## 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-D18_supernatant_DMSO_2.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D18_supernatant_DMSO_2.samtools-coordinate-dupmarked.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/qc/markdup/GRCh38.p13-D18_supernatant_DMSO_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 01:48:23 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	1426	24358018	19730406	0	1257	3093213	0	0.127012	87601712

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	20064733	20064733
2.0	1.757256	860989	860989
3.0	2.330692	145103	145103
4.0	2.76493	60687	60687
5.0	3.09376	33658	33658
6.0	3.342767	21022	21022
7.0	3.53133	14351	14351
8.0	3.67412	10366	10366
9.0	3.782249	7788	7788
10.0	3.86413	5964	5964
11.0	3.926135	4738	4738
12.0	3.973089	3948	3948
13.0	4.008645	3256	3256
14.0	4.035569	2684	2684
15.0	4.055958	2205	2205
16.0	4.071398	1955	1955
17.0	4.08309	1667	1667
18.0	4.091944	1447	1447
19.0	4.098648	1323	1323
20.0	4.103725	1056	1056
21.0	4.10757	1015	1015
22.0	4.110481	885	885
23.0	4.112686	858	858
24.0	4.114355	712	712
25.0	4.11562	689	689
26.0	4.116577	612	612
27.0	4.117302	551	551
28.0	4.117851	515	515
29.0	4.118267	455	455
30.0	4.118581	417	417
31.0	4.11882	412	412
32.0	4.119	365	365
33.0	4.119137	342	342
34.0	4.11924	339	339
35.0	4.119319	303	303
36.0	4.119378	264	264
37.0	4.119423	253	253
38.0	4.119457	232	232
39.0	4.119483	236	236
40.0	4.119502	200	200
41.0	4.119517	199	199
42.0	4.119528	207	207
43.0	4.119537	191	191
44.0	4.119543	165	165
45.0	4.119548	148	148
46.0	4.119552	141	141
47.0	4.119555	150	150
48.0	4.119557	165	165
49.0	4.119558	129	129
50.0	4.11956	129	129
51.0	4.119561	135	135
52.0	4.119561	111	111
53.0	4.119562	113	113
54.0	4.119562	105	105
55.0	4.119562	104	104
56.0	4.119563	112	112
57.0	4.119563	100	100
58.0	4.119563	76	76
59.0	4.119563	78	78
60.0	4.119563	68	68
61.0	4.119563	71	71
62.0	4.119563	70	70
63.0	4.119563	68	68
64.0	4.119563	69	69
65.0	4.119563	70	70
66.0	4.119563	64	64
67.0	4.119563	62	62
68.0	4.119563	74	74
69.0	4.119563	51	51
70.0	4.119563	56	56
71.0	4.119563	49	49
72.0	4.119563	65	65
73.0	4.119563	59	59
74.0	4.119563	51	51
75.0	4.119563	51	51
76.0	4.119563	42	42
77.0	4.119563	37	37
78.0	4.119563	46	46
79.0	4.119563	43	43
80.0	4.119563	46	46
81.0	4.119563	38	38
82.0	4.119563	45	45
83.0	4.119563	46	46
84.0	4.119563	39	39
85.0	4.119563	36	36
86.0	4.119563	39	39
87.0	4.119563	36	36
88.0	4.119563	27	27
89.0	4.119563	31	31
90.0	4.119563	30	30
91.0	4.119563	36	36
92.0	4.119563	37	37
93.0	4.119563	28	28
94.0	4.119563	33	33
95.0	4.119563	34	34
96.0	4.119563	20	20
97.0	4.119563	25	25
98.0	4.119563	24	24
99.0	4.119563	26	26
100.0	4.119563	22	22
101.0	0	33	33
102.0	0	21	21
103.0	0	18	18
104.0	0	15	15
105.0	0	14	14
106.0	0	25	25
107.0	0	21	21
108.0	0	16	16
109.0	0	17	17
110.0	0	20	20
111.0	0	28	28
112.0	0	27	27
113.0	0	19	19
114.0	0	22	22
115.0	0	18	18
116.0	0	17	17
117.0	0	19	19
118.0	0	19	19
119.0	0	20	20
120.0	0	17	17
121.0	0	17	17
122.0	0	21	21
123.0	0	18	18
124.0	0	14	14
125.0	0	18	18
126.0	0	10	10
127.0	0	16	16
128.0	0	20	20
129.0	0	11	11
130.0	0	17	17
131.0	0	10	10
132.0	0	23	23
133.0	0	18	18
134.0	0	10	10
135.0	0	13	13
136.0	0	15	15
137.0	0	14	14
138.0	0	12	12
139.0	0	10	10
140.0	0	7	7
141.0	0	13	13
142.0	0	8	8
143.0	0	12	12
144.0	0	12	12
145.0	0	7	7
146.0	0	10	10
147.0	0	14	14
148.0	0	9	9
149.0	0	18	18
150.0	0	13	13
151.0	0	10	10
152.0	0	10	10
153.0	0	5	5
154.0	0	7	7
155.0	0	8	8
156.0	0	8	8
157.0	0	8	8
158.0	0	5	5
159.0	0	3	3
160.0	0	9	9
161.0	0	5	5
162.0	0	12	12
163.0	0	11	11
164.0	0	10	10
165.0	0	11	11
166.0	0	10	10
167.0	0	9	9
168.0	0	13	13
169.0	0	6	6
170.0	0	8	8
171.0	0	13	13
172.0	0	7	7
173.0	0	11	11
174.0	0	6	6
175.0	0	8	8
176.0	0	9	9
177.0	0	8	8
178.0	0	9	9
179.0	0	4	4
180.0	0	5	5
181.0	0	6	6
182.0	0	9	9
183.0	0	6	6
184.0	0	8	8
185.0	0	10	10
186.0	0	3	3
187.0	0	7	7
188.0	0	10	10
189.0	0	8	8
190.0	0	8	8
191.0	0	5	5
192.0	0	2	2
193.0	0	10	10
194.0	0	4	4
195.0	0	1	1
196.0	0	6	6
197.0	0	3	3
198.0	0	2	2
199.0	0	4	4
200.0	0	5	5
201.0	0	8	8
202.0	0	3	3
203.0	0	6	6
204.0	0	6	6
205.0	0	5	5
206.0	0	6	6
207.0	0	1	1
208.0	0	5	5
209.0	0	6	6
210.0	0	6	6
211.0	0	4	4
212.0	0	4	4
213.0	0	6	6
214.0	0	5	5
215.0	0	7	7
216.0	0	6	6
217.0	0	7	7
218.0	0	9	9
219.0	0	6	6
220.0	0	4	4
221.0	0	3	3
222.0	0	8	8
223.0	0	3	3
224.0	0	3	3
225.0	0	5	5
226.0	0	2	2
227.0	0	2	2
228.0	0	2	2
229.0	0	7	7
231.0	0	2	2
232.0	0	6	6
233.0	0	2	2
234.0	0	4	4
235.0	0	3	3
236.0	0	5	5
237.0	0	4	4
238.0	0	7	7
239.0	0	1	1
240.0	0	6	6
241.0	0	3	3
242.0	0	1	1
243.0	0	3	3
244.0	0	2	2
245.0	0	1	1
246.0	0	5	5
247.0	0	3	3
248.0	0	5	5
249.0	0	1	1
250.0	0	3	3
251.0	0	3	3
252.0	0	2	2
253.0	0	2	2
254.0	0	3	3
255.0	0	3	3
256.0	0	4	4
257.0	0	2	2
258.0	0	2	2
259.0	0	2	2
260.0	0	1	1
261.0	0	2	2
262.0	0	3	3
263.0	0	4	4
264.0	0	5	5
265.0	0	1	1
267.0	0	4	4
268.0	0	2	2
269.0	0	1	1
270.0	0	2	2
271.0	0	7	7
272.0	0	3	3
273.0	0	3	3
274.0	0	2	2
276.0	0	3	3
277.0	0	2	2
278.0	0	2	2
279.0	0	2	2
280.0	0	1	1
281.0	0	2	2
282.0	0	5	5
283.0	0	1	1
285.0	0	1	1
286.0	0	2	2
287.0	0	3	3
288.0	0	3	3
289.0	0	1	1
290.0	0	3	3
291.0	0	3	3
293.0	0	2	2
294.0	0	5	5
295.0	0	1	1
296.0	0	2	2
298.0	0	3	3
300.0	0	1	1
301.0	0	2	2
302.0	0	3	3
303.0	0	1	1
304.0	0	1	1
307.0	0	3	3
308.0	0	1	1
309.0	0	2	2
310.0	0	1	1
311.0	0	1	1
312.0	0	1	1
313.0	0	1	1
314.0	0	1	1
315.0	0	2	2
316.0	0	3	3
317.0	0	1	1
318.0	0	1	1
320.0	0	2	2
321.0	0	2	2
322.0	0	1	1
323.0	0	2	2
324.0	0	1	1
326.0	0	3	3
327.0	0	6	6
328.0	0	1	1
331.0	0	1	1
332.0	0	2	2
334.0	0	1	1
336.0	0	1	1
338.0	0	2	2
339.0	0	2	2
340.0	0	3	3
341.0	0	2	2
342.0	0	3	3
343.0	0	2	2
344.0	0	1	1
345.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	2	2
352.0	0	2	2
353.0	0	2	2
354.0	0	1	1
355.0	0	4	4
356.0	0	1	1
357.0	0	1	1
358.0	0	2	2
359.0	0	2	2
360.0	0	2	2
361.0	0	1	1
362.0	0	1	1
363.0	0	1	1
364.0	0	2	2
365.0	0	2	2
367.0	0	1	1
369.0	0	1	1
370.0	0	1	1
371.0	0	1	1
373.0	0	1	1
374.0	0	2	2
375.0	0	1	1
376.0	0	1	1
377.0	0	1	1
378.0	0	1	1
381.0	0	1	1
383.0	0	2	2
385.0	0	1	1
387.0	0	1	1
390.0	0	1	1
391.0	0	1	1
392.0	0	1	1
393.0	0	1	1
394.0	0	1	1
396.0	0	1	1
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
402.0	0	1	1
403.0	0	2	2
407.0	0	1	1
408.0	0	1	1
411.0	0	1	1
412.0	0	2	2
414.0	0	1	1
415.0	0	1	1
417.0	0	2	2
419.0	0	1	1
421.0	0	2	2
423.0	0	1	1
424.0	0	1	1
425.0	0	1	1
427.0	0	1	1
428.0	0	1	1
429.0	0	2	2
434.0	0	2	2
435.0	0	1	1
436.0	0	2	2
439.0	0	1	1
442.0	0	1	1
443.0	0	3	3
445.0	0	2	2
448.0	0	1	1
450.0	0	1	1
451.0	0	1	1
452.0	0	1	1
455.0	0	1	1
457.0	0	1	1
458.0	0	1	1
460.0	0	2	2
461.0	0	1	1
463.0	0	1	1
465.0	0	2	2
466.0	0	2	2
469.0	0	1	1
471.0	0	1	1
472.0	0	2	2
473.0	0	1	1
475.0	0	2	2
478.0	0	1	1
479.0	0	1	1
480.0	0	4	4
488.0	0	1	1
493.0	0	1	1
499.0	0	1	1
502.0	0	1	1
508.0	0	1	1
516.0	0	1	1
517.0	0	1	1
520.0	0	1	1
526.0	0	1	1
528.0	0	1	1
532.0	0	1	1
533.0	0	1	1
540.0	0	1	1
541.0	0	1	1
543.0	0	1	1
546.0	0	1	1
547.0	0	1	1
548.0	0	2	2
560.0	0	1	1
563.0	0	1	1
571.0	0	1	1
577.0	0	1	1
578.0	0	1	1
581.0	0	2	2
587.0	0	1	1
589.0	0	1	1
591.0	0	1	1
593.0	0	1	1
594.0	0	1	1
605.0	0	1	1
608.0	0	1	1
610.0	0	2	2
611.0	0	2	2
615.0	0	2	2
632.0	0	1	1
644.0	0	2	2
651.0	0	1	1
659.0	0	3	3
672.0	0	1	1
677.0	0	1	1
685.0	0	1	1
701.0	0	1	1
711.0	0	1	1
719.0	0	1	1
722.0	0	1	1
729.0	0	1	1
748.0	0	1	1
753.0	0	1	1
758.0	0	1	1
761.0	0	1	1
769.0	0	3	3
781.0	0	1	1
783.0	0	1	1
786.0	0	1	1
816.0	0	1	1
827.0	0	1	1
834.0	0	1	1
854.0	0	1	1
899.0	0	1	1
970.0	0	1	1
980.0	0	1	1
982.0	0	1	1
997.0	0	1	1
1030.0	0	1	1
1032.0	0	1	1
1040.0	0	1	1
1042.0	0	1	1
1115.0	0	1	1
1123.0	0	1	1
1144.0	0	1	1
1184.0	0	1	1
1218.0	0	1	1
1232.0	0	1	1
1299.0	0	1	1
1302.0	0	1	1
1313.0	0	1	1
1322.0	0	1	1
1345.0	0	1	1
1377.0	0	1	1
1427.0	0	1	1
1445.0	0	1	1
1467.0	0	1	1
1503.0	0	1	1
1539.0	0	1	1
1549.0	0	1	1
1575.0	0	1	1
1591.0	0	1	1
1617.0	0	1	1
1721.0	0	1	1
1744.0	0	1	1
1750.0	0	1	1
1954.0	0	1	1
1994.0	0	1	1
3766.0	0	1	1
4869.0	0	1	1