## 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_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_supernatant_RU1uMTA100nM_3.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_3.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 02:44:01 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	540	21608037	18649891	0	452	3410121	0	0.157826	61049069

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	16885303	16885303
2.0	1.701913	909261	909261
3.0	2.194596	171721	171721
4.0	2.540416	73407	73407
5.0	2.783152	40873	40873
6.0	2.953531	25774	25774
7.0	3.073123	17226	17226
8.0	3.157066	12476	12476
9.0	3.215986	9275	9275
10.0	3.257344	7249	7249
11.0	3.286373	5481	5481
12.0	3.306749	4482	4482
13.0	3.321051	3661	3661
14.0	3.33109	3185	3185
15.0	3.338136	2685	2685
16.0	3.343082	2288	2288
17.0	3.346554	1915	1915
18.0	3.348991	1624	1624
19.0	3.350701	1491	1491
20.0	3.351902	1349	1349
21.0	3.352744	1169	1169
22.0	3.353336	997	997
23.0	3.353751	948	948
24.0	3.354042	831	831
25.0	3.354247	735	735
26.0	3.35439	699	699
27.0	3.354491	584	584
28.0	3.354562	572	572
29.0	3.354612	497	497
30.0	3.354647	469	469
31.0	3.354671	462	462
32.0	3.354688	419	419
33.0	3.3547	371	371
34.0	3.354709	316	316
35.0	3.354715	344	344
36.0	3.354719	278	278
37.0	3.354722	324	324
38.0	3.354724	263	263
39.0	3.354725	275	275
40.0	3.354726	243	243
41.0	3.354727	226	226
42.0	3.354727	234	234
43.0	3.354728	210	210
44.0	3.354728	193	193
45.0	3.354728	184	184
46.0	3.354728	162	162
47.0	3.354728	163	163
48.0	3.354728	146	146
49.0	3.354728	142	142
50.0	3.354729	148	148
51.0	3.354729	121	121
52.0	3.354729	122	122
53.0	3.354729	101	101
54.0	3.354729	108	108
55.0	3.354729	112	112
56.0	3.354729	110	110
57.0	3.354729	102	102
58.0	3.354729	87	87
59.0	3.354729	103	103
60.0	3.354729	82	82
61.0	3.354729	64	64
62.0	3.354729	80	80
63.0	3.354729	86	86
64.0	3.354729	68	68
65.0	3.354729	75	75
66.0	3.354729	72	72
67.0	3.354729	55	55
68.0	3.354729	73	73
69.0	3.354729	52	52
70.0	3.354729	65	65
71.0	3.354729	50	50
72.0	3.354729	46	46
73.0	3.354729	52	52
74.0	3.354729	65	65
75.0	3.354729	56	56
76.0	3.354729	44	44
77.0	3.354729	62	62
78.0	3.354729	43	43
79.0	3.354729	50	50
80.0	3.354729	45	45
81.0	3.354729	46	46
82.0	3.354729	38	38
83.0	3.354729	29	29
84.0	3.354729	40	40
85.0	3.354729	36	36
86.0	3.354729	38	38
87.0	3.354729	31	31
88.0	3.354729	31	31
89.0	3.354729	31	31
90.0	3.354729	24	24
91.0	3.354729	33	33
92.0	3.354729	34	34
93.0	3.354729	22	22
94.0	3.354729	32	32
95.0	3.354729	20	20
96.0	3.354729	38	38
97.0	3.354729	28	28
98.0	3.354729	34	34
99.0	3.354729	30	30
100.0	3.354729	22	22
101.0	0	23	23
102.0	0	25	25
103.0	0	16	16
104.0	0	20	20
105.0	0	22	22
106.0	0	22	22
107.0	0	24	24
108.0	0	22	22
109.0	0	20	20
110.0	0	16	16
111.0	0	21	21
112.0	0	18	18
113.0	0	20	20
114.0	0	19	19
115.0	0	19	19
116.0	0	23	23
117.0	0	14	14
118.0	0	19	19
119.0	0	20	20
120.0	0	14	14
121.0	0	16	16
122.0	0	14	14
123.0	0	14	14
124.0	0	10	10
125.0	0	18	18
126.0	0	11	11
127.0	0	20	20
128.0	0	17	17
129.0	0	15	15
130.0	0	17	17
131.0	0	18	18
132.0	0	15	15
133.0	0	16	16
134.0	0	13	13
135.0	0	11	11
136.0	0	10	10
137.0	0	9	9
138.0	0	16	16
139.0	0	16	16
140.0	0	11	11
141.0	0	14	14
142.0	0	17	17
143.0	0	9	9
144.0	0	10	10
145.0	0	17	17
146.0	0	11	11
147.0	0	10	10
148.0	0	10	10
149.0	0	10	10
150.0	0	10	10
151.0	0	9	9
152.0	0	7	7
153.0	0	4	4
154.0	0	16	16
155.0	0	11	11
156.0	0	10	10
157.0	0	4	4
158.0	0	11	11
159.0	0	5	5
160.0	0	9	9
161.0	0	9	9
162.0	0	12	12
163.0	0	10	10
164.0	0	9	9
165.0	0	7	7
166.0	0	5	5
167.0	0	12	12
168.0	0	8	8
169.0	0	9	9
170.0	0	11	11
171.0	0	3	3
172.0	0	11	11
173.0	0	5	5
174.0	0	8	8
175.0	0	9	9
176.0	0	5	5
177.0	0	6	6
178.0	0	5	5
179.0	0	9	9
180.0	0	3	3
181.0	0	4	4
182.0	0	9	9
183.0	0	6	6
184.0	0	4	4
185.0	0	4	4
186.0	0	5	5
187.0	0	3	3
188.0	0	7	7
189.0	0	4	4
190.0	0	2	2
191.0	0	5	5
192.0	0	3	3
193.0	0	5	5
194.0	0	2	2
195.0	0	2	2
196.0	0	5	5
197.0	0	4	4
198.0	0	5	5
199.0	0	3	3
200.0	0	6	6
201.0	0	6	6
202.0	0	5	5
203.0	0	4	4
204.0	0	4	4
205.0	0	9	9
206.0	0	4	4
207.0	0	5	5
208.0	0	5	5
209.0	0	4	4
210.0	0	4	4
211.0	0	3	3
212.0	0	6	6
213.0	0	3	3
214.0	0	4	4
215.0	0	4	4
216.0	0	6	6
217.0	0	5	5
219.0	0	5	5
220.0	0	3	3
221.0	0	5	5
222.0	0	10	10
223.0	0	2	2
224.0	0	8	8
225.0	0	3	3
226.0	0	4	4
227.0	0	5	5
228.0	0	3	3
229.0	0	2	2
230.0	0	5	5
231.0	0	6	6
232.0	0	1	1
233.0	0	3	3
234.0	0	2	2
235.0	0	1	1
236.0	0	3	3
237.0	0	5	5
238.0	0	2	2
239.0	0	2	2
240.0	0	1	1
241.0	0	3	3
242.0	0	5	5
243.0	0	2	2
244.0	0	6	6
245.0	0	1	1
246.0	0	4	4
247.0	0	1	1
248.0	0	1	1
249.0	0	5	5
250.0	0	3	3
251.0	0	1	1
252.0	0	2	2
253.0	0	5	5
254.0	0	1	1
255.0	0	2	2
256.0	0	6	6
257.0	0	2	2
258.0	0	2	2
259.0	0	3	3
260.0	0	4	4
261.0	0	1	1
262.0	0	2	2
263.0	0	2	2
264.0	0	3	3
265.0	0	1	1
266.0	0	1	1
267.0	0	5	5
268.0	0	3	3
269.0	0	1	1
270.0	0	3	3
271.0	0	2	2
272.0	0	4	4
273.0	0	2	2
274.0	0	3	3
275.0	0	1	1
276.0	0	1	1
277.0	0	1	1
278.0	0	1	1
279.0	0	3	3
280.0	0	5	5
281.0	0	1	1
282.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	6	6
286.0	0	1	1
287.0	0	2	2
288.0	0	3	3
289.0	0	2	2
290.0	0	1	1
291.0	0	2	2
292.0	0	3	3
293.0	0	1	1
294.0	0	2	2
295.0	0	1	1
296.0	0	2	2
297.0	0	3	3
298.0	0	4	4
299.0	0	2	2
300.0	0	3	3
301.0	0	2	2
302.0	0	4	4
303.0	0	1	1
305.0	0	4	4
306.0	0	1	1
307.0	0	1	1
308.0	0	2	2
309.0	0	4	4
310.0	0	1	1
313.0	0	3	3
314.0	0	1	1
316.0	0	2	2
317.0	0	2	2
318.0	0	2	2
319.0	0	2	2
320.0	0	1	1
325.0	0	4	4
326.0	0	2	2
327.0	0	4	4
328.0	0	2	2
329.0	0	1	1
330.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
335.0	0	1	1
336.0	0	1	1
338.0	0	2	2
341.0	0	1	1
342.0	0	1	1
343.0	0	2	2
346.0	0	1	1
347.0	0	1	1
351.0	0	2	2
352.0	0	2	2
353.0	0	1	1
359.0	0	3	3
360.0	0	2	2
362.0	0	2	2
364.0	0	1	1
365.0	0	1	1
366.0	0	1	1
367.0	0	3	3
368.0	0	1	1
371.0	0	1	1
372.0	0	1	1
375.0	0	1	1
376.0	0	1	1
377.0	0	1	1
378.0	0	1	1
381.0	0	2	2
382.0	0	1	1
383.0	0	3	3
384.0	0	3	3
385.0	0	1	1
386.0	0	1	1
388.0	0	2	2
391.0	0	1	1
392.0	0	3	3
393.0	0	2	2
397.0	0	1	1
398.0	0	2	2
399.0	0	1	1
400.0	0	2	2
402.0	0	1	1
403.0	0	1	1
405.0	0	1	1
411.0	0	1	1
412.0	0	3	3
415.0	0	2	2
416.0	0	1	1
417.0	0	1	1
418.0	0	2	2
424.0	0	1	1
426.0	0	2	2
428.0	0	2	2
429.0	0	1	1
435.0	0	2	2
436.0	0	1	1
437.0	0	1	1
441.0	0	3	3
443.0	0	2	2
444.0	0	1	1
445.0	0	1	1
446.0	0	2	2
449.0	0	1	1
454.0	0	2	2
472.0	0	2	2
474.0	0	1	1
475.0	0	1	1
476.0	0	1	1
483.0	0	1	1
484.0	0	1	1
485.0	0	1	1
486.0	0	1	1
487.0	0	2	2
489.0	0	1	1
491.0	0	2	2
493.0	0	1	1
500.0	0	1	1
506.0	0	2	2
508.0	0	2	2
515.0	0	1	1
517.0	0	1	1
519.0	0	1	1
520.0	0	1	1
522.0	0	1	1
532.0	0	1	1
545.0	0	1	1
554.0	0	1	1
563.0	0	2	2
565.0	0	1	1
568.0	0	1	1
576.0	0	1	1
586.0	0	1	1
592.0	0	2	2
593.0	0	2	2
594.0	0	1	1
596.0	0	1	1
600.0	0	1	1
603.0	0	3	3
604.0	0	1	1
605.0	0	1	1
616.0	0	1	1
620.0	0	1	1
636.0	0	1	1
644.0	0	1	1
650.0	0	1	1
659.0	0	1	1
662.0	0	1	1
666.0	0	1	1
672.0	0	2	2
676.0	0	1	1
682.0	0	2	2
686.0	0	1	1
687.0	0	1	1
693.0	0	1	1
707.0	0	1	1
713.0	0	1	1
715.0	0	1	1
718.0	0	1	1
731.0	0	1	1
777.0	0	1	1
810.0	0	1	1
872.0	0	1	1
896.0	0	1	1
912.0	0	1	1
914.0	0	1	1
917.0	0	1	1
920.0	0	1	1
925.0	0	2	2
934.0	0	1	1
951.0	0	1	1
984.0	0	1	1
998.0	0	1	1
1005.0	0	1	1
1006.0	0	1	1
1025.0	0	1	1
1026.0	0	1	1
1051.0	0	1	1
1054.0	0	1	1
1061.0	0	1	1
1092.0	0	1	1
1101.0	0	1	1
1139.0	0	1	1
1154.0	0	1	1
1178.0	0	1	1
1185.0	0	1	1
1199.0	0	1	1
1241.0	0	1	1
1251.0	0	1	1
1275.0	0	1	1
1380.0	0	1	1
1399.0	0	1	1
1420.0	0	1	1
1471.0	0	1	1
1577.0	0	1	1
1594.0	0	1	1
1622.0	0	1	1
1647.0	0	1	1
1799.0	0	1	1
1816.0	0	1	1
1841.0	0	1	1
1954.0	0	1	1
2600.0	0	1	1
4073.0	0	1	1