## 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-GSM4728093.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-GSM4728093.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-GSM4728093.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 16:45:58 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	5662	45929543	0	0	3092	9754965	0	0.21241	92202095

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	28686029	28686029
2.0	1.60766	5958086	5958086
3.0	1.97691	1180596	1180596
4.0	2.201289	238408	238408
5.0	2.337635	52293	52293
6.0	2.420487	13493	13493
7.0	2.470833	4561	4561
8.0	2.501426	2018	2018
9.0	2.520016	1094	1094
10.0	2.531313	696	696
11.0	2.538177	532	532
12.0	2.542349	404	404
13.0	2.544883	299	299
14.0	2.546424	260	260
15.0	2.54736	243	243
16.0	2.547928	220	220
17.0	2.548274	181	181
18.0	2.548484	172	172
19.0	2.548611	176	176
20.0	2.548689	129	129
21.0	2.548736	108	108
22.0	2.548765	101	101
23.0	2.548782	108	108
24.0	2.548793	88	88
25.0	2.548799	90	90
26.0	2.548803	94	94
27.0	2.548805	70	70
28.0	2.548807	82	82
29.0	2.548808	63	63
30.0	2.548808	62	62
31.0	2.548809	60	60
32.0	2.548809	67	67
33.0	2.548809	57	57
34.0	2.548809	55	55
35.0	2.548809	51	51
36.0	2.548809	50	50
37.0	2.548809	52	52
38.0	2.548809	40	40
39.0	2.548809	40	40
40.0	2.548809	37	37
41.0	2.548809	43	43
42.0	2.548809	30	30
43.0	2.548809	28	28
44.0	2.548809	23	23
45.0	2.548809	30	30
46.0	2.548809	34	34
47.0	2.548809	27	27
48.0	2.548809	29	29
49.0	2.548809	32	32
50.0	2.548809	21	21
51.0	2.548809	28	28
52.0	2.548809	19	19
53.0	2.548809	25	25
54.0	2.548809	25	25
55.0	2.548809	25	25
56.0	2.548809	19	19
57.0	2.548809	23	23
58.0	2.548809	22	22
59.0	2.548809	18	18
60.0	2.548809	24	24
61.0	2.548809	19	19
62.0	2.548809	18	18
63.0	2.548809	20	20
64.0	2.548809	18	18
65.0	2.548809	20	20
66.0	2.548809	22	22
67.0	2.548809	22	22
68.0	2.548809	9	9
69.0	2.548809	19	19
70.0	2.548809	11	11
71.0	2.548809	12	12
72.0	2.548809	11	11
73.0	2.548809	16	16
74.0	2.548809	9	9
75.0	2.548809	11	11
76.0	2.548809	11	11
77.0	2.548809	7	7
78.0	2.548809	4	4
79.0	2.548809	14	14
80.0	2.548809	13	13
81.0	2.548809	9	9
82.0	2.548809	11	11
83.0	2.548809	9	9
84.0	2.548809	10	10
85.0	2.548809	9	9
86.0	2.548809	16	16
87.0	2.548809	8	8
88.0	2.548809	10	10
89.0	2.548809	8	8
90.0	2.548809	8	8
91.0	2.548809	8	8
92.0	2.548809	9	9
93.0	2.548809	9	9
94.0	2.548809	9	9
95.0	2.548809	11	11
96.0	2.548809	7	7
97.0	2.548809	12	12
98.0	2.548809	5	5
99.0	2.548809	14	14
100.0	2.548809	9	9
101.0	0	5	5
102.0	0	14	14
103.0	0	4	4
104.0	0	9	9
105.0	0	5	5
106.0	0	7	7
107.0	0	6	6
108.0	0	5	5
109.0	0	4	4
110.0	0	5	5
111.0	0	8	8
112.0	0	11	11
113.0	0	6	6
114.0	0	10	10
115.0	0	8	8
116.0	0	5	5
117.0	0	13	13
118.0	0	8	8
119.0	0	7	7
120.0	0	6	6
121.0	0	10	10
122.0	0	11	11
123.0	0	5	5
124.0	0	3	3
125.0	0	3	3
126.0	0	4	4
127.0	0	9	9
128.0	0	5	5
129.0	0	4	4
130.0	0	7	7
131.0	0	4	4
132.0	0	5	5
133.0	0	5	5
134.0	0	3	3
135.0	0	4	4
136.0	0	4	4
137.0	0	6	6
138.0	0	4	4
139.0	0	3	3
140.0	0	4	4
141.0	0	5	5
142.0	0	8	8
143.0	0	5	5
144.0	0	6	6
145.0	0	9	9
146.0	0	9	9
147.0	0	7	7
148.0	0	4	4
149.0	0	6	6
150.0	0	3	3
151.0	0	5	5
152.0	0	4	4
153.0	0	5	5
154.0	0	3	3
155.0	0	3	3
156.0	0	4	4
157.0	0	3	3
158.0	0	7	7
159.0	0	8	8
160.0	0	6	6
161.0	0	4	4
162.0	0	2	2
163.0	0	4	4
164.0	0	5	5
165.0	0	2	2
166.0	0	3	3
167.0	0	1	1
168.0	0	5	5
169.0	0	3	3
170.0	0	5	5
171.0	0	2	2
172.0	0	9	9
173.0	0	1	1
174.0	0	1	1
175.0	0	3	3
176.0	0	3	3
177.0	0	6	6
178.0	0	3	3
179.0	0	1	1
180.0	0	4	4
181.0	0	2	2
182.0	0	3	3
183.0	0	3	3
184.0	0	2	2
185.0	0	3	3
186.0	0	5	5
187.0	0	8	8
188.0	0	1	1
189.0	0	1	1
190.0	0	2	2
191.0	0	1	1
192.0	0	4	4
193.0	0	2	2
194.0	0	1	1
195.0	0	1	1
196.0	0	2	2
197.0	0	2	2
198.0	0	3	3
199.0	0	1	1
200.0	0	2	2
202.0	0	3	3
203.0	0	2	2
204.0	0	1	1
205.0	0	3	3
206.0	0	1	1
207.0	0	5	5
208.0	0	1	1
209.0	0	4	4
210.0	0	3	3
212.0	0	3	3
213.0	0	1	1
214.0	0	3	3
215.0	0	3	3
216.0	0	6	6
218.0	0	1	1
219.0	0	3	3
221.0	0	3	3
222.0	0	4	4
223.0	0	2	2
224.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	3	3
229.0	0	8	8
230.0	0	5	5
231.0	0	3	3
232.0	0	1	1
233.0	0	1	1
234.0	0	3	3
235.0	0	1	1
237.0	0	2	2
238.0	0	2	2
239.0	0	1	1
240.0	0	5	5
241.0	0	2	2
242.0	0	3	3
243.0	0	3	3
244.0	0	2	2
245.0	0	1	1
246.0	0	6	6
248.0	0	1	1
249.0	0	1	1
250.0	0	2	2
251.0	0	1	1
252.0	0	4	4
253.0	0	1	1
254.0	0	1	1
255.0	0	2	2
256.0	0	3	3
257.0	0	2	2
259.0	0	4	4
260.0	0	1	1
262.0	0	1	1
263.0	0	2	2
265.0	0	2	2
266.0	0	1	1
267.0	0	4	4
268.0	0	1	1
269.0	0	2	2
270.0	0	2	2
271.0	0	1	1
272.0	0	2	2
274.0	0	2	2
275.0	0	1	1
276.0	0	1	1
278.0	0	3	3
279.0	0	3	3
280.0	0	3	3
281.0	0	1	1
285.0	0	2	2
286.0	0	2	2
287.0	0	3	3
288.0	0	1	1
289.0	0	1	1
291.0	0	2	2
292.0	0	3	3
294.0	0	4	4
295.0	0	1	1
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	1	1
302.0	0	1	1
303.0	0	1	1
304.0	0	3	3
305.0	0	3	3
306.0	0	1	1
308.0	0	1	1
310.0	0	2	2
311.0	0	2	2
312.0	0	1	1
314.0	0	1	1
315.0	0	1	1
316.0	0	1	1
317.0	0	2	2
318.0	0	1	1
319.0	0	1	1
320.0	0	1	1
321.0	0	1	1
322.0	0	2	2
323.0	0	2	2
324.0	0	1	1
325.0	0	1	1
326.0	0	1	1
328.0	0	1	1
330.0	0	1	1
331.0	0	2	2
332.0	0	3	3
333.0	0	1	1
335.0	0	2	2
336.0	0	4	4
337.0	0	2	2
339.0	0	2	2
340.0	0	2	2
343.0	0	2	2
344.0	0	3	3
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
352.0	0	1	1
353.0	0	3	3
354.0	0	1	1
355.0	0	1	1
356.0	0	3	3
358.0	0	1	1
360.0	0	1	1
361.0	0	2	2
363.0	0	1	1
364.0	0	1	1
366.0	0	1	1
367.0	0	2	2
372.0	0	1	1
376.0	0	2	2
377.0	0	2	2
380.0	0	1	1
381.0	0	2	2
383.0	0	1	1
384.0	0	2	2
385.0	0	1	1
386.0	0	1	1
387.0	0	1	1
389.0	0	1	1
396.0	0	1	1
397.0	0	1	1
398.0	0	1	1
399.0	0	1	1
401.0	0	1	1
404.0	0	2	2
405.0	0	1	1
407.0	0	1	1
414.0	0	1	1
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
421.0	0	1	1
422.0	0	1	1
423.0	0	2	2
424.0	0	2	2
425.0	0	1	1
430.0	0	2	2
439.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	1	1
445.0	0	1	1
447.0	0	2	2
448.0	0	1	1
454.0	0	1	1
459.0	0	1	1
460.0	0	3	3
463.0	0	2	2
464.0	0	2	2
466.0	0	1	1
468.0	0	1	1
473.0	0	1	1
478.0	0	1	1
480.0	0	2	2
484.0	0	1	1
488.0	0	1	1
494.0	0	1	1
495.0	0	2	2
496.0	0	1	1
500.0	0	1	1
502.0	0	1	1
503.0	0	1	1
510.0	0	2	2
513.0	0	1	1
516.0	0	1	1
517.0	0	1	1
519.0	0	1	1
525.0	0	1	1
528.0	0	1	1
535.0	0	1	1
540.0	0	1	1
543.0	0	1	1
545.0	0	1	1
551.0	0	1	1
564.0	0	1	1
566.0	0	1	1
572.0	0	2	2
578.0	0	1	1
579.0	0	2	2
583.0	0	1	1
587.0	0	1	1
590.0	0	2	2
596.0	0	1	1
597.0	0	1	1
602.0	0	2	2
604.0	0	2	2
621.0	0	1	1
622.0	0	1	1
623.0	0	1	1
624.0	0	2	2
629.0	0	1	1
635.0	0	1	1
641.0	0	1	1
644.0	0	1	1
646.0	0	1	1
651.0	0	1	1
652.0	0	1	1
654.0	0	1	1
661.0	0	2	2
664.0	0	1	1
675.0	0	2	2
677.0	0	1	1
684.0	0	1	1
712.0	0	1	1
722.0	0	1	1
723.0	0	3	3
725.0	0	1	1
728.0	0	1	1
735.0	0	1	1
736.0	0	1	1
746.0	0	1	1
748.0	0	1	1
749.0	0	1	1
751.0	0	1	1
754.0	0	1	1
762.0	0	1	1
773.0	0	1	1
775.0	0	1	1
799.0	0	1	1
802.0	0	1	1
815.0	0	1	1
841.0	0	1	1
851.0	0	1	1
886.0	0	1	1
894.0	0	1	1
926.0	0	1	1
984.0	0	1	1
990.0	0	1	1
991.0	0	1	1
1045.0	0	1	1
1067.0	0	1	1
1105.0	0	2	2
1113.0	0	1	1
1169.0	0	1	1
1180.0	0	1	1
1204.0	0	1	1
1206.0	0	1	1
1235.0	0	1	1
1330.0	0	1	1
1384.0	0	1	1
1711.0	0	1	1
1806.0	0	1	1
1949.0	0	1	1
2058.0	0	1	1
2079.0	0	1	1
2991.0	0	1	1
5512.0	0	1	1