## 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_TA_3.samtools-coordinate-unsieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/slrinzema/ghe/2023_s2s_run/results_no_replicates/star/GRCh38.p13-D12_adherent_TA_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_adherent_TA_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 01:59:50 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	641	24480772	18568752	0	561	4331970	0	0.176963	60745987

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	18216416	18216416
2.0	1.668311	1481232	1481232
3.0	2.11495	224422	224422
4.0	2.413443	77470	77470
5.0	2.61293	39723	39723
6.0	2.746248	24247	24247
7.0	2.835347	15866	15866
8.0	2.894892	11109	11109
9.0	2.934687	8466	8466
10.0	2.961282	6351	6351
11.0	2.979056	4925	4925
12.0	2.990935	3987	3987
13.0	2.998873	3204	3204
14.0	3.004179	2778	2778
15.0	3.007724	2245	2245
16.0	3.010094	2074	2074
17.0	3.011678	1693	1693
18.0	3.012736	1580	1580
19.0	3.013443	1379	1379
20.0	3.013916	1233	1233
21.0	3.014232	1031	1031
22.0	3.014443	919	919
23.0	3.014584	911	911
24.0	3.014678	790	790
25.0	3.014741	741	741
26.0	3.014784	631	631
27.0	3.014812	589	589
28.0	3.014831	569	569
29.0	3.014843	510	510
30.0	3.014851	470	470
31.0	3.014857	451	451
32.0	3.014861	390	390
33.0	3.014863	353	353
34.0	3.014865	350	350
35.0	3.014866	326	326
36.0	3.014867	346	346
37.0	3.014867	264	264
38.0	3.014868	276	276
39.0	3.014868	257	257
40.0	3.014868	265	265
41.0	3.014868	216	216
42.0	3.014868	218	218
43.0	3.014868	210	210
44.0	3.014868	187	187
45.0	3.014868	206	206
46.0	3.014868	181	181
47.0	3.014868	183	183
48.0	3.014868	187	187
49.0	3.014868	167	167
50.0	3.014868	159	159
51.0	3.014868	140	140
52.0	3.014868	149	149
53.0	3.014868	151	151
54.0	3.014868	130	130
55.0	3.014868	118	118
56.0	3.014868	106	106
57.0	3.014868	102	102
58.0	3.014868	90	90
59.0	3.014868	110	110
60.0	3.014868	86	86
61.0	3.014868	89	89
62.0	3.014868	91	91
63.0	3.014868	99	99
64.0	3.014868	81	81
65.0	3.014868	104	104
66.0	3.014868	67	67
67.0	3.014868	73	73
68.0	3.014868	83	83
69.0	3.014868	64	64
70.0	3.014868	67	67
71.0	3.014868	60	60
72.0	3.014868	68	68
73.0	3.014868	67	67
74.0	3.014868	58	58
75.0	3.014868	66	66
76.0	3.014868	47	47
77.0	3.014868	65	65
78.0	3.014868	60	60
79.0	3.014868	53	53
80.0	3.014868	41	41
81.0	3.014868	46	46
82.0	3.014868	50	50
83.0	3.014868	39	39
84.0	3.014868	52	52
85.0	3.014868	56	56
86.0	3.014868	43	43
87.0	3.014868	52	52
88.0	3.014868	48	48
89.0	3.014868	36	36
90.0	3.014868	43	43
91.0	3.014868	40	40
92.0	3.014868	31	31
93.0	3.014868	43	43
94.0	3.014868	42	42
95.0	3.014868	32	32
96.0	3.014868	35	35
97.0	3.014868	31	31
98.0	3.014868	38	38
99.0	3.014868	29	29
100.0	3.014868	27	27
101.0	0	25	25
102.0	0	31	31
103.0	0	31	31
104.0	0	25	25
105.0	0	24	24
106.0	0	25	25
107.0	0	36	36
108.0	0	31	31
109.0	0	26	26
110.0	0	35	35
111.0	0	34	34
112.0	0	26	26
113.0	0	23	23
114.0	0	21	21
115.0	0	21	21
116.0	0	24	24
117.0	0	15	15
118.0	0	19	19
119.0	0	20	20
120.0	0	24	24
121.0	0	20	20
122.0	0	18	18
123.0	0	27	27
124.0	0	14	14
125.0	0	22	22
126.0	0	25	25
127.0	0	16	16
128.0	0	18	18
129.0	0	25	25
130.0	0	15	15
131.0	0	24	24
132.0	0	18	18
133.0	0	19	19
134.0	0	21	21
135.0	0	11	11
136.0	0	20	20
137.0	0	10	10
138.0	0	19	19
139.0	0	11	11
140.0	0	9	9
141.0	0	14	14
142.0	0	22	22
143.0	0	15	15
144.0	0	21	21
145.0	0	13	13
146.0	0	12	12
147.0	0	17	17
148.0	0	18	18
149.0	0	15	15
150.0	0	12	12
151.0	0	15	15
152.0	0	14	14
153.0	0	11	11
154.0	0	15	15
155.0	0	16	16
156.0	0	18	18
157.0	0	9	9
158.0	0	7	7
159.0	0	11	11
160.0	0	12	12
161.0	0	16	16
162.0	0	10	10
163.0	0	20	20
164.0	0	14	14
165.0	0	11	11
166.0	0	15	15
167.0	0	11	11
168.0	0	10	10
169.0	0	5	5
170.0	0	9	9
171.0	0	10	10
172.0	0	9	9
173.0	0	9	9
174.0	0	13	13
175.0	0	24	24
176.0	0	10	10
177.0	0	7	7
178.0	0	11	11
179.0	0	14	14
180.0	0	7	7
181.0	0	11	11
182.0	0	8	8
183.0	0	10	10
184.0	0	13	13
185.0	0	2	2
186.0	0	11	11
187.0	0	17	17
188.0	0	9	9
189.0	0	9	9
190.0	0	8	8
191.0	0	4	4
192.0	0	12	12
193.0	0	9	9
194.0	0	9	9
195.0	0	5	5
196.0	0	5	5
197.0	0	8	8
198.0	0	9	9
199.0	0	12	12
200.0	0	4	4
201.0	0	8	8
202.0	0	12	12
203.0	0	7	7
204.0	0	8	8
205.0	0	10	10
206.0	0	5	5
207.0	0	9	9
208.0	0	7	7
209.0	0	10	10
210.0	0	8	8
211.0	0	9	9
212.0	0	4	4
213.0	0	4	4
214.0	0	6	6
215.0	0	3	3
216.0	0	3	3
217.0	0	9	9
218.0	0	5	5
219.0	0	7	7
220.0	0	6	6
221.0	0	6	6
222.0	0	11	11
223.0	0	6	6
224.0	0	5	5
225.0	0	3	3
226.0	0	5	5
227.0	0	9	9
228.0	0	5	5
229.0	0	5	5
230.0	0	7	7
231.0	0	8	8
232.0	0	5	5
233.0	0	6	6
234.0	0	7	7
235.0	0	8	8
236.0	0	5	5
237.0	0	8	8
238.0	0	2	2
239.0	0	2	2
240.0	0	7	7
241.0	0	3	3
242.0	0	8	8
243.0	0	6	6
244.0	0	5	5
245.0	0	6	6
246.0	0	3	3
247.0	0	9	9
248.0	0	6	6
249.0	0	4	4
250.0	0	4	4
251.0	0	2	2
252.0	0	2	2
253.0	0	4	4
254.0	0	4	4
255.0	0	9	9
256.0	0	4	4
257.0	0	8	8
258.0	0	4	4
259.0	0	4	4
260.0	0	6	6
261.0	0	5	5
262.0	0	4	4
263.0	0	3	3
264.0	0	5	5
265.0	0	4	4
266.0	0	4	4
267.0	0	6	6
268.0	0	2	2
269.0	0	2	2
270.0	0	4	4
271.0	0	3	3
272.0	0	2	2
273.0	0	5	5
274.0	0	5	5
275.0	0	5	5
276.0	0	4	4
277.0	0	6	6
278.0	0	4	4
279.0	0	5	5
280.0	0	3	3
281.0	0	5	5
282.0	0	3	3
283.0	0	2	2
284.0	0	3	3
285.0	0	4	4
286.0	0	1	1
287.0	0	5	5
288.0	0	6	6
289.0	0	4	4
290.0	0	1	1
291.0	0	3	3
292.0	0	7	7
293.0	0	2	2
294.0	0	4	4
295.0	0	4	4
296.0	0	3	3
297.0	0	4	4
298.0	0	5	5
299.0	0	6	6
300.0	0	4	4
301.0	0	5	5
302.0	0	3	3
303.0	0	3	3
304.0	0	2	2
305.0	0	4	4
306.0	0	1	1
307.0	0	3	3
308.0	0	6	6
309.0	0	2	2
310.0	0	4	4
311.0	0	6	6
312.0	0	1	1
313.0	0	4	4
314.0	0	5	5
316.0	0	3	3
317.0	0	2	2
318.0	0	4	4
319.0	0	2	2
320.0	0	1	1
321.0	0	1	1
322.0	0	2	2
323.0	0	1	1
324.0	0	2	2
325.0	0	3	3
326.0	0	2	2
327.0	0	5	5
328.0	0	2	2
329.0	0	2	2
330.0	0	2	2
331.0	0	3	3
332.0	0	6	6
333.0	0	4	4
334.0	0	3	3
335.0	0	4	4
336.0	0	5	5
337.0	0	4	4
338.0	0	1	1
339.0	0	2	2
340.0	0	1	1
342.0	0	1	1
343.0	0	3	3
344.0	0	2	2
345.0	0	3	3
346.0	0	2	2
347.0	0	1	1
348.0	0	1	1
349.0	0	2	2
350.0	0	2	2
351.0	0	3	3
352.0	0	2	2
353.0	0	1	1
354.0	0	3	3
355.0	0	3	3
356.0	0	2	2
357.0	0	4	4
358.0	0	3	3
359.0	0	1	1
360.0	0	2	2
361.0	0	1	1
362.0	0	2	2
365.0	0	1	1
366.0	0	2	2
367.0	0	1	1
368.0	0	5	5
369.0	0	2	2
370.0	0	3	3
371.0	0	4	4
372.0	0	2	2
373.0	0	1	1
374.0	0	2	2
375.0	0	2	2
376.0	0	5	5
377.0	0	3	3
379.0	0	2	2
380.0	0	4	4
382.0	0	2	2
385.0	0	3	3
386.0	0	2	2
387.0	0	2	2
388.0	0	3	3
389.0	0	2	2
390.0	0	1	1
391.0	0	3	3
393.0	0	2	2
395.0	0	1	1
396.0	0	1	1
397.0	0	1	1
398.0	0	2	2
399.0	0	3	3
400.0	0	2	2
401.0	0	4	4
402.0	0	2	2
405.0	0	1	1
406.0	0	3	3
407.0	0	4	4
409.0	0	2	2
411.0	0	3	3
413.0	0	1	1
415.0	0	4	4
418.0	0	1	1
419.0	0	3	3
420.0	0	3	3
421.0	0	1	1
422.0	0	1	1
425.0	0	2	2
426.0	0	1	1
428.0	0	1	1
429.0	0	3	3
430.0	0	1	1
431.0	0	1	1
432.0	0	5	5
433.0	0	4	4
434.0	0	1	1
436.0	0	1	1
437.0	0	2	2
438.0	0	1	1
439.0	0	1	1
440.0	0	2	2
441.0	0	2	2
443.0	0	1	1
444.0	0	1	1
445.0	0	1	1
446.0	0	2	2
447.0	0	1	1
448.0	0	2	2
449.0	0	1	1
451.0	0	4	4
453.0	0	1	1
454.0	0	3	3
455.0	0	1	1
456.0	0	3	3
458.0	0	1	1
459.0	0	2	2
460.0	0	4	4
461.0	0	1	1
462.0	0	2	2
463.0	0	1	1
465.0	0	1	1
466.0	0	2	2
467.0	0	1	1
468.0	0	2	2
470.0	0	1	1
471.0	0	1	1
473.0	0	1	1
474.0	0	3	3
475.0	0	2	2
476.0	0	2	2
479.0	0	1	1
482.0	0	1	1
483.0	0	2	2
484.0	0	2	2
485.0	0	1	1
488.0	0	1	1
491.0	0	2	2
493.0	0	2	2
494.0	0	2	2
495.0	0	2	2
499.0	0	2	2
504.0	0	1	1
505.0	0	1	1
506.0	0	1	1
508.0	0	1	1
509.0	0	1	1
510.0	0	1	1
511.0	0	1	1
514.0	0	1	1
517.0	0	1	1
520.0	0	1	1
521.0	0	1	1
522.0	0	3	3
523.0	0	1	1
524.0	0	1	1
527.0	0	1	1
528.0	0	2	2
532.0	0	1	1
533.0	0	1	1
534.0	0	1	1
535.0	0	4	4
538.0	0	2	2
539.0	0	2	2
541.0	0	2	2
543.0	0	2	2
544.0	0	1	1
546.0	0	1	1
548.0	0	1	1
554.0	0	1	1
557.0	0	1	1
559.0	0	1	1
562.0	0	1	1
563.0	0	2	2
564.0	0	4	4
567.0	0	1	1
574.0	0	1	1
576.0	0	1	1
578.0	0	1	1
581.0	0	1	1
583.0	0	2	2
585.0	0	1	1
587.0	0	1	1
588.0	0	1	1
590.0	0	1	1
591.0	0	1	1
592.0	0	1	1
593.0	0	1	1
598.0	0	1	1
603.0	0	1	1
604.0	0	3	3
605.0	0	1	1
606.0	0	1	1
608.0	0	1	1
609.0	0	1	1
611.0	0	1	1
612.0	0	1	1
613.0	0	1	1
616.0	0	1	1
618.0	0	1	1
621.0	0	1	1
622.0	0	1	1
626.0	0	1	1
629.0	0	1	1
635.0	0	1	1
637.0	0	1	1
638.0	0	1	1
641.0	0	1	1
643.0	0	1	1
645.0	0	1	1
649.0	0	1	1
651.0	0	1	1
652.0	0	1	1
656.0	0	1	1
659.0	0	1	1
660.0	0	1	1
672.0	0	1	1
674.0	0	1	1
678.0	0	2	2
680.0	0	1	1
681.0	0	1	1
682.0	0	1	1
686.0	0	1	1
691.0	0	1	1
692.0	0	1	1
694.0	0	2	2
706.0	0	1	1
707.0	0	3	3
715.0	0	1	1
719.0	0	2	2
728.0	0	1	1
735.0	0	1	1
746.0	0	1	1
748.0	0	1	1
750.0	0	1	1
751.0	0	2	2
754.0	0	1	1
756.0	0	1	1
761.0	0	2	2
766.0	0	1	1
768.0	0	1	1
779.0	0	1	1
792.0	0	2	2
799.0	0	1	1
805.0	0	1	1
810.0	0	1	1
811.0	0	2	2
813.0	0	1	1
814.0	0	1	1
821.0	0	1	1
827.0	0	1	1
828.0	0	1	1
836.0	0	1	1
840.0	0	1	1
841.0	0	2	2
848.0	0	1	1
852.0	0	1	1
854.0	0	1	1
856.0	0	1	1
859.0	0	1	1
864.0	0	1	1
871.0	0	1	1
886.0	0	1	1
897.0	0	1	1
903.0	0	1	1
905.0	0	2	2
908.0	0	1	1
913.0	0	2	2
929.0	0	1	1
947.0	0	1	1
954.0	0	1	1
970.0	0	2	2
972.0	0	1	1
977.0	0	1	1
982.0	0	1	1
988.0	0	1	1
990.0	0	1	1
1051.0	0	1	1
1060.0	0	1	1
1076.0	0	1	1
1114.0	0	1	1
1168.0	0	1	1
1231.0	0	1	1
1247.0	0	1	1
1262.0	0	1	1
1302.0	0	1	1
1315.0	0	1	1
1362.0	0	1	1
1398.0	0	1	1
1405.0	0	1	1
1421.0	0	1	1
1466.0	0	1	1
1489.0	0	1	1
1556.0	0	1	1
1586.0	0	1	1
1614.0	0	1	1
1755.0	0	1	1
1794.0	0	1	1
1799.0	0	1	1
1816.0	0	1	1
1842.0	0	1	1
1863.0	0	1	1
1887.0	0	1	1
2037.0	0	1	1
2042.0	0	1	1
2061.0	0	1	1
2267.0	0	1	1
2596.0	0	1	1
2616.0	0	1	1
2699.0	0	1	1
3590.0	0	1	1
3857.0	0	1	1
3912.0	0	1	1
4730.0	0	1	1