## 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_adherent_TA_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_adherent_TA_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D12_adherent_TA_2.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 02:37:17 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	559	9467166	10839572	0	494	1491089	0	0.157523	26807940

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	7365092	7365092
2.0	1.702473	448972	448972
3.0	2.195942	69955	69955
4.0	2.542591	28074	28074
5.0	2.786102	15822	15822
6.0	2.957163	9937	9937
7.0	3.077328	6825	6825
8.0	3.161741	4779	4779
9.0	3.221039	3731	3731
10.0	3.262694	2866	2866
11.0	3.291955	2311	2311
12.0	3.312511	1881	1881
13.0	3.326951	1550	1550
14.0	3.337094	1291	1291
15.0	3.34422	1084	1084
16.0	3.349225	986	986
17.0	3.352741	854	854
18.0	3.355211	775	775
19.0	3.356947	622	622
20.0	3.358165	589	589
21.0	3.359022	510	510
22.0	3.359623	517	517
23.0	3.360046	397	397
24.0	3.360342	360	360
25.0	3.360551	365	365
26.0	3.360697	323	323
27.0	3.3608	265	265
28.0	3.360873	278	278
29.0	3.360923	221	221
30.0	3.360959	227	227
31.0	3.360984	186	186
32.0	3.361002	192	192
33.0	3.361014	190	190
34.0	3.361023	164	164
35.0	3.361029	148	148
36.0	3.361033	152	152
37.0	3.361036	141	141
38.0	3.361038	147	147
39.0	3.36104	134	134
40.0	3.361041	128	128
41.0	3.361042	121	121
42.0	3.361042	91	91
43.0	3.361042	96	96
44.0	3.361043	101	101
45.0	3.361043	86	86
46.0	3.361043	67	67
47.0	3.361043	70	70
48.0	3.361043	61	61
49.0	3.361043	68	68
50.0	3.361043	56	56
51.0	3.361043	68	68
52.0	3.361043	44	44
53.0	3.361043	55	55
54.0	3.361043	60	60
55.0	3.361043	67	67
56.0	3.361043	51	51
57.0	3.361043	64	64
58.0	3.361043	41	41
59.0	3.361043	56	56
60.0	3.361043	35	35
61.0	3.361043	37	37
62.0	3.361043	31	31
63.0	3.361043	45	45
64.0	3.361043	37	37
65.0	3.361043	34	34
66.0	3.361043	43	43
67.0	3.361043	40	40
68.0	3.361043	33	33
69.0	3.361043	31	31
70.0	3.361043	32	32
71.0	3.361043	25	25
72.0	3.361043	24	24
73.0	3.361043	20	20
74.0	3.361043	27	27
75.0	3.361043	20	20
76.0	3.361043	25	25
77.0	3.361043	29	29
78.0	3.361043	24	24
79.0	3.361043	25	25
80.0	3.361043	24	24
81.0	3.361043	16	16
82.0	3.361043	19	19
83.0	3.361043	19	19
84.0	3.361043	14	14
85.0	3.361043	20	20
86.0	3.361043	14	14
87.0	3.361043	14	14
88.0	3.361043	10	10
89.0	3.361043	25	25
90.0	3.361043	17	17
91.0	3.361043	12	12
92.0	3.361043	12	12
93.0	3.361043	17	17
94.0	3.361043	15	15
95.0	3.361043	13	13
96.0	3.361043	14	14
97.0	3.361043	13	13
98.0	3.361043	8	8
99.0	3.361043	5	5
100.0	3.361043	8	8
101.0	0	11	11
102.0	0	9	9
103.0	0	12	12
104.0	0	9	9
105.0	0	13	13
106.0	0	8	8
107.0	0	10	10
108.0	0	16	16
109.0	0	16	16
110.0	0	12	12
111.0	0	6	6
112.0	0	7	7
113.0	0	10	10
114.0	0	9	9
115.0	0	6	6
116.0	0	7	7
117.0	0	10	10
118.0	0	9	9
119.0	0	12	12
120.0	0	10	10
121.0	0	4	4
122.0	0	9	9
123.0	0	14	14
124.0	0	12	12
125.0	0	9	9
126.0	0	4	4
127.0	0	7	7
128.0	0	10	10
129.0	0	9	9
130.0	0	13	13
131.0	0	4	4
132.0	0	9	9
133.0	0	12	12
134.0	0	10	10
135.0	0	6	6
136.0	0	10	10
137.0	0	6	6
138.0	0	12	12
139.0	0	8	8
140.0	0	1	1
141.0	0	3	3
142.0	0	7	7
143.0	0	3	3
144.0	0	2	2
145.0	0	6	6
146.0	0	3	3
147.0	0	7	7
148.0	0	10	10
149.0	0	10	10
150.0	0	2	2
151.0	0	3	3
152.0	0	7	7
153.0	0	4	4
154.0	0	1	1
155.0	0	8	8
156.0	0	3	3
157.0	0	5	5
158.0	0	6	6
159.0	0	4	4
160.0	0	4	4
161.0	0	5	5
162.0	0	4	4
163.0	0	4	4
164.0	0	2	2
165.0	0	2	2
166.0	0	4	4
167.0	0	3	3
168.0	0	6	6
169.0	0	4	4
170.0	0	4	4
172.0	0	3	3
173.0	0	4	4
174.0	0	4	4
175.0	0	5	5
176.0	0	7	7
177.0	0	3	3
178.0	0	4	4
179.0	0	3	3
180.0	0	3	3
181.0	0	2	2
182.0	0	4	4
183.0	0	4	4
184.0	0	3	3
185.0	0	2	2
187.0	0	4	4
188.0	0	2	2
189.0	0	2	2
190.0	0	2	2
191.0	0	2	2
192.0	0	4	4
193.0	0	4	4
194.0	0	1	1
195.0	0	3	3
196.0	0	3	3
197.0	0	1	1
198.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	4	4
202.0	0	2	2
203.0	0	5	5
204.0	0	1	1
206.0	0	4	4
207.0	0	4	4
208.0	0	3	3
209.0	0	3	3
210.0	0	3	3
211.0	0	2	2
212.0	0	1	1
213.0	0	1	1
215.0	0	2	2
216.0	0	2	2
217.0	0	2	2
218.0	0	1	1
219.0	0	3	3
220.0	0	3	3
221.0	0	1	1
222.0	0	1	1
223.0	0	3	3
224.0	0	1	1
226.0	0	1	1
228.0	0	4	4
229.0	0	1	1
230.0	0	3	3
231.0	0	2	2
232.0	0	1	1
234.0	0	2	2
236.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	1	1
242.0	0	2	2
243.0	0	2	2
244.0	0	2	2
247.0	0	3	3
248.0	0	1	1
250.0	0	1	1
251.0	0	1	1
253.0	0	1	1
254.0	0	2	2
255.0	0	1	1
256.0	0	2	2
257.0	0	2	2
260.0	0	2	2
262.0	0	3	3
263.0	0	1	1
265.0	0	1	1
267.0	0	1	1
268.0	0	3	3
270.0	0	2	2
273.0	0	1	1
274.0	0	1	1
275.0	0	1	1
276.0	0	2	2
279.0	0	1	1
281.0	0	2	2
283.0	0	1	1
286.0	0	3	3
288.0	0	1	1
294.0	0	2	2
295.0	0	1	1
298.0	0	1	1
304.0	0	1	1
305.0	0	1	1
307.0	0	2	2
309.0	0	1	1
312.0	0	1	1
314.0	0	3	3
316.0	0	1	1
317.0	0	4	4
321.0	0	1	1
322.0	0	1	1
324.0	0	2	2
334.0	0	1	1
338.0	0	1	1
340.0	0	2	2
346.0	0	1	1
354.0	0	1	1
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
366.0	0	2	2
377.0	0	1	1
401.0	0	1	1
405.0	0	1	1
408.0	0	1	1
409.0	0	1	1
410.0	0	1	1
411.0	0	1	1
413.0	0	1	1
417.0	0	1	1
431.0	0	1	1
434.0	0	1	1
435.0	0	1	1
439.0	0	1	1
456.0	0	1	1
461.0	0	1	1
472.0	0	1	1
480.0	0	1	1
481.0	0	1	1
487.0	0	1	1
491.0	0	1	1
495.0	0	1	1
506.0	0	1	1
515.0	0	1	1
518.0	0	1	1
527.0	0	1	1
532.0	0	1	1
549.0	0	1	1
560.0	0	1	1
584.0	0	1	1
601.0	0	1	1
605.0	0	1	1
628.0	0	1	1
639.0	0	1	1
647.0	0	1	1
755.0	0	1	1
795.0	0	1	1
809.0	0	1	1
882.0	0	1	1
957.0	0	1	1
966.0	0	1	1
974.0	0	1	1
999.0	0	1	1
1022.0	0	1	1
1052.0	0	1	1
1074.0	0	1	1
1077.0	0	1	1
1111.0	0	1	1
1950.0	0	1	1