## 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-D10_supernatant_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D10_supernatant_DMSO_1.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D10_supernatant_DMSO_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 03:18:02 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	1054	19748834	25036058	0	865	5462207	0	0.276598	28759788

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	11077580	11077580
2.0	1.503243	2409082	2409082
3.0	1.756496	517528	517528
4.0	1.883944	130142	130142
5.0	1.948082	47762	47762
6.0	1.980358	24726	24726
7.0	1.996601	15751	15751
8.0	2.004776	11058	11058
9.0	2.008889	8133	8133
10.0	2.010959	6290	6290
11.0	2.012001	4847	4847
12.0	2.012525	3959	3959
13.0	2.012789	3126	3126
14.0	2.012922	2735	2735
15.0	2.012989	2265	2265
16.0	2.013022	1940	1940
17.0	2.013039	1671	1671
18.0	2.013048	1445	1445
19.0	2.013052	1290	1290
20.0	2.013054	1123	1123
21.0	2.013055	1005	1005
22.0	2.013056	874	874
23.0	2.013056	773	773
24.0	2.013056	704	704
25.0	2.013056	654	654
26.0	2.013057	573	573
27.0	2.013057	529	529
28.0	2.013057	477	477
29.0	2.013057	419	419
30.0	2.013057	423	423
31.0	2.013057	400	400
32.0	2.013057	372	372
33.0	2.013057	335	335
34.0	2.013057	297	297
35.0	2.013057	260	260
36.0	2.013057	239	239
37.0	2.013057	261	261
38.0	2.013057	235	235
39.0	2.013057	218	218
40.0	2.013057	232	232
41.0	2.013057	180	180
42.0	2.013057	197	197
43.0	2.013057	183	183
44.0	2.013057	157	157
45.0	2.013057	139	139
46.0	2.013057	129	129
47.0	2.013057	131	131
48.0	2.013057	130	130
49.0	2.013057	88	88
50.0	2.013057	110	110
51.0	2.013057	113	113
52.0	2.013057	84	84
53.0	2.013057	93	93
54.0	2.013057	97	97
55.0	2.013057	104	104
56.0	2.013057	81	81
57.0	2.013057	85	85
58.0	2.013057	75	75
59.0	2.013057	73	73
60.0	2.013057	64	64
61.0	2.013057	68	68
62.0	2.013057	78	78
63.0	2.013057	67	67
64.0	2.013057	52	52
65.0	2.013057	56	56
66.0	2.013057	52	52
67.0	2.013057	43	43
68.0	2.013057	52	52
69.0	2.013057	56	56
70.0	2.013057	43	43
71.0	2.013057	38	38
72.0	2.013057	36	36
73.0	2.013057	38	38
74.0	2.013057	31	31
75.0	2.013057	36	36
76.0	2.013057	39	39
77.0	2.013057	39	39
78.0	2.013057	38	38
79.0	2.013057	33	33
80.0	2.013057	23	23
81.0	2.013057	41	41
82.0	2.013057	30	30
83.0	2.013057	36	36
84.0	2.013057	40	40
85.0	2.013057	23	23
86.0	2.013057	28	28
87.0	2.013057	24	24
88.0	2.013057	36	36
89.0	2.013057	22	22
90.0	2.013057	26	26
91.0	2.013057	12	12
92.0	2.013057	26	26
93.0	2.013057	19	19
94.0	2.013057	22	22
95.0	2.013057	22	22
96.0	2.013057	23	23
97.0	2.013057	13	13
98.0	2.013057	19	19
99.0	2.013057	25	25
100.0	2.013057	20	20
101.0	0	14	14
102.0	0	13	13
103.0	0	18	18
104.0	0	17	17
105.0	0	15	15
106.0	0	15	15
107.0	0	16	16
108.0	0	17	17
109.0	0	12	12
110.0	0	14	14
111.0	0	22	22
112.0	0	18	18
113.0	0	10	10
114.0	0	13	13
115.0	0	19	19
116.0	0	13	13
117.0	0	11	11
118.0	0	16	16
119.0	0	9	9
120.0	0	18	18
121.0	0	8	8
122.0	0	14	14
123.0	0	13	13
124.0	0	6	6
125.0	0	14	14
126.0	0	8	8
127.0	0	13	13
128.0	0	16	16
129.0	0	11	11
130.0	0	13	13
131.0	0	10	10
132.0	0	14	14
133.0	0	6	6
134.0	0	5	5
135.0	0	8	8
136.0	0	6	6
137.0	0	10	10
138.0	0	3	3
139.0	0	8	8
140.0	0	6	6
141.0	0	10	10
142.0	0	6	6
143.0	0	8	8
144.0	0	7	7
145.0	0	12	12
146.0	0	11	11
147.0	0	7	7
148.0	0	6	6
149.0	0	10	10
150.0	0	5	5
151.0	0	6	6
152.0	0	8	8
153.0	0	9	9
154.0	0	9	9
155.0	0	7	7
156.0	0	4	4
157.0	0	4	4
158.0	0	8	8
159.0	0	3	3
160.0	0	12	12
161.0	0	11	11
162.0	0	6	6
163.0	0	5	5
164.0	0	7	7
165.0	0	6	6
166.0	0	5	5
167.0	0	5	5
168.0	0	4	4
169.0	0	6	6
170.0	0	5	5
171.0	0	2	2
172.0	0	7	7
173.0	0	2	2
174.0	0	6	6
175.0	0	8	8
176.0	0	9	9
177.0	0	6	6
178.0	0	1	1
179.0	0	3	3
180.0	0	5	5
181.0	0	2	2
182.0	0	5	5
183.0	0	3	3
184.0	0	4	4
185.0	0	8	8
186.0	0	2	2
187.0	0	3	3
188.0	0	3	3
189.0	0	3	3
190.0	0	5	5
191.0	0	5	5
192.0	0	6	6
193.0	0	6	6
194.0	0	6	6
195.0	0	3	3
196.0	0	4	4
197.0	0	1	1
198.0	0	5	5
199.0	0	4	4
200.0	0	2	2
201.0	0	2	2
202.0	0	3	3
203.0	0	3	3
204.0	0	6	6
205.0	0	5	5
206.0	0	3	3
207.0	0	1	1
208.0	0	4	4
209.0	0	3	3
210.0	0	2	2
211.0	0	5	5
212.0	0	2	2
213.0	0	5	5
214.0	0	2	2
215.0	0	3	3
216.0	0	5	5
217.0	0	1	1
218.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	3	3
222.0	0	1	1
223.0	0	3	3
224.0	0	5	5
225.0	0	3	3
226.0	0	3	3
227.0	0	2	2
228.0	0	2	2
229.0	0	1	1
230.0	0	4	4
231.0	0	1	1
233.0	0	2	2
234.0	0	1	1
235.0	0	3	3
237.0	0	2	2
238.0	0	3	3
240.0	0	2	2
241.0	0	5	5
242.0	0	2	2
243.0	0	2	2
244.0	0	3	3
245.0	0	4	4
246.0	0	1	1
247.0	0	2	2
248.0	0	2	2
249.0	0	2	2
250.0	0	3	3
251.0	0	1	1
252.0	0	3	3
253.0	0	1	1
254.0	0	1	1
256.0	0	2	2
257.0	0	1	1
258.0	0	2	2
259.0	0	2	2
260.0	0	4	4
261.0	0	4	4
262.0	0	1	1
263.0	0	2	2
265.0	0	3	3
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
270.0	0	2	2
271.0	0	1	1
272.0	0	1	1
273.0	0	3	3
275.0	0	2	2
276.0	0	1	1
277.0	0	1	1
280.0	0	1	1
281.0	0	2	2
282.0	0	2	2
283.0	0	2	2
286.0	0	1	1
287.0	0	3	3
290.0	0	1	1
291.0	0	3	3
292.0	0	2	2
293.0	0	1	1
294.0	0	1	1
296.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	2	2
302.0	0	2	2
304.0	0	1	1
305.0	0	1	1
309.0	0	1	1
311.0	0	1	1
315.0	0	3	3
316.0	0	1	1
317.0	0	3	3
320.0	0	1	1
326.0	0	1	1
327.0	0	1	1
332.0	0	1	1
333.0	0	1	1
334.0	0	3	3
337.0	0	1	1
339.0	0	1	1
341.0	0	1	1
344.0	0	2	2
345.0	0	1	1
348.0	0	2	2
349.0	0	1	1
350.0	0	1	1
356.0	0	1	1
357.0	0	1	1
358.0	0	1	1
359.0	0	1	1
361.0	0	1	1
364.0	0	1	1
366.0	0	1	1
367.0	0	1	1
368.0	0	1	1
370.0	0	1	1
372.0	0	1	1
373.0	0	2	2
374.0	0	2	2
378.0	0	1	1
379.0	0	1	1
380.0	0	1	1
382.0	0	1	1
383.0	0	1	1
389.0	0	1	1
393.0	0	1	1
395.0	0	1	1
398.0	0	2	2
400.0	0	1	1
405.0	0	1	1
407.0	0	1	1
408.0	0	1	1
421.0	0	1	1
423.0	0	1	1
425.0	0	1	1
426.0	0	1	1
431.0	0	1	1
451.0	0	1	1
453.0	0	1	1
462.0	0	1	1
464.0	0	1	1
469.0	0	2	2
471.0	0	1	1
474.0	0	1	1
483.0	0	1	1
485.0	0	1	1
495.0	0	1	1
496.0	0	1	1
497.0	0	1	1
503.0	0	1	1
505.0	0	1	1
507.0	0	1	1
508.0	0	1	1
519.0	0	1	1
530.0	0	1	1
531.0	0	1	1
539.0	0	1	1
551.0	0	1	1
554.0	0	1	1
562.0	0	1	1
587.0	0	1	1
593.0	0	2	2
595.0	0	1	1
600.0	0	1	1
609.0	0	1	1
617.0	0	1	1
618.0	0	1	1
619.0	0	1	1
628.0	0	1	1
632.0	0	1	1
637.0	0	1	1
645.0	0	1	1
649.0	0	1	1
655.0	0	1	1
658.0	0	1	1
693.0	0	1	1
709.0	0	1	1
742.0	0	1	1
763.0	0	1	1
789.0	0	1	1
804.0	0	1	1
843.0	0	2	2
844.0	0	1	1
847.0	0	1	1
849.0	0	1	1
879.0	0	1	1
884.0	0	1	1
888.0	0	1	1
892.0	0	1	1
933.0	0	1	1
936.0	0	1	1
944.0	0	1	1
970.0	0	1	1
1004.0	0	1	1
1041.0	0	1	1
1078.0	0	1	1
1211.0	0	1	1
1235.0	0	1	1
1260.0	0	1	1
1295.0	0	1	1
1329.0	0	1	1
1453.0	0	1	1