
373.0	0	1	1
374.0	0	1	1
382.0	0	1	1
390.0	0	1	1
399.0	0	1	1
401.0	0	1	1
403.0	0	1	1
429.0	0	1	1
432.0	0	1	1
446.0	0	1	1
448.0	0	1	1
466.0	0	1	1
469.0	0	1	1
478.0	0	1	1
479.0	0	1	1
489.0	0	1	1
500.0	0	1	1
502.0	0	1	1
519.0	0	1	1
526.0	0	1	1
530.0	0	1	1
535.0	0	1	1
540.0	0	1	1
542.0	0	1	1
550.0	0	1	1
554.0	0	1	1
583.0	0	1	1
589.0	0	1	1
593.0	0	1	1
601.0	0	1	1
604.0	0	1	1
609.0	0	1	1
616.0	0	1	1
639.0	0	1	1
649.0	0	1	1
650.0	0	1	1
654.0	0	1	1
673.0	0	1	1
676.0	0	1	1
677.0	0	1	1
708.0	0	1	1
753.0	0	1	1
760.0	0	1	1
786.0	0	2	2
788.0	0	1	1
871.0	0	1	1
900.0	0	1	1
918.0	0	1	1
921.0	0	1	1
927.0	0	1	1
957.0	0	1	1
1071.0	0	1	1
1115.0	0	1	1
1116.0	0	1	1
1140.0	0	1	1
1146.0	0	1	1
1203.0	0	1	1
1211.0	0	1	1
1219.0	0	1	1
1239.0	0	1	1
1274.0	0	1	1
1315.0	0	1	1
1422.0	0	2	2
1629.0	0	1	1
1875.0	0	1	1