## 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-GSM2400261.samtools-coordinate-sievsort.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/final_bam/hg38-GSM2400261.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/zhou/jsmits/Ananse_test_data/ATAC/results/qc/markdup/hg38-GSM2400261.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: Fri Feb 19 02:07:45 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	245239	89587863	0	0	95314	25554042	0	0.285381	125488963

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	46704534	46704534
2.0	1.489725	12982557	12982557
3.0	1.729557	3084495	3084495
4.0	1.847008	703476	703476
5.0	1.904527	153176	153176
6.0	1.932695	33574	33574
7.0	1.94649	8256	8256
8.0	1.953246	2706	2706
9.0	1.956554	1229	1229
10.0	1.958174	720	720
11.0	1.958968	494	494
12.0	1.959356	352	352
13.0	1.959547	265	265
14.0	1.95964	244	244
15.0	1.959686	181	181
16.0	1.959708	129	129
17.0	1.959719	117	117
18.0	1.959724	100	100
19.0	1.959727	85	85
20.0	1.959728	83	83
21.0	1.959729	73	73
22.0	1.959729	59	59
23.0	1.959729	45	45
24.0	1.959729	37	37
25.0	1.959729	43	43
26.0	1.959729	47	47
27.0	1.959729	32	32
28.0	1.959729	31	31
29.0	1.959729	31	31
30.0	1.959729	26	26
31.0	1.959729	20	20
32.0	1.959729	22	22
33.0	1.959729	21	21
34.0	1.959729	24	24
35.0	1.959729	16	16
36.0	1.959729	16	16
37.0	1.959729	18	18
38.0	1.959729	20	20
39.0	1.959729	13	13
40.0	1.959729	11	11
41.0	1.959729	20	20
42.0	1.959729	13	13
43.0	1.959729	20	20
44.0	1.959729	14	14
45.0	1.959729	14	14
46.0	1.959729	16	16
47.0	1.959729	5	5
48.0	1.959729	9	9
49.0	1.959729	12	12
50.0	1.959729	10	10
51.0	1.959729	4	4
52.0	1.959729	6	6
53.0	1.959729	2	2
54.0	1.959729	6	6
55.0	1.959729	9	9
56.0	1.959729	11	11
57.0	1.959729	11	11
58.0	1.959729	11	11
59.0	1.959729	5	5
60.0	1.959729	6	6
61.0	1.959729	4	4
62.0	1.959729	4	4
63.0	1.959729	5	5
64.0	1.959729	5	5
65.0	1.959729	5	5
66.0	1.959729	7	7
67.0	1.959729	4	4
68.0	1.959729	3	3
69.0	1.959729	12	12
70.0	1.959729	6	6
71.0	1.959729	7	7
72.0	1.959729	13	13
73.0	1.959729	6	6
74.0	1.959729	5	5
75.0	1.959729	10	10
76.0	1.959729	3	3
77.0	1.959729	5	5
78.0	1.959729	3	3
79.0	1.959729	5	5
80.0	1.959729	7	7
81.0	1.959729	6	6
82.0	1.959729	4	4
83.0	1.959729	3	3
84.0	1.959729	5	5
85.0	1.959729	4	4
86.0	1.959729	3	3
87.0	1.959729	4	4
88.0	1.959729	5	5
89.0	1.959729	5	5
90.0	1.959729	4	4
91.0	1.959729	4	4
92.0	1.959729	11	11
93.0	1.959729	3	3
94.0	1.959729	3	3
95.0	1.959729	2	2
96.0	1.959729	2	2
97.0	1.959729	5	5
98.0	1.959729	5	5
99.0	1.959729	4	4
100.0	1.959729	3	3
101.0	0	3	3
102.0	0	5	5
103.0	0	3	3
104.0	0	2	2
105.0	0	1	1
106.0	0	4	4
107.0	0	2	2
110.0	0	5	5
111.0	0	2	2
112.0	0	3	3
113.0	0	3	3
114.0	0	3	3
117.0	0	3	3
118.0	0	5	5
119.0	0	2	2
122.0	0	2	2
123.0	0	4	4
124.0	0	5	5
126.0	0	2	2
127.0	0	2	2
128.0	0	6	6
129.0	0	1	1
130.0	0	1	1
131.0	0	5	5
132.0	0	1	1
133.0	0	1	1
134.0	0	6	6
137.0	0	2	2
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
142.0	0	1	1
143.0	0	3	3
144.0	0	2	2
145.0	0	3	3
146.0	0	5	5
147.0	0	4	4
148.0	0	1	1
149.0	0	3	3
150.0	0	2	2
152.0	0	1	1
153.0	0	2	2
154.0	0	1	1
155.0	0	2	2
156.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	2	2
160.0	0	2	2
161.0	0	3	3
163.0	0	1	1
164.0	0	2	2
166.0	0	1	1
167.0	0	2	2
168.0	0	1	1
169.0	0	5	5
170.0	0	3	3
171.0	0	3	3
172.0	0	2	2
173.0	0	2	2
174.0	0	1	1
175.0	0	2	2
176.0	0	2	2
177.0	0	2	2
179.0	0	1	1
180.0	0	1	1
181.0	0	3	3
182.0	0	3	3
183.0	0	3	3
184.0	0	3	3
186.0	0	1	1
187.0	0	1	1
188.0	0	1	1
189.0	0	1	1
191.0	0	3	3
192.0	0	2	2
193.0	0	3	3
196.0	0	1	1
197.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	2	2
201.0	0	2	2
203.0	0	1	1
204.0	0	1	1
205.0	0	1	1
206.0	0	1	1
208.0	0	1	1
210.0	0	2	2
211.0	0	1	1
213.0	0	1	1
214.0	0	2	2
215.0	0	1	1
216.0	0	1	1
217.0	0	1	1
218.0	0	2	2
219.0	0	1	1
225.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
229.0	0	3	3
230.0	0	1	1
231.0	0	1	1
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
236.0	0	1	1
238.0	0	1	1
241.0	0	1	1
244.0	0	2	2
245.0	0	1	1
246.0	0	1	1
249.0	0	1	1
251.0	0	1	1
253.0	0	1	1
255.0	0	1	1
259.0	0	2	2
261.0	0	4	4
262.0	0	2	2
263.0	0	1	1
264.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	2	2
271.0	0	1	1
273.0	0	3	3
276.0	0	2	2
282.0	0	1	1
283.0	0	2	2
286.0	0	1	1
289.0	0	2	2
290.0	0	1	1
292.0	0	2	2
293.0	0	1	1
295.0	0	1	1
296.0	0	1	1
297.0	0	2	2
298.0	0	2	2
302.0	0	1	1
303.0	0	1	1
306.0	0	1	1
308.0	0	2	2
313.0	0	1	1
316.0	0	1	1
318.0	0	1	1
323.0	0	1	1
324.0	0	1	1
329.0	0	2	2
331.0	0	1	1
335.0	0	1	1
336.0	0	1	1
337.0	0	1	1
338.0	0	2	2
340.0	0	1	1
343.0	0	2	2
344.0	0	1	1
345.0	0	2	2
349.0	0	2	2
352.0	0	1	1
355.0	0	1	1
357.0	0	1	1
368.0	0	1	1
370.0	0	1	1
372.0	0	1	1
375.0	0	1	1
377.0	0	1	1
379.0	0	1	1
384.0	0	2	2
386.0	0	1	1
390.0	0	1	1
391.0	0	2	2
392.0	0	1	1
399.0	0	1	1
408.0	0	1	1
409.0	0	2	2
417.0	0	1	1
419.0	0	1	1
420.0	0	1	1
425.0	0	2	2
429.0	0	1	1
431.0	0	1	1
436.0	0	1	1
437.0	0	1	1
438.0	0	1	1
440.0	0	1	1
443.0	0	1	1
446.0	0	1	1
450.0	0	1	1
451.0	0	1	1
453.0	0	1	1
454.0	0	2	2
455.0	0	1	1
459.0	0	2	2
469.0	0	1	1
470.0	0	2	2
472.0	0	1	1
474.0	0	1	1
479.0	0	1	1
480.0	0	1	1
487.0	0	1	1
488.0	0	1	1
496.0	0	3	3
501.0	0	1	1
505.0	0	1	1
506.0	0	1	1
515.0	0	1	1
516.0	0	1	1
534.0	0	1	1
536.0	0	1	1
537.0	0	1	1
539.0	0	1	1
543.0	0	1	1
545.0	0	1	1
554.0	0	1	1
560.0	0	1	1
570.0	0	1	1
574.0	0	1	1
585.0	0	1	1
596.0	0	1	1
598.0	0	1	1
604.0	0	1	1
623.0	0	1	1
637.0	0	2	2
638.0	0	2	2
641.0	0	1	1
642.0	0	1	1
652.0	0	1	1
668.0	0	1	1
673.0	0	1	1
706.0	0	1	1
710.0	0	1	1
713.0	0	1	1
720.0	0	1	1
724.0	0	1	1
728.0	0	1	1
761.0	0	1	1
765.0	0	1	1
771.0	0	1	1
776.0	0	1	1
777.0	0	1	1
783.0	0	1	1
790.0	0	1	1
795.0	0	1	1
797.0	0	1	1
819.0	0	1	1
823.0	0	1	1
824.0	0	1	1
837.0	0	1	1
840.0	0	1	1
852.0	0	1	1
861.0	0	1	1
864.0	0	1	1
865.0	0	1	1
868.0	0	1	1
874.0	0	2	2
876.0	0	1	1
879.0	0	1	1
883.0	0	1	1
904.0	0	1	1
905.0	0	1	1
909.0	0	1	1
926.0	0	1	1
927.0	0	1	1
931.0	0	1	1
935.0	0	1	1
940.0	0	1	1
977.0	0	1	1
986.0	0	2	2
988.0	0	1	1
996.0	0	1	1
1037.0	0	1	1
1053.0	0	1	1
1057.0	0	1	1
1088.0	0	1	1
1104.0	0	1	1
1126.0	0	1	1
1131.0	0	1	1
1143.0	0	1	1
1149.0	0	1	1
1151.0	0	1	1
1156.0	0	1	1
1160.0	0	1	1
1183.0	0	1	1
1195.0	0	1	1
1239.0	0	1	1
1248.0	0	1	1
1255.0	0	2	2
1261.0	0	1	1
1319.0	0	1	1
1339.0	0	1	1
1353.0	0	1	1
1392.0	0	1	1
1402.0	0	1	1
1475.0	0	1	1
1482.0	0	1	1
1651.0	0	1	1
1685.0	0	1	1
1695.0	0	1	1
1773.0	0	1	1
1822.0	0	1	1
1825.0	0	1	1
1841.0	0	1	1
1859.0	0	1	1
1885.0	0	1	1
1940.0	0	1	1
2070.0	0	1	1
2107.0	0	1	1
2272.0	0	1	1
2294.0	0	1	1
2431.0	0	1	1
2459.0	0	1	1
2475.0	0	1	1
2588.0	0	1	1
2595.0	0	1	1
2762.0	0	1	1
2826.0	0	1	1
2835.0	0	1	1
3101.0	0	1	1
3147.0	0	1	1
3191.0	0	1	1
3280.0	0	1	1
3447.0	0	1	1
3522.0	0	1	1
3790.0	0	1	1
3805.0	0	1	1
3839.0	0	1	1
4223.0	0	1	1
5087.0	0	1	1
5765.0	0	1	1
6373.0	0	1	1
9279.0	0	1	1
18691.0	0	1	1
3067264.0	0	1	1