## 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_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_adherent_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-D12_adherent_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 01:20:33 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	1248	30914382	25329024	0	1121	5457621	0	0.176554	76915963

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	22402757	22402757
2.0	1.669031	2398275	2398275
3.0	2.116635	362972	362972
4.0	2.416095	109448	109448
5.0	2.616444	53589	53589
6.0	2.750483	31458	31458
7.0	2.84016	20449	20449
8.0	2.900156	14362	14362
9.0	2.940296	10481	10481
10.0	2.967151	7851	7851
11.0	2.985117	6144	6144
12.0	2.997137	4873	4873
13.0	3.005179	3830	3830
14.0	3.01056	3241	3241
15.0	3.014159	2617	2617
16.0	3.016567	2244	2244
17.0	3.018179	1886	1886
18.0	3.019257	1698	1698
19.0	3.019978	1455	1455
20.0	3.02046	1214	1214
21.0	3.020783	1168	1168
22.0	3.020999	991	991
23.0	3.021143	874	874
24.0	3.02124	776	776
25.0	3.021305	737	737
26.0	3.021348	650	650
27.0	3.021377	581	581
28.0	3.021396	538	538
29.0	3.021409	478	478
30.0	3.021418	444	444
31.0	3.021424	437	437
32.0	3.021428	378	378
33.0	3.02143	371	371
34.0	3.021432	276	276
35.0	3.021433	306	306
36.0	3.021434	290	290
37.0	3.021435	268	268
38.0	3.021435	242	242
39.0	3.021435	214	214
40.0	3.021435	241	241
41.0	3.021435	184	184
42.0	3.021435	198	198
43.0	3.021435	184	184
44.0	3.021435	161	161
45.0	3.021436	159	159
46.0	3.021436	129	129
47.0	3.021436	146	146
48.0	3.021436	144	144
49.0	3.021436	130	130
50.0	3.021436	117	117
51.0	3.021436	119	119
52.0	3.021436	105	105
53.0	3.021436	102	102
54.0	3.021436	100	100
55.0	3.021436	101	101
56.0	3.021436	99	99
57.0	3.021436	86	86
58.0	3.021436	88	88
59.0	3.021436	89	89
60.0	3.021436	82	82
61.0	3.021436	88	88
62.0	3.021436	66	66
63.0	3.021436	65	65
64.0	3.021436	62	62
65.0	3.021436	54	54
66.0	3.021436	56	56
67.0	3.021436	55	55
68.0	3.021436	57	57
69.0	3.021436	51	51
70.0	3.021436	69	69
71.0	3.021436	42	42
72.0	3.021436	66	66
73.0	3.021436	43	43
74.0	3.021436	37	37
75.0	3.021436	39	39
76.0	3.021436	33	33
77.0	3.021436	49	49
78.0	3.021436	44	44
79.0	3.021436	38	38
80.0	3.021436	31	31
81.0	3.021436	34	34
82.0	3.021436	41	41
83.0	3.021436	39	39
84.0	3.021436	32	32
85.0	3.021436	33	33
86.0	3.021436	36	36
87.0	3.021436	39	39
88.0	3.021436	17	17
89.0	3.021436	38	38
90.0	3.021436	28	28
91.0	3.021436	36	36
92.0	3.021436	32	32
93.0	3.021436	25	25
94.0	3.021436	35	35
95.0	3.021436	19	19
96.0	3.021436	29	29
97.0	3.021436	21	21
98.0	3.021436	26	26
99.0	3.021436	21	21
100.0	3.021436	14	14
101.0	0	23	23
102.0	0	22	22
103.0	0	18	18
104.0	0	20	20
105.0	0	16	16
106.0	0	22	22
107.0	0	11	11
108.0	0	24	24
109.0	0	15	15
110.0	0	22	22
111.0	0	10	10
112.0	0	23	23
113.0	0	19	19
114.0	0	21	21
115.0	0	10	10
116.0	0	13	13
117.0	0	13	13
118.0	0	19	19
119.0	0	17	17
120.0	0	11	11
121.0	0	11	11
122.0	0	14	14
123.0	0	15	15
124.0	0	14	14
125.0	0	14	14
126.0	0	6	6
127.0	0	18	18
128.0	0	4	4
129.0	0	15	15
130.0	0	12	12
131.0	0	8	8
132.0	0	6	6
133.0	0	10	10
134.0	0	9	9
135.0	0	10	10
136.0	0	12	12
137.0	0	11	11
138.0	0	10	10
139.0	0	10	10
140.0	0	9	9
141.0	0	10	10
142.0	0	7	7
143.0	0	8	8
144.0	0	13	13
145.0	0	8	8
146.0	0	4	4
147.0	0	7	7
148.0	0	9	9
149.0	0	9	9
150.0	0	9	9
151.0	0	8	8
152.0	0	11	11
153.0	0	4	4
154.0	0	9	9
155.0	0	5	5
156.0	0	10	10
157.0	0	11	11
158.0	0	10	10
159.0	0	8	8
160.0	0	6	6
161.0	0	2	2
162.0	0	12	12
163.0	0	9	9
164.0	0	5	5
165.0	0	7	7
166.0	0	7	7
167.0	0	8	8
168.0	0	9	9
169.0	0	6	6
170.0	0	7	7
171.0	0	4	4
172.0	0	6	6
173.0	0	3	3
174.0	0	11	11
175.0	0	8	8
176.0	0	8	8
177.0	0	4	4
178.0	0	6	6
179.0	0	2	2
180.0	0	11	11
181.0	0	9	9
182.0	0	2	2
183.0	0	9	9
184.0	0	4	4
185.0	0	6	6
186.0	0	3	3
187.0	0	3	3
188.0	0	2	2
189.0	0	10	10
190.0	0	2	2
191.0	0	5	5
192.0	0	6	6
193.0	0	5	5
194.0	0	6	6
195.0	0	2	2
196.0	0	3	3
197.0	0	1	1
198.0	0	5	5
199.0	0	2	2
200.0	0	7	7
201.0	0	6	6
202.0	0	3	3
203.0	0	1	1
204.0	0	4	4
205.0	0	2	2
206.0	0	6	6
207.0	0	2	2
208.0	0	7	7
209.0	0	8	8
210.0	0	3	3
211.0	0	9	9
212.0	0	2	2
213.0	0	1	1
214.0	0	3	3
215.0	0	4	4
216.0	0	3	3
217.0	0	5	5
218.0	0	4	4
219.0	0	2	2
220.0	0	6	6
221.0	0	5	5
222.0	0	5	5
223.0	0	3	3
224.0	0	2	2
225.0	0	2	2
226.0	0	5	5
227.0	0	3	3
228.0	0	4	4
229.0	0	1	1
230.0	0	3	3
231.0	0	3	3
232.0	0	4	4
233.0	0	1	1
234.0	0	5	5
235.0	0	1	1
236.0	0	5	5
237.0	0	3	3
238.0	0	4	4
239.0	0	2	2
240.0	0	1	1
241.0	0	1	1
242.0	0	1	1
243.0	0	1	1
245.0	0	4	4
246.0	0	2	2
247.0	0	3	3
248.0	0	4	4
249.0	0	2	2
250.0	0	2	2
251.0	0	4	4
252.0	0	3	3
253.0	0	2	2
254.0	0	1	1
256.0	0	3	3
257.0	0	3	3
258.0	0	1	1
259.0	0	2	2
260.0	0	3	3
261.0	0	1	1
262.0	0	4	4
263.0	0	3	3
264.0	0	2	2
266.0	0	1	1
267.0	0	4	4
268.0	0	2	2
269.0	0	4	4
270.0	0	4	4
271.0	0	1	1
273.0	0	2	2
274.0	0	3	3
275.0	0	4	4
276.0	0	1	1
277.0	0	2	2
278.0	0	1	1
279.0	0	1	1
280.0	0	1	1
282.0	0	4	4
283.0	0	1	1
285.0	0	5	5
286.0	0	1	1
287.0	0	3	3
288.0	0	3	3
289.0	0	1	1
290.0	0	1	1
291.0	0	1	1
292.0	0	1	1
293.0	0	2	2
294.0	0	1	1
295.0	0	2	2
296.0	0	4	4
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
303.0	0	2	2
304.0	0	4	4
305.0	0	2	2
307.0	0	1	1
308.0	0	1	1
309.0	0	1	1
310.0	0	1	1
311.0	0	3	3
312.0	0	3	3
313.0	0	3	3
315.0	0	3	3
316.0	0	1	1
317.0	0	1	1
319.0	0	3	3
320.0	0	1	1
321.0	0	1	1
322.0	0	3	3
324.0	0	1	1
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
328.0	0	1	1
330.0	0	2	2
331.0	0	1	1
333.0	0	2	2
334.0	0	1	1
336.0	0	2	2
338.0	0	3	3
339.0	0	3	3
340.0	0	1	1
341.0	0	1	1
343.0	0	1	1
344.0	0	2	2
347.0	0	1	1
349.0	0	2	2
351.0	0	1	1
352.0	0	1	1
353.0	0	2	2
356.0	0	2	2
357.0	0	3	3
359.0	0	1	1
360.0	0	1	1
361.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	2	2
365.0	0	1	1
366.0	0	3	3
369.0	0	1	1
373.0	0	1	1
375.0	0	1	1
377.0	0	1	1
378.0	0	1	1
379.0	0	1	1
382.0	0	1	1
383.0	0	2	2
388.0	0	2	2
389.0	0	1	1
390.0	0	2	2
391.0	0	2	2
393.0	0	1	1
397.0	0	1	1
398.0	0	2	2
400.0	0	2	2
402.0	0	1	1
404.0	0	1	1
405.0	0	2	2
406.0	0	1	1
410.0	0	2	2
411.0	0	2	2
413.0	0	2	2
414.0	0	1	1
415.0	0	1	1
416.0	0	1	1
417.0	0	1	1
420.0	0	1	1
421.0	0	3	3
425.0	0	2	2
431.0	0	2	2
434.0	0	1	1
435.0	0	1	1
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	1	1
445.0	0	1	1
446.0	0	1	1
449.0	0	1	1
450.0	0	1	1
451.0	0	1	1
453.0	0	2	2
455.0	0	1	1
457.0	0	2	2
459.0	0	1	1
461.0	0	1	1
473.0	0	2	2
475.0	0	1	1
477.0	0	1	1
479.0	0	1	1
481.0	0	1	1
482.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
488.0	0	2	2
490.0	0	3	3
492.0	0	1	1
496.0	0	1	1
497.0	0	1	1
501.0	0	2	2
502.0	0	1	1
507.0	0	1	1
509.0	0	1	1
510.0	0	1	1
511.0	0	1	1
519.0	0	1	1
522.0	0	2	2
524.0	0	1	1
528.0	0	1	1
532.0	0	1	1
539.0	0	1	1
541.0	0	1	1
547.0	0	1	1
552.0	0	1	1
553.0	0	1	1
561.0	0	1	1
568.0	0	1	1
571.0	0	1	1
573.0	0	1	1
588.0	0	1	1
592.0	0	1	1
597.0	0	2	2
601.0	0	1	1
604.0	0	1	1
606.0	0	1	1
607.0	0	3	3
609.0	0	2	2
618.0	0	2	2
620.0	0	1	1
629.0	0	1	1
634.0	0	1	1
642.0	0	2	2
643.0	0	1	1
651.0	0	1	1
654.0	0	2	2
656.0	0	2	2
666.0	0	1	1
689.0	0	1	1
699.0	0	1	1
700.0	0	1	1
701.0	0	1	1
702.0	0	1	1
715.0	0	1	1
724.0	0	1	1
756.0	0	1	1
762.0	0	1	1
778.0	0	1	1
782.0	0	1	1
794.0	0	1	1
805.0	0	1	1
810.0	0	1	1
836.0	0	1	1
849.0	0	1	1
852.0	0	1	1
856.0	0	1	1
868.0	0	1	1
870.0	0	1	1
883.0	0	1	1
895.0	0	1	1
898.0	0	1	1
915.0	0	1	1
935.0	0	1	1
938.0	0	2	2
945.0	0	1	1
963.0	0	2	2
1002.0	0	1	1
1015.0	0	1	1
1023.0	0	1	1
1050.0	0	1	1
1061.0	0	1	1
1067.0	0	1	1
1078.0	0	1	1
1080.0	0	1	1
1097.0	0	1	1
1143.0	0	1	1
1223.0	0	1	1
1234.0	0	1	1
1242.0	0	1	1
1248.0	0	1	1
1263.0	0	1	1
1301.0	0	1	1
1303.0	0	1	1
1343.0	0	1	1
1361.0	0	1	1
1367.0	0	1	1
1378.0	0	1	1
1433.0	0	1	1
1575.0	0	1	1
1585.0	0	1	1
1607.0	0	1	1
1812.0	0	1	1
1835.0	0	1	1
1867.0	0	1	1
2062.0	0	1	1
2163.0	0	1	1
2530.0	0	1	1
3510.0	0	1	1