## 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_TA_1.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D10_supernatant_TA_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_TA_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 03:20:25 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	855	20285545	67649651	0	713	7902408	0	0.389568	18710962

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	9239859	9239859
2.0	1.338188	2218467	2218467
3.0	1.452559	502040	502040
4.0	1.491238	141192	141192
5.0	1.504319	61955	61955
6.0	1.508743	38319	38319
7.0	1.510239	26975	26975
8.0	1.510745	20166	20166
9.0	1.510916	16026	16026
10.0	1.510974	12777	12777
11.0	1.510993	10696	10696
12.0	1.511	8910	8910
13.0	1.511002	7455	7455
14.0	1.511003	6466	6466
15.0	1.511003	5569	5569
16.0	1.511003	4970	4970
17.0	1.511003	4310	4310
18.0	1.511003	3879	3879
19.0	1.511003	3437	3437
20.0	1.511003	3109	3109
21.0	1.511003	2740	2740
22.0	1.511003	2540	2540
23.0	1.511003	2374	2374
24.0	1.511003	2074	2074
25.0	1.511003	1995	1995
26.0	1.511003	1757	1757
27.0	1.511003	1645	1645
28.0	1.511003	1469	1469
29.0	1.511003	1374	1374
30.0	1.511003	1272	1272
31.0	1.511003	1244	1244
32.0	1.511003	1126	1126
33.0	1.511003	1054	1054
34.0	1.511003	928	928
35.0	1.511003	874	874
36.0	1.511003	825	825
37.0	1.511003	790	790
38.0	1.511003	771	771
39.0	1.511003	743	743
40.0	1.511003	663	663
41.0	1.511003	632	632
42.0	1.511003	605	605
43.0	1.511003	592	592
44.0	1.511003	503	503
45.0	1.511003	496	496
46.0	1.511003	473	473
47.0	1.511003	449	449
48.0	1.511003	434	434
49.0	1.511003	431	431
50.0	1.511003	387	387
51.0	1.511003	383	383
52.0	1.511003	372	372
53.0	1.511003	356	356
54.0	1.511003	332	332
55.0	1.511003	318	318
56.0	1.511003	286	286
57.0	1.511003	253	253
58.0	1.511003	286	286
59.0	1.511003	279	279
60.0	1.511003	252	252
61.0	1.511003	249	249
62.0	1.511003	229	229
63.0	1.511003	232	232
64.0	1.511003	248	248
65.0	1.511003	224	224
66.0	1.511003	205	205
67.0	1.511003	200	200
68.0	1.511003	186	186
69.0	1.511003	185	185
70.0	1.511003	214	214
71.0	1.511003	168	168
72.0	1.511003	203	203
73.0	1.511003	149	149
74.0	1.511003	166	166
75.0	1.511003	185	185
76.0	1.511003	148	148
77.0	1.511003	150	150
78.0	1.511003	134	134
79.0	1.511003	140	140
80.0	1.511003	133	133
81.0	1.511003	143	143
82.0	1.511003	127	127
83.0	1.511003	132	132
84.0	1.511003	131	131
85.0	1.511003	107	107
86.0	1.511003	110	110
87.0	1.511003	120	120
88.0	1.511003	109	109
89.0	1.511003	99	99
90.0	1.511003	104	104
91.0	1.511003	105	105
92.0	1.511003	82	82
93.0	1.511003	91	91
94.0	1.511003	85	85
95.0	1.511003	81	81
96.0	1.511003	76	76
97.0	1.511003	66	66
98.0	1.511003	71	71
99.0	1.511003	81	81
100.0	1.511003	78	78
101.0	0	66	66
102.0	0	67	67
103.0	0	72	72
104.0	0	69	69
105.0	0	73	73
106.0	0	65	65
107.0	0	76	76
108.0	0	72	72
109.0	0	67	67
110.0	0	42	42
111.0	0	60	60
112.0	0	46	46
113.0	0	66	66
114.0	0	55	55
115.0	0	48	48
116.0	0	52	52
117.0	0	43	43
118.0	0	48	48
119.0	0	63	63
120.0	0	56	56
121.0	0	46	46
122.0	0	53	53
123.0	0	44	44
124.0	0	38	38
125.0	0	43	43
126.0	0	41	41
127.0	0	36	36
128.0	0	37	37
129.0	0	47	47
130.0	0	38	38
131.0	0	34	34
132.0	0	42	42
133.0	0	43	43
134.0	0	45	45
135.0	0	32	32
136.0	0	31	31
137.0	0	32	32
138.0	0	38	38
139.0	0	33	33
140.0	0	34	34
141.0	0	31	31
142.0	0	30	30
143.0	0	23	23
144.0	0	24	24
145.0	0	35	35
146.0	0	32	32
147.0	0	21	21
148.0	0	24	24
149.0	0	24	24
150.0	0	27	27
151.0	0	23	23
152.0	0	25	25
153.0	0	28	28
154.0	0	25	25
155.0	0	22	22
156.0	0	29	29
157.0	0	15	15
158.0	0	20	20
159.0	0	29	29
160.0	0	28	28
161.0	0	23	23
162.0	0	22	22
163.0	0	22	22
164.0	0	15	15
165.0	0	20	20
166.0	0	20	20
167.0	0	22	22
168.0	0	21	21
169.0	0	23	23
170.0	0	15	15
171.0	0	24	24
172.0	0	17	17
173.0	0	17	17
174.0	0	21	21
175.0	0	19	19
176.0	0	22	22
177.0	0	20	20
178.0	0	17	17
179.0	0	17	17
180.0	0	17	17
181.0	0	15	15
182.0	0	15	15
183.0	0	10	10
184.0	0	18	18
185.0	0	18	18
186.0	0	13	13
187.0	0	17	17
188.0	0	16	16
189.0	0	19	19
190.0	0	18	18
191.0	0	10	10
192.0	0	12	12
193.0	0	13	13
194.0	0	18	18
195.0	0	14	14
196.0	0	16	16
197.0	0	15	15
198.0	0	10	10
199.0	0	17	17
200.0	0	12	12
201.0	0	15	15
202.0	0	11	11
203.0	0	12	12
204.0	0	5	5
205.0	0	10	10
206.0	0	13	13
207.0	0	6	6
208.0	0	9	9
209.0	0	9	9
210.0	0	17	17
211.0	0	14	14
212.0	0	14	14
213.0	0	16	16
214.0	0	10	10
215.0	0	8	8
216.0	0	13	13
217.0	0	12	12
218.0	0	8	8
219.0	0	7	7
220.0	0	14	14
221.0	0	8	8
222.0	0	10	10
223.0	0	14	14
224.0	0	9	9
225.0	0	13	13
226.0	0	8	8
227.0	0	5	5
228.0	0	7	7
229.0	0	14	14
230.0	0	5	5
231.0	0	6	6
232.0	0	9	9
233.0	0	7	7
234.0	0	4	4
235.0	0	7	7
236.0	0	8	8
237.0	0	9	9
238.0	0	6	6
239.0	0	9	9
240.0	0	7	7
241.0	0	10	10
242.0	0	5	5
243.0	0	9	9
244.0	0	8	8
245.0	0	6	6
246.0	0	6	6
247.0	0	7	7
248.0	0	8	8
249.0	0	5	5
250.0	0	10	10
251.0	0	6	6
252.0	0	7	7
253.0	0	4	4
254.0	0	4	4
255.0	0	5	5
256.0	0	5	5
257.0	0	8	8
258.0	0	3	3
259.0	0	7	7
260.0	0	9	9
261.0	0	7	7
262.0	0	3	3
263.0	0	5	5
264.0	0	4	4
265.0	0	4	4
266.0	0	8	8
267.0	0	7	7
268.0	0	5	5
269.0	0	6	6
270.0	0	5	5
271.0	0	6	6
272.0	0	6	6
273.0	0	5	5
274.0	0	5	5
275.0	0	2	2
276.0	0	3	3
277.0	0	4	4
278.0	0	3	3
279.0	0	4	4
280.0	0	5	5
281.0	0	5	5
282.0	0	4	4
283.0	0	6	6
284.0	0	2	2
285.0	0	5	5
286.0	0	2	2
287.0	0	5	5
288.0	0	2	2
289.0	0	1	1
290.0	0	1	1
291.0	0	5	5
292.0	0	4	4
293.0	0	9	9
294.0	0	5	5
295.0	0	3	3
296.0	0	6	6
297.0	0	4	4
298.0	0	4	4
299.0	0	5	5
300.0	0	1	1
301.0	0	1	1
302.0	0	1	1
303.0	0	4	4
304.0	0	5	5
305.0	0	5	5
306.0	0	3	3
307.0	0	5	5
308.0	0	4	4
309.0	0	8	8
310.0	0	2	2
311.0	0	3	3
312.0	0	4	4
313.0	0	5	5
314.0	0	6	6
315.0	0	5	5
316.0	0	5	5
317.0	0	2	2
318.0	0	1	1
319.0	0	2	2
320.0	0	4	4
321.0	0	1	1
322.0	0	1	1
323.0	0	1	1
324.0	0	1	1
325.0	0	6	6
326.0	0	3	3
327.0	0	3	3
328.0	0	5	5
329.0	0	4	4
330.0	0	3	3
331.0	0	2	2
332.0	0	5	5
333.0	0	2	2
334.0	0	5	5
336.0	0	5	5
337.0	0	3	3
338.0	0	1	1
339.0	0	2	2
340.0	0	2	2
341.0	0	4	4
342.0	0	2	2
344.0	0	3	3
345.0	0	1	1
346.0	0	2	2
347.0	0	2	2
348.0	0	3	3
349.0	0	3	3
350.0	0	2	2
351.0	0	2	2
352.0	0	2	2
353.0	0	3	3
355.0	0	2	2
357.0	0	4	4
358.0	0	1	1
359.0	0	1	1
360.0	0	1	1
361.0	0	2	2
362.0	0	1	1
363.0	0	2	2
364.0	0	3	3
365.0	0	1	1
366.0	0	2	2
367.0	0	3	3
368.0	0	1	1
369.0	0	3	3
370.0	0	1	1
371.0	0	2	2
372.0	0	1	1
373.0	0	1	1
374.0	0	1	1
375.0	0	4	4
376.0	0	4	4
377.0	0	2	2
378.0	0	4	4
380.0	0	7	7
382.0	0	1	1
383.0	0	2	2
384.0	0	3	3
385.0	0	2	2
386.0	0	2	2
387.0	0	4	4
388.0	0	2	2
389.0	0	4	4
390.0	0	1	1
391.0	0	3	3
392.0	0	1	1
393.0	0	2	2
394.0	0	1	1
395.0	0	2	2
396.0	0	3	3
397.0	0	1	1
399.0	0	1	1
400.0	0	2	2
401.0	0	1	1
403.0	0	2	2
405.0	0	4	4
406.0	0	2	2
407.0	0	1	1
409.0	0	1	1
410.0	0	1	1
411.0	0	6	6
413.0	0	2	2
414.0	0	3	3
415.0	0	1	1
416.0	0	1	1
417.0	0	1	1
418.0	0	1	1
419.0	0	1	1
420.0	0	1	1
421.0	0	3	3
423.0	0	7	7
424.0	0	1	1
425.0	0	1	1
429.0	0	3	3
431.0	0	2	2
432.0	0	1	1
433.0	0	2	2
434.0	0	1	1
436.0	0	1	1
437.0	0	1	1
438.0	0	2	2
439.0	0	1	1
440.0	0	4	4
443.0	0	1	1
444.0	0	3	3
446.0	0	2	2
447.0	0	1	1
448.0	0	1	1
449.0	0	1	1
450.0	0	1	1
453.0	0	1	1
455.0	0	1	1
457.0	0	1	1
458.0	0	1	1
460.0	0	1	1
461.0	0	1	1
464.0	0	1	1
465.0	0	1	1
466.0	0	1	1
469.0	0	1	1
471.0	0	2	2
472.0	0	2	2
473.0	0	1	1
474.0	0	1	1
476.0	0	4	4
477.0	0	1	1
479.0	0	1	1
481.0	0	2	2
482.0	0	3	3
485.0	0	2	2
486.0	0	1	1
487.0	0	2	2
489.0	0	4	4
490.0	0	1	1
492.0	0	1	1
494.0	0	2	2
496.0	0	2	2
498.0	0	1	1
500.0	0	1	1
501.0	0	2	2
502.0	0	2	2
503.0	0	1	1
504.0	0	1	1
506.0	0	1	1
507.0	0	2	2
508.0	0	1	1
509.0	0	1	1
511.0	0	1	1
512.0	0	1	1
514.0	0	2	2
516.0	0	1	1
517.0	0	1	1
520.0	0	2	2
521.0	0	2	2
524.0	0	1	1
525.0	0	1	1
526.0	0	2	2
528.0	0	1	1
535.0	0	2	2
536.0	0	2	2
537.0	0	1	1
538.0	0	1	1
539.0	0	2	2
540.0	0	1	1
542.0	0	1	1
544.0	0	1	1
545.0	0	1	1
549.0	0	1	1
552.0	0	1	1
554.0	0	2	2
555.0	0	2	2
562.0	0	2	2
563.0	0	1	1
565.0	0	1	1
566.0	0	1	1
567.0	0	1	1
569.0	0	1	1
573.0	0	1	1
577.0	0	1	1
581.0	0	1	1
585.0	0	1	1
590.0	0	1	1
592.0	0	1	1
594.0	0	1	1
596.0	0	1	1
597.0	0	1	1
601.0	0	1	1
603.0	0	1	1
607.0	0	2	2
610.0	0	1	1
614.0	0	1	1
618.0	0	1	1
619.0	0	1	1
621.0	0	2	2
622.0	0	1	1
627.0	0	3	3
629.0	0	1	1
631.0	0	1	1
633.0	0	1	1
640.0	0	1	1
647.0	0	1	1
648.0	0	1	1
655.0	0	1	1
657.0	0	1	1
662.0	0	1	1
663.0	0	1	1
665.0	0	1	1
667.0	0	1	1
673.0	0	1	1
675.0	0	1	1
678.0	0	1	1
696.0	0	1	1
699.0	0	1	1
703.0	0	1	1
715.0	0	2	2
720.0	0	1	1
727.0	0	1	1
738.0	0	1	1
740.0	0	1	1
743.0	0	1	1
746.0	0	1	1
753.0	0	1	1
755.0	0	1	1
759.0	0	1	1
760.0	0	2	2
763.0	0	1	1
764.0	0	1	1
784.0	0	1	1
791.0	0	1	1
822.0	0	1	1
832.0	0	1	1
843.0	0	1	1
845.0	0	1	1
846.0	0	1	1
860.0	0	1	1
863.0	0	1	1
867.0	0	1	1
869.0	0	1	1
890.0	0	1	1
891.0	0	1	1
892.0	0	1	1
897.0	0	1	1
898.0	0	1	1
907.0	0	1	1
912.0	0	1	1
919.0	0	1	1
921.0	0	1	1
925.0	0	1	1
930.0	0	1	1
936.0	0	1	1
978.0	0	1	1
981.0	0	1	1
986.0	0	1	1
992.0	0	1	1
994.0	0	1	1
999.0	0	1	1
1009.0	0	1	1
1025.0	0	1	1
1041.0	0	1	1
1047.0	0	1	1
1053.0	0	1	1
1065.0	0	1	1
1095.0	0	1	1
1123.0	0	1	1
1127.0	0	1	1
1131.0	0	1	1
1139.0	0	1	1
1140.0	0	1	1
1145.0	0	1	1
1203.0	0	1	1
1206.0	0	2	2
1241.0	0	1	1
1277.0	0	1	1
1291.0	0	1	1
1312.0	0	1	1
1327.0	0	1	1
1378.0	0	1	1
1438.0	0	1	1
1442.0	0	1	1
1452.0	0	1	1
1462.0	0	1	1
1505.0	0	1	1
1515.0	0	1	1
1535.0	0	1	1
1582.0	0	1	1
1635.0	0	1	1
1642.0	0	1	1
1645.0	0	1	1
1646.0	0	1	1
1713.0	0	1	1
1764.0	0	1	1
1787.0	0	1	1
1968.0	0	1	1
2192.0	0	1	1
2325.0	0	1	1
3393.0	0	1	1
3575.0	0	1	1
5197.0	0	1	1
5487.0	0	1	1