## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/standard/BerglandTeach/mapping_output/ExpEvo_PRJNA657615_L180_2_1999-10-DD/ExpEvo_PRJNA657615_L180_2_1999-10-DD.sorted_merged.bam] OUTPUT=/standard/BerglandTeach/mapping_output/ExpEvo_PRJNA657615_L180_2_1999-10-DD/ExpEvo_PRJNA657615_L180_2_1999-10-DD.dedup.bam METRICS_FILE=/standard/BerglandTeach/mapping_output/ExpEvo_PRJNA657615_L180_2_1999-10-DD/ExpEvo_PRJNA657615_L180_2_1999-10-DD.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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 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 Sep 17 16:42:03 UTC 2024

## 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
lib1	123474	28553738	0	0	39483	532820	0	0.01931	755547298

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	27224745	27224745
2.0	1.962913	425840	425840
3.0	2.890115	13381	13381
4.0	3.782929	1794	1794
5.0	4.642632	571	571
6.0	5.470451	250	250
7.0	6.267569	135	135
8.0	7.035124	71	71
9.0	7.774213	58	58
10.0	8.485892	46	46
11.0	9.171176	30	30
12.0	9.831045	18	18
13.0	10.466442	16	16
14.0	11.078274	9	9
15.0	11.667415	9	9
16.0	12.234707	15	15
17.0	12.780959	14	14
18.0	13.306953	16	16
19.0	13.813439	9	9
20.0	14.301141	6	6
21.0	14.770756	9	9
22.0	15.222954	6	6
23.0	15.658382	7	7
24.0	16.077661	4	4
25.0	16.48139	4	4
26.0	16.870146	4	4
27.0	17.244484	6	6
28.0	17.60494	3	3
29.0	17.952027	4	4
30.0	18.286242	3	3
31.0	18.608061	4	4
32.0	18.917946	4	4
33.0	19.216337	4	4
34.0	19.503663	5	5
35.0	19.780332	2	2
36.0	20.046741	4	4
37.0	20.303269	1	1
38.0	20.550283	2	2
39.0	20.788137	5	5
40.0	21.017169	0	0
41.0	21.237707	5	5
42.0	21.450066	0	0
43.0	21.654549	2	2
44.0	21.851449	3	3
45.0	22.041046	4	4
46.0	22.223612	1	1
47.0	22.399406	2	2
48.0	22.568681	1	1
49.0	22.731679	0	0
50.0	22.888631	2	2
51.0	23.039762	0	0
52.0	23.185289	2	2
53.0	23.325418	0	0
54.0	23.46035	1	1
55.0	23.590278	4	4
56.0	23.715387	1	1
57.0	23.835857	0	0
58.0	23.951858	5	5
59.0	24.063558	2	2
60.0	24.171115	1	1
61.0	24.274683	0	0
62.0	24.37441	0	0
63.0	24.470438	0	0
64.0	24.562905	1	1
65.0	24.651943	0	0
66.0	24.737678	1	1
67.0	24.820234	3	3
68.0	24.899728	0	0
69.0	24.976274	0	0
70.0	25.049981	1	1
71.0	25.120955	1	1
72.0	25.189296	1	1
73.0	25.255103	0	0
74.0	25.318469	2	2
75.0	25.379485	0	0
76.0	25.438238	0	0
77.0	25.494812	2	2
78.0	25.549288	1	1
79.0	25.601744	0	0
80.0	25.652254	3	3
81.0	25.700891	0	0
82.0	25.747725	1	1
83.0	25.792821	0	0
84.0	25.836245	0	0
85.0	25.878058	1	1
86.0	25.918321	0	0
87.0	25.95709	1	1
88.0	25.994422	0	0
89.0	26.030369	0	0
90.0	26.064983	1	1
91.0	26.098313	1	1
92.0	26.130407	0	0
93.0	26.161311	0	0
94.0	26.191069	0	0
95.0	26.219723	2	2
96.0	26.247314	0	0
97.0	26.273882	1	1
98.0	26.299465	0	0
99.0	26.324099	1	1
100.0	26.34782	1	1
103.0	0	1	1
109.0	0	1	1
110.0	0	1	1
112.0	0	1	1
113.0	0	1	1
118.0	0	1	1
120.0	0	1	1
121.0	0	1	1
123.0	0	1	1
125.0	0	1	1
127.0	0	1	1
130.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
141.0	0	1	1
142.0	0	1	1
144.0	0	1	1
151.0	0	2	2
165.0	0	2	2
166.0	0	1	1
170.0	0	1	1
199.0	0	1	1
219.0	0	1	1
227.0	0	1	1
231.0	0	1	1
234.0	0	1	1
244.0	0	1	1
246.0	0	1	1
254.0	0	1	1
263.0	0	1	1
264.0	0	1	1
267.0	0	1	1
268.0	0	1	1
282.0	0	1	1
286.0	0	1	1
312.0	0	1	1
318.0	0	1	1
336.0	0	1	1
347.0	0	1	1
350.0	0	1	1
375.0	0	1	1
385.0	0	1	1
391.0	0	1	1
402.0	0	1	1
411.0	0	1	1
449.0	0	1	1
459.0	0	1	1
485.0	0	1	1
494.0	0	1	1
495.0	0	1	1
505.0	0	1	1
516.0	0	1	1
517.0	0	1	1
550.0	0	1	1
551.0	0	1	1
590.0	0	1	1
668.0	0	1	1
688.0	0	1	1
691.0	0	1	1
813.0	0	1	1
908.0	0	1	1
914.0	0	1	1
1029.0	0	2	2
1070.0	0	1	1
1170.0	0	1	1
1185.0	0	1	1
1271.0	0	1	1
2052.0	0	1	1
2438.0	0	1	1
2518.0	0	1	1
3096.0	0	1	1
3160.0	0	1	1
3621.0	0	1	1
3741.0	0	1	1
3814.0	0	1	1
4447.0	0	1	1
4967.0	0	1	1