## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_3.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/slrinzema/ghe_2022/metta/star/GRCh38-DMSO_3.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/slrinzema/ghe_2022/metta/qc/markdup/GRCh38-DMSO_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 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 GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Oct 11 13:25:17 CEST 2022

## 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	216	6858910	4584962	0	174	698691	0	0.101877	31338891

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	5853276	5853276
2.0	1.803432	221528	221528
3.0	2.448935	38362	38362
4.0	2.967553	15960	15960
5.0	3.384228	8413	8413
6.0	3.718997	5077	5077
7.0	3.987962	3419	3419
8.0	4.204057	2485	2485
9.0	4.377674	1767	1767
10.0	4.517164	1394	1394
11.0	4.629235	1029	1029
12.0	4.719276	863	863
13.0	4.791618	708	708
14.0	4.84974	582	582
15.0	4.896437	496	496
16.0	4.933955	420	420
17.0	4.964098	380	380
18.0	4.988316	300	300
19.0	5.007773	273	273
20.0	5.023406	261	261
21.0	5.035966	213	213
22.0	5.046057	167	167
23.0	5.054164	178	178
24.0	5.060678	158	158
25.0	5.065911	130	130
26.0	5.070116	155	155
27.0	5.073494	108	108
28.0	5.076208	109	109
29.0	5.078389	93	93
30.0	5.080141	79	79
31.0	5.081548	74	74
32.0	5.082679	77	77
33.0	5.083588	78	78
34.0	5.084318	55	55
35.0	5.084904	48	48
36.0	5.085375	60	60
37.0	5.085754	59	59
38.0	5.086058	57	57
39.0	5.086303	68	68
40.0	5.086499	51	51
41.0	5.086657	46	46
42.0	5.086783	43	43
43.0	5.086885	39	39
44.0	5.086967	47	47
45.0	5.087033	33	33
46.0	5.087086	31	31
47.0	5.087128	39	39
48.0	5.087162	35	35
49.0	5.087189	24	24
50.0	5.087212	34	34
51.0	5.087229	24	24
52.0	5.087243	21	21
53.0	5.087255	23	23
54.0	5.087264	18	18
55.0	5.087271	29	29
56.0	5.087277	16	16
57.0	5.087282	18	18
58.0	5.087286	21	21
59.0	5.087289	19	19
60.0	5.087291	19	19
61.0	5.087293	15	15
62.0	5.087295	16	16
63.0	5.087296	13	13
64.0	5.087297	10	10
65.0	5.087298	14	14
66.0	5.087299	10	10
67.0	5.087299	8	8
68.0	5.0873	7	7
69.0	5.0873	13	13
70.0	5.0873	12	12
71.0	5.087301	16	16
72.0	5.087301	10	10
73.0	5.087301	8	8
74.0	5.087301	12	12
75.0	5.087301	10	10
76.0	5.087301	9	9
77.0	5.087301	5	5
78.0	5.087301	11	11
79.0	5.087301	16	16
80.0	5.087301	12	12
81.0	5.087301	14	14
82.0	5.087301	9	9
83.0	5.087301	12	12
84.0	5.087301	6	6
85.0	5.087301	11	11
86.0	5.087301	11	11
87.0	5.087301	8	8
88.0	5.087301	8	8
89.0	5.087301	4	4
90.0	5.087301	3	3
91.0	5.087301	4	4
92.0	5.087301	7	7
93.0	5.087301	11	11
94.0	5.087301	8	8
95.0	5.087301	8	8
96.0	5.087301	6	6
97.0	5.087301	3	3
98.0	5.087301	4	4
99.0	5.087301	4	4
100.0	5.087301	7	7
101.0	0	3	3
102.0	0	1	1
103.0	0	4	4
104.0	0	5	5
105.0	0	5	5
106.0	0	6	6
107.0	0	6	6
108.0	0	4	4
109.0	0	2	2
110.0	0	6	6
111.0	0	1	1
112.0	0	5	5
113.0	0	2	2
114.0	0	3	3
115.0	0	2	2
116.0	0	3	3
117.0	0	3	3
118.0	0	1	1
119.0	0	4	4
120.0	0	5	5
121.0	0	5	5
122.0	0	3	3
123.0	0	2	2
125.0	0	2	2
126.0	0	4	4
127.0	0	2	2
128.0	0	4	4
129.0	0	4	4
130.0	0	2	2
131.0	0	2	2
132.0	0	2	2
133.0	0	3	3
134.0	0	2	2
135.0	0	4	4
136.0	0	2	2
137.0	0	2	2
138.0	0	3	3
139.0	0	3	3
140.0	0	1	1
141.0	0	1	1
142.0	0	1	1
143.0	0	3	3
144.0	0	1	1
145.0	0	2	2
146.0	0	2	2
147.0	0	1	1
148.0	0	1	1
149.0	0	3	3
150.0	0	1	1
151.0	0	2	2
152.0	0	3	3
153.0	0	1	1
154.0	0	2	2
155.0	0	3	3
156.0	0	2	2
157.0	0	1	1
158.0	0	1	1
159.0	0	3	3
160.0	0	1	1
162.0	0	1	1
163.0	0	1	1
164.0	0	2	2
165.0	0	3	3
166.0	0	1	1
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
172.0	0	1	1
173.0	0	2	2
174.0	0	2	2
175.0	0	2	2
176.0	0	1	1
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
182.0	0	2	2
184.0	0	2	2
186.0	0	1	1
190.0	0	2	2
192.0	0	2	2
193.0	0	1	1
195.0	0	1	1
198.0	0	1	1
200.0	0	1	1
202.0	0	1	1
206.0	0	2	2
207.0	0	1	1
211.0	0	1	1
212.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	1	1
224.0	0	1	1
226.0	0	1	1
229.0	0	2	2
230.0	0	1	1
234.0	0	1	1
239.0	0	1	1
241.0	0	1	1
243.0	0	1	1
246.0	0	1	1
249.0	0	1	1
253.0	0	2	2
257.0	0	1	1
258.0	0	1	1
261.0	0	1	1
263.0	0	1	1
271.0	0	1	1
276.0	0	1	1
287.0	0	2	2
294.0	0	1	1
306.0	0	1	1
308.0	0	1	1
312.0	0	1	1
317.0	0	1	1
318.0	0	1	1
328.0	0	1	1
343.0	0	1	1
344.0	0	1	1
350.0	0	1	1
373.0	0	1	1
380.0	0	1	1
388.0	0	2	2
391.0	0	1	1
408.0	0	1	1
411.0	0	1	1
417.0	0	1	1
422.0	0	2	2
445.0	0	1	1
454.0	0	1	1
491.0	0	1	1
533.0	0	1	1
536.0	0	1	1
540.0	0	1	1
600.0	0	1	1
613.0	0	1	1
981.0	0	1	1
1081.0	0	1	1
1348.0	0	1	1