## 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_RU1uMTA100nM_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA100nM_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_RU1uMTA100nM_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 03:55:52 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	667	14707738	12198318	0	553	1702616	0	0.115779	58521554

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	12251465	12251465
2.0	1.777772	537180	537180
3.0	2.382702	96526	96526
4.0	2.853199	40033	40033
5.0	3.219138	21791	21791
6.0	3.503756	13527	13527
7.0	3.725124	9011	9011
8.0	3.897297	6266	6266
9.0	4.031209	4700	4700
10.0	4.135362	3611	3611
11.0	4.216369	2798	2798
12.0	4.279374	2199	2199
13.0	4.328378	1844	1844
14.0	4.366492	1488	1488
15.0	4.396135	1261	1261
16.0	4.419191	1041	1041
17.0	4.437124	944	944
18.0	4.451071	779	779
19.0	4.461919	682	682
20.0	4.470356	605	605
21.0	4.476918	534	534
22.0	4.482022	455	455
23.0	4.485992	454	454
24.0	4.489079	376	376
25.0	4.491481	331	331
26.0	4.493348	296	296
27.0	4.494801	268	268
28.0	4.495931	247	247
29.0	4.49681	230	230
30.0	4.497493	256	256
31.0	4.498025	172	172
32.0	4.498438	178	178
33.0	4.49876	149	149
34.0	4.49901	150	150
35.0	4.499204	133	133
36.0	4.499356	122	122
37.0	4.499473	140	140
38.0	4.499565	116	116
39.0	4.499636	110	110
40.0	4.499691	97	97
41.0	4.499734	97	97
42.0	4.499768	91	91
43.0	4.499794	111	111
44.0	4.499814	87	87
45.0	4.49983	80	80
46.0	4.499842	75	75
47.0	4.499852	64	64
48.0	4.499859	69	69
49.0	4.499865	59	59
50.0	4.499869	58	58
51.0	4.499873	57	57
52.0	4.499876	59	59
53.0	4.499878	53	53
54.0	4.499879	48	48
55.0	4.499881	36	36
56.0	4.499882	46	46
57.0	4.499882	42	42
58.0	4.499883	40	40
59.0	4.499883	43	43
60.0	4.499884	32	32
61.0	4.499884	41	41
62.0	4.499884	33	33
63.0	4.499884	45	45
64.0	4.499885	28	28
65.0	4.499885	31	31
66.0	4.499885	38	38
67.0	4.499885	25	25
68.0	4.499885	22	22
69.0	4.499885	23	23
70.0	4.499885	35	35
71.0	4.499885	22	22
72.0	4.499885	27	27
73.0	4.499885	28	28
74.0	4.499885	18	18
75.0	4.499885	23	23
76.0	4.499885	15	15
77.0	4.499885	19	19
78.0	4.499885	11	11
79.0	4.499885	17	17
80.0	4.499885	19	19
81.0	4.499885	16	16
82.0	4.499885	14	14
83.0	4.499885	18	18
84.0	4.499885	14	14
85.0	4.499885	8	8
86.0	4.499885	12	12
87.0	4.499885	16	16
88.0	4.499885	15	15
89.0	4.499885	11	11
90.0	4.499885	12	12
91.0	4.499885	12	12
92.0	4.499885	15	15
93.0	4.499885	12	12
94.0	4.499885	11	11
95.0	4.499885	12	12
96.0	4.499885	11	11
97.0	4.499885	18	18
98.0	4.499885	11	11
99.0	4.499885	10	10
100.0	4.499885	8	8
101.0	0	14	14
102.0	0	11	11
103.0	0	6	6
104.0	0	10	10
105.0	0	10	10
106.0	0	5	5
107.0	0	9	9
108.0	0	8	8
109.0	0	8	8
110.0	0	6	6
111.0	0	8	8
112.0	0	9	9
113.0	0	8	8
114.0	0	7	7
115.0	0	7	7
116.0	0	3	3
117.0	0	4	4
118.0	0	5	5
119.0	0	5	5
120.0	0	10	10
121.0	0	1	1
122.0	0	3	3
123.0	0	11	11
124.0	0	4	4
125.0	0	6	6
126.0	0	4	4
127.0	0	8	8
128.0	0	6	6
129.0	0	2	2
130.0	0	8	8
131.0	0	5	5
132.0	0	3	3
133.0	0	2	2
134.0	0	9	9
135.0	0	3	3
136.0	0	4	4
137.0	0	3	3
138.0	0	2	2
139.0	0	7	7
140.0	0	6	6
141.0	0	4	4
142.0	0	7	7
143.0	0	3	3
144.0	0	4	4
145.0	0	5	5
146.0	0	2	2
147.0	0	2	2
148.0	0	3	3
149.0	0	4	4
150.0	0	3	3
151.0	0	3	3
152.0	0	2	2
153.0	0	5	5
154.0	0	2	2
155.0	0	3	3
156.0	0	3	3
157.0	0	3	3
158.0	0	4	4
159.0	0	2	2
160.0	0	2	2
161.0	0	1	1
162.0	0	4	4
163.0	0	4	4
164.0	0	4	4
165.0	0	3	3
166.0	0	3	3
167.0	0	1	1
168.0	0	4	4
169.0	0	2	2
171.0	0	4	4
172.0	0	2	2
173.0	0	3	3
174.0	0	3	3
175.0	0	1	1
176.0	0	3	3
177.0	0	4	4
178.0	0	3	3
179.0	0	1	1
180.0	0	3	3
181.0	0	1	1
182.0	0	2	2
184.0	0	2	2
185.0	0	4	4
186.0	0	3	3
188.0	0	1	1
191.0	0	3	3
194.0	0	1	1
195.0	0	1	1
196.0	0	1	1
197.0	0	1	1
198.0	0	1	1
199.0	0	4	4
200.0	0	1	1
201.0	0	3	3
202.0	0	3	3
203.0	0	2	2
204.0	0	1	1
205.0	0	3	3
206.0	0	3	3
207.0	0	2	2
208.0	0	2	2
209.0	0	2	2
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
214.0	0	1	1
215.0	0	1	1
217.0	0	1	1
218.0	0	3	3
222.0	0	1	1
224.0	0	1	1
225.0	0	1	1
228.0	0	1	1
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
237.0	0	3	3
238.0	0	1	1
239.0	0	1	1
240.0	0	1	1
243.0	0	1	1
247.0	0	1	1
248.0	0	1	1
249.0	0	1	1
250.0	0	1	1
251.0	0	2	2
253.0	0	2	2
254.0	0	1	1
257.0	0	1	1
258.0	0	1	1
259.0	0	1	1
260.0	0	2	2
261.0	0	1	1
262.0	0	1	1
264.0	0	1	1
265.0	0	1	1
270.0	0	1	1
272.0	0	1	1
273.0	0	1	1
275.0	0	1	1
277.0	0	2	2
283.0	0	1	1
285.0	0	1	1
288.0	0	2	2
293.0	0	1	1
300.0	0	1	1
302.0	0	1	1
314.0	0	1	1
322.0	0	1	1
329.0	0	1	1
331.0	0	1	1
333.0	0	1	1
334.0	0	2	2
339.0	0	1	1
343.0	0	1	1
345.0	0	1	1
350.0	0	1	1
363.0	0	1	1
364.0	0	1	1
370.0	0	1	1
371.0	0	1	1
373.0	0	1	1
388.0	0	1	1
392.0	0	1	1
399.0	0	1	1
400.0	0	1	1
401.0	0	1	1
408.0	0	1	1
419.0	0	1	1
428.0	0	1	1
433.0	0	1	1
437.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	1	1
450.0	0	1	1
455.0	0	1	1
463.0	0	1	1
474.0	0	1	1
486.0	0	1	1
487.0	0	1	1
490.0	0	1	1
491.0	0	1	1
493.0	0	1	1
501.0	0	1	1
506.0	0	1	1
516.0	0	1	1
526.0	0	1	1
527.0	0	1	1
542.0	0	1	1
551.0	0	1	1
557.0	0	1	1
580.0	0	1	1
587.0	0	1	1
599.0	0	1	1
629.0	0	1	1
634.0	0	1	1
637.0	0	1	1
639.0	0	1	1
665.0	0	1	1
666.0	0	1	1
684.0	0	1	1
691.0	0	1	1
715.0	0	1	1
792.0	0	1	1
882.0	0	1	1
934.0	0	1	1
1114.0	0	1	1
1619.0	0	1	1
1731.0	0	1	1