## 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_DMSO_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_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-D12_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 01:08:36 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	1705	46808658	42764306	0	1498	10004136	0	0.213736	93274470

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	32176596	32176596
2.0	1.605417	3397330	3397330
3.0	1.971947	623469	623469
4.0	2.19385	207381	207381
5.0	2.328194	104877	104877
6.0	2.409528	64256	64256
7.0	2.458769	43479	43479
8.0	2.488581	31349	31349
9.0	2.506629	23531	23531
10.0	2.517556	17966	17966
11.0	2.524171	14284	14284
12.0	2.528176	11628	11628
13.0	2.530601	9555	9555
14.0	2.532069	8047	8047
15.0	2.532957	6698	6698
16.0	2.533495	5813	5813
17.0	2.533821	4899	4899
18.0	2.534018	4351	4351
19.0	2.534138	3681	3681
20.0	2.53421	3392	3392
21.0	2.534254	2959	2959
22.0	2.53428	2586	2586
23.0	2.534296	2316	2316
24.0	2.534306	2094	2094
25.0	2.534312	1875	1875
26.0	2.534315	1693	1693
27.0	2.534318	1536	1536
28.0	2.534319	1485	1485
29.0	2.53432	1256	1256
30.0	2.53432	1203	1203
31.0	2.53432	1092	1092
32.0	2.534321	1036	1036
33.0	2.534321	982	982
34.0	2.534321	885	885
35.0	2.534321	822	822
36.0	2.534321	787	787
37.0	2.534321	701	701
38.0	2.534321	617	617
39.0	2.534321	590	590
40.0	2.534321	637	637
41.0	2.534321	603	603
42.0	2.534321	511	511
43.0	2.534321	472	472
44.0	2.534321	448	448
45.0	2.534321	437	437
46.0	2.534321	395	395
47.0	2.534321	405	405
48.0	2.534321	351	351
49.0	2.534321	366	366
50.0	2.534321	362	362
51.0	2.534321	298	298
52.0	2.534321	297	297
53.0	2.534321	273	273
54.0	2.534321	263	263
55.0	2.534321	257	257
56.0	2.534321	259	259
57.0	2.534321	245	245
58.0	2.534321	225	225
59.0	2.534321	226	226
60.0	2.534321	203	203
61.0	2.534321	200	200
62.0	2.534321	209	209
63.0	2.534321	190	190
64.0	2.534321	173	173
65.0	2.534321	166	166
66.0	2.534321	153	153
67.0	2.534321	169	169
68.0	2.534321	146	146
69.0	2.534321	145	145
70.0	2.534321	142	142
71.0	2.534321	172	172
72.0	2.534321	126	126
73.0	2.534321	127	127
74.0	2.534321	116	116
75.0	2.534321	115	115
76.0	2.534321	122	122
77.0	2.534321	94	94
78.0	2.534321	94	94
79.0	2.534321	94	94
80.0	2.534321	107	107
81.0	2.534321	83	83
82.0	2.534321	77	77
83.0	2.534321	92	92
84.0	2.534321	88	88
85.0	2.534321	84	84
86.0	2.534321	90	90
87.0	2.534321	101	101
88.0	2.534321	80	80
89.0	2.534321	67	67
90.0	2.534321	87	87
91.0	2.534321	92	92
92.0	2.534321	60	60
93.0	2.534321	73	73
94.0	2.534321	70	70
95.0	2.534321	47	47
96.0	2.534321	53	53
97.0	2.534321	59	59
98.0	2.534321	63	63
99.0	2.534321	54	54
100.0	2.534321	53	53
101.0	0	52	52
102.0	0	48	48
103.0	0	53	53
104.0	0	44	44
105.0	0	56	56
106.0	0	38	38
107.0	0	47	47
108.0	0	37	37
109.0	0	57	57
110.0	0	49	49
111.0	0	45	45
112.0	0	49	49
113.0	0	36	36
114.0	0	38	38
115.0	0	43	43
116.0	0	43	43
117.0	0	30	30
118.0	0	45	45
119.0	0	39	39
120.0	0	29	29
121.0	0	34	34
122.0	0	41	41
123.0	0	25	25
124.0	0	27	27
125.0	0	27	27
126.0	0	41	41
127.0	0	35	35
128.0	0	33	33
129.0	0	28	28
130.0	0	23	23
131.0	0	25	25
132.0	0	29	29
133.0	0	32	32
134.0	0	28	28
135.0	0	23	23
136.0	0	18	18
137.0	0	24	24
138.0	0	21	21
139.0	0	25	25
140.0	0	18	18
141.0	0	26	26
142.0	0	17	17
143.0	0	29	29
144.0	0	25	25
145.0	0	22	22
146.0	0	25	25
147.0	0	18	18
148.0	0	21	21
149.0	0	23	23
150.0	0	18	18
151.0	0	23	23
152.0	0	13	13
153.0	0	18	18
154.0	0	19	19
155.0	0	19	19
156.0	0	12	12
157.0	0	12	12
158.0	0	9	9
159.0	0	13	13
160.0	0	13	13
161.0	0	18	18
162.0	0	14	14
163.0	0	13	13
164.0	0	10	10
165.0	0	12	12
166.0	0	14	14
167.0	0	17	17
168.0	0	9	9
169.0	0	11	11
170.0	0	14	14
171.0	0	21	21
172.0	0	20	20
173.0	0	18	18
174.0	0	21	21
175.0	0	14	14
176.0	0	12	12
177.0	0	14	14
178.0	0	11	11
179.0	0	18	18
180.0	0	12	12
181.0	0	11	11
182.0	0	12	12
183.0	0	17	17
184.0	0	5	5
185.0	0	15	15
186.0	0	12	12
187.0	0	9	9
188.0	0	11	11
189.0	0	15	15
190.0	0	9	9
191.0	0	8	8
192.0	0	13	13
193.0	0	10	10
194.0	0	13	13
195.0	0	14	14
196.0	0	18	18
197.0	0	10	10
198.0	0	5	5
199.0	0	14	14
200.0	0	10	10
201.0	0	13	13
202.0	0	8	8
203.0	0	11	11
204.0	0	7	7
205.0	0	12	12
206.0	0	7	7
207.0	0	15	15
208.0	0	11	11
209.0	0	9	9
210.0	0	8	8
211.0	0	15	15
212.0	0	1	1
213.0	0	8	8
214.0	0	6	6
215.0	0	6	6
216.0	0	6	6
217.0	0	9	9
218.0	0	8	8
219.0	0	8	8
220.0	0	5	5
221.0	0	10	10
222.0	0	11	11
223.0	0	3	3
224.0	0	11	11
225.0	0	6	6
226.0	0	5	5
227.0	0	7	7
228.0	0	7	7
229.0	0	8	8
230.0	0	9	9
231.0	0	9	9
232.0	0	6	6
233.0	0	8	8
234.0	0	9	9
235.0	0	6	6
236.0	0	8	8
237.0	0	2	2
238.0	0	6	6
239.0	0	12	12
240.0	0	3	3
241.0	0	9	9
242.0	0	7	7
243.0	0	8	8
244.0	0	11	11
245.0	0	7	7
246.0	0	3	3
247.0	0	6	6
248.0	0	3	3
249.0	0	10	10
250.0	0	5	5
251.0	0	2	2
252.0	0	10	10
253.0	0	7	7
254.0	0	5	5
255.0	0	4	4
256.0	0	7	7
257.0	0	4	4
258.0	0	7	7
259.0	0	4	4
260.0	0	5	5
261.0	0	2	2
262.0	0	5	5
263.0	0	9	9
264.0	0	5	5
265.0	0	3	3
266.0	0	4	4
267.0	0	4	4
268.0	0	4	4
269.0	0	8	8
270.0	0	5	5
271.0	0	5	5
272.0	0	4	4
273.0	0	5	5
274.0	0	3	3
275.0	0	6	6
277.0	0	2	2
278.0	0	6	6
279.0	0	4	4
280.0	0	3	3
281.0	0	5	5
282.0	0	3	3
283.0	0	1	1
284.0	0	7	7
285.0	0	4	4
286.0	0	7	7
287.0	0	6	6
288.0	0	4	4
289.0	0	4	4
290.0	0	9	9
291.0	0	5	5
292.0	0	5	5
293.0	0	6	6
294.0	0	1	1
295.0	0	5	5
296.0	0	3	3
297.0	0	2	2
298.0	0	2	2
299.0	0	4	4
300.0	0	6	6
301.0	0	6	6
302.0	0	5	5
303.0	0	4	4
304.0	0	7	7
305.0	0	2	2
306.0	0	6	6
307.0	0	2	2
309.0	0	2	2
310.0	0	3	3
311.0	0	6	6
312.0	0	3	3
313.0	0	2	2
314.0	0	2	2
315.0	0	4	4
316.0	0	4	4
317.0	0	6	6
318.0	0	5	5
319.0	0	5	5
320.0	0	5	5
321.0	0	2	2
322.0	0	1	1
323.0	0	3	3
324.0	0	5	5
325.0	0	4	4
326.0	0	2	2
327.0	0	2	2
328.0	0	1	1
329.0	0	2	2
330.0	0	5	5
331.0	0	5	5
332.0	0	5	5
333.0	0	2	2
334.0	0	3	3
335.0	0	3	3
336.0	0	5	5
337.0	0	2	2
338.0	0	2	2
339.0	0	2	2
340.0	0	3	3
341.0	0	3	3
342.0	0	2	2
343.0	0	2	2
344.0	0	4	4
345.0	0	5	5
346.0	0	3	3
347.0	0	2	2
348.0	0	1	1
349.0	0	3	3
350.0	0	4	4
351.0	0	5	5
352.0	0	1	1
354.0	0	2	2
355.0	0	4	4
356.0	0	2	2
357.0	0	1	1
358.0	0	4	4
359.0	0	4	4
361.0	0	2	2
362.0	0	1	1
363.0	0	3	3
364.0	0	1	1
365.0	0	1	1
366.0	0	6	6
367.0	0	2	2
370.0	0	3	3
371.0	0	3	3
372.0	0	7	7
374.0	0	2	2
375.0	0	3	3
376.0	0	3	3
377.0	0	4	4
378.0	0	2	2
379.0	0	1	1
382.0	0	1	1
384.0	0	2	2
385.0	0	3	3
386.0	0	1	1
388.0	0	2	2
389.0	0	1	1
390.0	0	3	3
391.0	0	1	1
392.0	0	1	1
393.0	0	1	1
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
401.0	0	1	1
402.0	0	2	2
403.0	0	2	2
404.0	0	3	3
406.0	0	2	2
407.0	0	2	2
408.0	0	2	2
409.0	0	1	1
410.0	0	3	3
411.0	0	3	3
412.0	0	2	2
413.0	0	3	3
415.0	0	1	1
416.0	0	2	2
417.0	0	1	1
418.0	0	1	1
419.0	0	3	3
420.0	0	1	1
421.0	0	1	1
422.0	0	1	1
423.0	0	1	1
427.0	0	1	1
428.0	0	2	2
430.0	0	1	1
432.0	0	3	3
433.0	0	3	3
434.0	0	1	1
435.0	0	2	2
436.0	0	2	2
437.0	0	2	2
438.0	0	2	2
439.0	0	1	1
440.0	0	1	1
441.0	0	1	1
443.0	0	1	1
444.0	0	2	2
450.0	0	3	3
451.0	0	2	2
452.0	0	1	1
453.0	0	2	2
455.0	0	1	1
456.0	0	1	1
458.0	0	1	1
459.0	0	2	2
460.0	0	1	1
464.0	0	3	3
467.0	0	1	1
468.0	0	1	1
469.0	0	2	2
470.0	0	2	2
471.0	0	1	1
473.0	0	1	1
474.0	0	1	1
475.0	0	1	1
480.0	0	1	1
481.0	0	1	1
483.0	0	2	2
484.0	0	1	1
487.0	0	1	1
490.0	0	3	3
493.0	0	2	2
494.0	0	2	2
495.0	0	2	2
496.0	0	2	2
497.0	0	1	1
498.0	0	3	3
500.0	0	1	1
501.0	0	1	1
504.0	0	3	3
505.0	0	1	1
507.0	0	2	2
509.0	0	1	1
510.0	0	2	2
512.0	0	2	2
513.0	0	1	1
514.0	0	3	3
517.0	0	2	2
518.0	0	2	2
522.0	0	2	2
524.0	0	1	1
526.0	0	2	2
527.0	0	1	1
529.0	0	2	2
530.0	0	1	1
533.0	0	3	3
534.0	0	1	1
535.0	0	1	1
536.0	0	2	2
538.0	0	1	1
539.0	0	1	1
542.0	0	1	1
543.0	0	2	2
545.0	0	2	2
546.0	0	2	2
547.0	0	1	1
549.0	0	1	1
552.0	0	1	1
555.0	0	3	3
556.0	0	2	2
560.0	0	1	1
562.0	0	3	3
564.0	0	1	1
565.0	0	1	1
566.0	0	1	1
567.0	0	1	1
568.0	0	1	1
571.0	0	1	1
573.0	0	2	2
574.0	0	1	1
579.0	0	1	1
586.0	0	1	1
589.0	0	1	1
590.0	0	1	1
605.0	0	1	1
607.0	0	1	1
611.0	0	1	1
614.0	0	1	1
615.0	0	2	2
618.0	0	1	1
621.0	0	1	1
624.0	0	1	1
625.0	0	1	1
626.0	0	1	1
627.0	0	1	1
630.0	0	2	2
631.0	0	1	1
632.0	0	2	2
638.0	0	2	2
639.0	0	1	1
641.0	0	1	1
643.0	0	1	1
644.0	0	1	1
650.0	0	2	2
651.0	0	1	1
652.0	0	1	1
653.0	0	1	1
657.0	0	1	1
658.0	0	1	1
660.0	0	1	1
662.0	0	1	1
665.0	0	1	1
666.0	0	1	1
670.0	0	1	1
674.0	0	1	1
677.0	0	1	1
680.0	0	1	1
681.0	0	1	1
683.0	0	2	2
689.0	0	1	1
690.0	0	1	1
691.0	0	1	1
693.0	0	2	2
694.0	0	1	1
703.0	0	2	2
705.0	0	1	1
708.0	0	1	1
710.0	0	1	1
711.0	0	1	1
713.0	0	1	1
715.0	0	1	1
724.0	0	1	1
727.0	0	1	1
734.0	0	1	1
738.0	0	1	1
755.0	0	1	1
757.0	0	1	1
762.0	0	1	1
768.0	0	2	2
773.0	0	1	1
774.0	0	1	1
775.0	0	2	2
779.0	0	1	1
788.0	0	1	1
797.0	0	1	1
808.0	0	1	1
811.0	0	1	1
812.0	0	1	1
827.0	0	1	1
838.0	0	1	1
848.0	0	2	2
853.0	0	2	2
860.0	0	1	1
864.0	0	1	1
866.0	0	2	2
870.0	0	1	1
877.0	0	1	1
879.0	0	2	2
882.0	0	1	1
889.0	0	1	1
893.0	0	1	1
918.0	0	1	1
923.0	0	1	1
924.0	0	1	1
928.0	0	1	1
979.0	0	1	1
985.0	0	1	1
992.0	0	1	1
1002.0	0	1	1
1006.0	0	1	1
1010.0	0	1	1
1049.0	0	1	1
1051.0	0	1	1
1084.0	0	1	1
1090.0	0	1	1
1099.0	0	1	1
1104.0	0	1	1
1114.0	0	1	1
1116.0	0	1	1
1121.0	0	1	1
1128.0	0	1	1
1135.0	0	1	1
1163.0	0	1	1
1185.0	0	1	1
1186.0	0	1	1
1190.0	0	2	2
1202.0	0	1	1
1227.0	0	2	2
1265.0	0	1	1
1290.0	0	1	1
1301.0	0	1	1
1302.0	0	1	1
1309.0	0	1	1
1312.0	0	1	1
1336.0	0	1	1
1339.0	0	1	1
1369.0	0	1	1
1374.0	0	1	1
1383.0	0	2	2
1385.0	0	1	1
1399.0	0	1	1
1416.0	0	1	1
1423.0	0	1	1
1428.0	0	1	1
1442.0	0	1	1
1515.0	0	1	1
1558.0	0	1	1
1594.0	0	1	1
1632.0	0	1	1
1717.0	0	1	1
1726.0	0	1	1
1728.0	0	1	1
1729.0	0	1	1
1741.0	0	1	1
1752.0	0	1	1
1771.0	0	1	1
1784.0	0	1	1
1842.0	0	1	1
1894.0	0	1	1
1955.0	0	1	1
2006.0	0	1	1
2019.0	0	1	1
2076.0	0	1	1
2093.0	0	1	1
2138.0	0	1	1
2177.0	0	1	1
2232.0	0	2	2
2258.0	0	1	1
2312.0	0	1	1
2332.0	0	1	1
2377.0	0	1	1
2447.0	0	1	1
2563.0	0	1	1
2664.0	0	1	1
2777.0	0	1	1
4218.0	0	1	1
4598.0	0	1	1