## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/bwa-mem2/hg38-GSM4728094.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-GSM4728094.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-GSM4728094.samtools-coordinate.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/scratch/jsmits/tmp/GZnl]    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 ADD_PG_TAG_TO_READS=true 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu Feb 18 16:57:08 CET 2021

## 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	7958	49446106	0	0	5281	10782472	0	0.218101	96211798

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	30638437	30638437
2.0	1.59814	6363568	6363568
3.0	1.955912	1270284	1270284
4.0	2.16991	261474	261474
5.0	2.297911	59721	59721
6.0	2.374473	16660	16660
7.0	2.420268	6094	6094
8.0	2.44766	2869	2869
9.0	2.464045	1730	1730
10.0	2.473845	1118	1118
11.0	2.479706	791	791
12.0	2.483213	615	615
13.0	2.48531	463	463
14.0	2.486564	404	404
15.0	2.487315	322	322
16.0	2.487763	285	285
17.0	2.488032	266	266
18.0	2.488192	216	216
19.0	2.488288	224	224
20.0	2.488346	194	194
21.0	2.48838	164	164
22.0	2.488401	153	153
23.0	2.488413	155	155
24.0	2.48842	135	135
25.0	2.488425	135	135
26.0	2.488427	142	142
27.0	2.488429	107	107
28.0	2.48843	90	90
29.0	2.48843	99	99
30.0	2.488431	106	106
31.0	2.488431	92	92
32.0	2.488431	91	91
33.0	2.488431	63	63
34.0	2.488431	71	71
35.0	2.488431	74	74
36.0	2.488431	75	75
37.0	2.488431	70	70
38.0	2.488431	74	74
39.0	2.488431	68	68
40.0	2.488431	65	65
41.0	2.488431	49	49
42.0	2.488431	39	39
43.0	2.488431	54	54
44.0	2.488431	44	44
45.0	2.488431	50	50
46.0	2.488431	50	50
47.0	2.488431	41	41
48.0	2.488431	39	39
49.0	2.488431	34	34
50.0	2.488431	28	28
51.0	2.488431	40	40
52.0	2.488431	26	26
53.0	2.488431	38	38
54.0	2.488431	32	32
55.0	2.488431	36	36
56.0	2.488431	32	32
57.0	2.488431	33	33
58.0	2.488431	25	25
59.0	2.488431	31	31
60.0	2.488431	25	25
61.0	2.488431	22	22
62.0	2.488431	35	35
63.0	2.488431	31	31
64.0	2.488431	27	27
65.0	2.488431	24	24
66.0	2.488431	28	28
67.0	2.488431	17	17
68.0	2.488431	31	31
69.0	2.488431	19	19
70.0	2.488431	31	31
71.0	2.488431	19	19
72.0	2.488431	20	20
73.0	2.488431	13	13
74.0	2.488431	28	28
75.0	2.488431	21	21
76.0	2.488431	14	14
77.0	2.488431	18	18
78.0	2.488431	17	17
79.0	2.488431	16	16
80.0	2.488431	14	14
81.0	2.488431	18	18
82.0	2.488431	18	18
83.0	2.488431	17	17
84.0	2.488431	12	12
85.0	2.488431	10	10
86.0	2.488431	7	7
87.0	2.488431	17	17
88.0	2.488431	10	10
89.0	2.488431	10	10
90.0	2.488431	10	10
91.0	2.488431	14	14
92.0	2.488431	11	11
93.0	2.488431	12	12
94.0	2.488431	14	14
95.0	2.488431	15	15
96.0	2.488431	9	9
97.0	2.488431	13	13
98.0	2.488431	22	22
99.0	2.488431	8	8
100.0	2.488431	7	7
101.0	0	8	8
102.0	0	11	11
103.0	0	3	3
104.0	0	7	7
105.0	0	13	13
106.0	0	7	7
107.0	0	15	15
108.0	0	8	8
109.0	0	13	13
110.0	0	6	6
111.0	0	11	11
112.0	0	14	14
113.0	0	7	7
114.0	0	8	8
115.0	0	8	8
116.0	0	11	11
117.0	0	10	10
118.0	0	11	11
119.0	0	6	6
120.0	0	5	5
121.0	0	6	6
122.0	0	9	9
123.0	0	11	11
124.0	0	11	11
125.0	0	9	9
126.0	0	4	4
127.0	0	4	4
128.0	0	9	9
129.0	0	6	6
130.0	0	10	10
131.0	0	3	3
132.0	0	8	8
133.0	0	4	4
134.0	0	5	5
135.0	0	4	4
136.0	0	8	8
137.0	0	6	6
138.0	0	5	5
139.0	0	4	4
140.0	0	5	5
141.0	0	4	4
142.0	0	3	3
143.0	0	7	7
144.0	0	13	13
145.0	0	4	4
146.0	0	3	3
147.0	0	4	4
148.0	0	5	5
149.0	0	5	5
150.0	0	4	4
151.0	0	8	8
152.0	0	3	3
153.0	0	2	2
154.0	0	5	5
155.0	0	6	6
156.0	0	4	4
157.0	0	9	9
158.0	0	5	5
159.0	0	4	4
160.0	0	10	10
161.0	0	4	4
162.0	0	4	4
163.0	0	7	7
164.0	0	8	8
165.0	0	4	4
166.0	0	3	3
167.0	0	4	4
168.0	0	4	4
169.0	0	3	3
170.0	0	2	2
171.0	0	4	4
172.0	0	5	5
173.0	0	11	11
174.0	0	5	5
175.0	0	5	5
176.0	0	5	5
177.0	0	6	6
178.0	0	6	6
179.0	0	3	3
180.0	0	3	3
181.0	0	5	5
182.0	0	8	8
183.0	0	4	4
185.0	0	5	5
186.0	0	6	6
187.0	0	3	3
188.0	0	4	4
189.0	0	4	4
190.0	0	5	5
191.0	0	5	5
192.0	0	4	4
193.0	0	7	7
194.0	0	3	3
195.0	0	6	6
196.0	0	7	7
197.0	0	3	3
198.0	0	3	3
199.0	0	5	5
200.0	0	4	4
201.0	0	3	3
202.0	0	1	1
203.0	0	5	5
204.0	0	5	5
205.0	0	4	4
206.0	0	4	4
207.0	0	7	7
208.0	0	2	2
209.0	0	3	3
210.0	0	7	7
211.0	0	4	4
212.0	0	3	3
213.0	0	5	5
214.0	0	1	1
215.0	0	3	3
216.0	0	2	2
217.0	0	1	1
218.0	0	5	5
219.0	0	3	3
220.0	0	3	3
221.0	0	5	5
222.0	0	1	1
223.0	0	5	5
224.0	0	3	3
225.0	0	4	4
226.0	0	2	2
227.0	0	1	1
228.0	0	3	3
229.0	0	4	4
231.0	0	2	2
232.0	0	3	3
233.0	0	5	5
234.0	0	1	1
235.0	0	4	4
236.0	0	3	3
237.0	0	6	6
238.0	0	4	4
239.0	0	2	2
240.0	0	5	5
241.0	0	2	2
242.0	0	2	2
243.0	0	2	2
245.0	0	2	2
246.0	0	1	1
247.0	0	2	2
248.0	0	3	3
249.0	0	2	2
250.0	0	2	2
251.0	0	5	5
252.0	0	5	5
253.0	0	1	1
255.0	0	1	1
256.0	0	4	4
257.0	0	1	1
258.0	0	3	3
259.0	0	2	2
260.0	0	2	2
261.0	0	2	2
262.0	0	2	2
263.0	0	3	3
264.0	0	1	1
265.0	0	5	5
266.0	0	1	1
267.0	0	1	1
268.0	0	2	2
269.0	0	3	3
270.0	0	4	4
271.0	0	3	3
272.0	0	3	3
273.0	0	4	4
274.0	0	2	2
276.0	0	3	3
277.0	0	1	1
278.0	0	1	1
279.0	0	2	2
281.0	0	4	4
282.0	0	2	2
283.0	0	3	3
284.0	0	1	1
285.0	0	1	1
287.0	0	1	1
288.0	0	4	4
289.0	0	6	6
290.0	0	2	2
291.0	0	1	1
293.0	0	3	3
294.0	0	1	1
295.0	0	3	3
296.0	0	2	2
297.0	0	5	5
299.0	0	3	3
300.0	0	1	1
301.0	0	4	4
304.0	0	3	3
305.0	0	2	2
306.0	0	4	4
307.0	0	2	2
308.0	0	1	1
310.0	0	1	1
311.0	0	1	1
312.0	0	2	2
313.0	0	2	2
314.0	0	2	2
315.0	0	5	5
317.0	0	1	1
318.0	0	3	3
319.0	0	1	1
320.0	0	2	2
321.0	0	1	1
322.0	0	2	2
323.0	0	2	2
324.0	0	3	3
325.0	0	2	2
328.0	0	1	1
331.0	0	1	1
332.0	0	1	1
333.0	0	1	1
334.0	0	1	1
336.0	0	3	3
338.0	0	2	2
339.0	0	3	3
340.0	0	1	1
341.0	0	4	4
343.0	0	1	1
344.0	0	1	1
345.0	0	1	1
346.0	0	2	2
348.0	0	2	2
349.0	0	2	2
350.0	0	1	1
352.0	0	3	3
354.0	0	1	1
355.0	0	1	1
357.0	0	3	3
358.0	0	4	4
359.0	0	1	1
360.0	0	3	3
361.0	0	1	1
364.0	0	1	1
366.0	0	3	3
368.0	0	1	1
369.0	0	2	2
370.0	0	2	2
371.0	0	1	1
375.0	0	1	1
376.0	0	3	3
378.0	0	2	2
379.0	0	5	5
380.0	0	2	2
381.0	0	2	2
382.0	0	2	2
383.0	0	2	2
385.0	0	1	1
386.0	0	1	1
387.0	0	2	2
388.0	0	2	2
389.0	0	2	2
391.0	0	1	1
393.0	0	1	1
394.0	0	2	2
396.0	0	1	1
397.0	0	1	1
399.0	0	1	1
400.0	0	1	1
401.0	0	1	1
404.0	0	1	1
405.0	0	2	2
407.0	0	1	1
408.0	0	2	2
409.0	0	2	2
410.0	0	2	2
411.0	0	1	1
412.0	0	2	2
413.0	0	1	1
415.0	0	1	1
417.0	0	1	1
421.0	0	1	1
422.0	0	2	2
423.0	0	1	1
428.0	0	3	3
429.0	0	2	2
432.0	0	1	1
433.0	0	1	1
435.0	0	1	1
436.0	0	1	1
437.0	0	1	1
439.0	0	1	1
440.0	0	2	2
441.0	0	1	1
442.0	0	1	1
444.0	0	1	1
447.0	0	1	1
450.0	0	2	2
452.0	0	3	3
454.0	0	1	1
455.0	0	1	1
457.0	0	2	2
459.0	0	1	1
460.0	0	1	1
461.0	0	1	1
463.0	0	2	2
468.0	0	1	1
469.0	0	2	2
471.0	0	2	2
472.0	0	1	1
473.0	0	1	1
475.0	0	1	1
476.0	0	1	1
477.0	0	1	1
478.0	0	2	2
479.0	0	1	1
480.0	0	3	3
483.0	0	2	2
484.0	0	2	2
485.0	0	1	1
487.0	0	4	4
488.0	0	4	4
489.0	0	1	1
493.0	0	2	2
494.0	0	1	1
495.0	0	1	1
497.0	0	1	1
499.0	0	2	2
501.0	0	2	2
502.0	0	4	4
503.0	0	2	2
509.0	0	1	1
510.0	0	1	1
511.0	0	1	1
514.0	0	1	1
518.0	0	2	2
520.0	0	1	1
521.0	0	1	1
523.0	0	1	1
526.0	0	1	1
533.0	0	1	1
535.0	0	1	1
539.0	0	1	1
541.0	0	2	2
542.0	0	1	1
543.0	0	1	1
546.0	0	1	1
547.0	0	1	1
548.0	0	1	1
551.0	0	1	1
552.0	0	1	1
556.0	0	1	1
561.0	0	1	1
563.0	0	2	2
564.0	0	1	1
565.0	0	2	2
568.0	0	1	1
575.0	0	1	1
577.0	0	1	1
580.0	0	1	1
582.0	0	1	1
583.0	0	2	2
586.0	0	1	1
589.0	0	1	1
596.0	0	1	1
598.0	0	1	1
602.0	0	3	3
606.0	0	1	1
607.0	0	2	2
614.0	0	1	1
617.0	0	1	1
619.0	0	1	1
620.0	0	1	1
623.0	0	1	1
625.0	0	1	1
627.0	0	1	1
630.0	0	1	1
636.0	0	1	1
637.0	0	1	1
639.0	0	1	1
642.0	0	1	1
644.0	0	1	1
652.0	0	1	1
658.0	0	1	1
661.0	0	1	1
663.0	0	1	1
665.0	0	1	1
673.0	0	1	1
677.0	0	1	1
678.0	0	1	1
679.0	0	1	1
684.0	0	1	1
688.0	0	1	1
689.0	0	1	1
690.0	0	1	1
694.0	0	2	2
715.0	0	1	1
717.0	0	1	1
728.0	0	1	1
732.0	0	1	1
733.0	0	1	1
734.0	0	1	1
736.0	0	1	1
738.0	0	1	1
739.0	0	1	1
754.0	0	1	1
762.0	0	1	1
763.0	0	1	1
764.0	0	1	1
766.0	0	1	1
772.0	0	1	1
777.0	0	1	1
778.0	0	1	1
784.0	0	1	1
790.0	0	1	1
792.0	0	1	1
795.0	0	1	1
796.0	0	1	1
802.0	0	1	1
803.0	0	1	1
816.0	0	1	1
830.0	0	1	1
833.0	0	1	1
835.0	0	1	1
841.0	0	1	1
846.0	0	2	2
848.0	0	1	1
853.0	0	1	1
863.0	0	1	1
865.0	0	1	1
866.0	0	1	1
873.0	0	1	1
876.0	0	1	1
879.0	0	1	1
884.0	0	1	1
887.0	0	1	1
893.0	0	1	1
907.0	0	3	3
909.0	0	1	1
910.0	0	1	1
916.0	0	1	1
919.0	0	1	1
923.0	0	1	1
940.0	0	1	1
944.0	0	1	1
953.0	0	1	1
959.0	0	1	1
975.0	0	1	1
980.0	0	1	1
990.0	0	1	1
992.0	0	1	1
1017.0	0	2	2
1018.0	0	1	1
1019.0	0	1	1
1025.0	0	1	1
1028.0	0	1	1
1035.0	0	1	1
1041.0	0	1	1
1045.0	0	1	1
1051.0	0	1	1
1061.0	0	1	1
1065.0	0	1	1
1074.0	0	1	1
1079.0	0	1	1
1093.0	0	1	1
1120.0	0	1	1
1128.0	0	1	1
1145.0	0	1	1
1163.0	0	1	1
1167.0	0	1	1
1202.0	0	1	1
1211.0	0	1	1
1259.0	0	1	1
1262.0	0	1	1
1265.0	0	1	1
1282.0	0	1	1
1288.0	0	1	1
1322.0	0	1	1
1331.0	0	1	1
1363.0	0	1	1
1367.0	0	1	1
1376.0	0	1	1
1439.0	0	1	1
1442.0	0	1	1
1457.0	0	1	1
1476.0	0	1	1
1483.0	0	1	1
1506.0	0	1	1
1507.0	0	1	1
1515.0	0	1	1
1530.0	0	1	1
1564.0	0	1	1
1587.0	0	1	1
1615.0	0	1	1
1636.0	0	1	1
1662.0	0	1	1
1864.0	0	1	1
1903.0	0	1	1
2012.0	0	1	1
2016.0	0	1	1
2111.0	0	1	1
2127.0	0	1	1
2154.0	0	1	1
2285.0	0	1	1
2305.0	0	1	1
2385.0	0	1	1
2454.0	0	1	1
2793.0	0	1	1
2806.0	0	1	1
2866.0	0	1	1
2934.0	0	1	1
2991.0	0	1	1
3074.0	0	1	1
3142.0	0	1	1
3281.0	0	1	1
3377.0	0	1	1
3448.0	0	1	1
3660.0	0	1	1
3673.0	0	1	1
3695.0	0	1	1
4060.0	0	1	1
4326.0	0	1	1
4569.0	0	1	1
4925.0	0	1	1
6299.0	0	1	1
6589.0	0	1	1
7320.0	0	1	1