## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//CA_es_13_spring/CA_es_13_spring.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/CA_es_13_spring/CA_es_13_spring.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/CA_es_13_spring/CA_es_13_spring.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: Sun Jun 07 07:13:06 UTC 2020

## 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	2693920	41221971	0	0	1120064	1501467	0	0.048427	552037817

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	37584308	37584308
2.0	1.928047	1307258	1307258
3.0	2.78932	47357	47357
4.0	3.588621	4176	4176
5.0	4.330411	1364	1364
6.0	5.018827	731	731
7.0	5.65771	432	432
8.0	6.250623	342	342
9.0	6.800875	210	210
10.0	7.311535	167	167
11.0	7.785452	130	130
12.0	8.225269	113	113
13.0	8.633441	94	94
14.0	9.012243	90	90
15.0	9.363789	78	78
16.0	9.690041	71	71
17.0	9.992819	59	59
18.0	10.27381	52	52
19.0	10.534584	49	49
20.0	10.776594	49	49
21.0	11.001191	34	34
22.0	11.209628	24	24
23.0	11.403067	27	27
24.0	11.582588	35	35
25.0	11.749192	22	22
26.0	11.903808	27	27
27.0	12.047299	29	29
28.0	12.180466	17	17
29.0	12.304051	22	22
30.0	12.418743	18	18
31.0	12.525184	20	20
32.0	12.623965	10	10
33.0	12.715639	18	18
34.0	12.800717	14	14
35.0	12.879674	18	18
36.0	12.952949	11	11
37.0	13.020952	12	12
38.0	13.084062	4	4
39.0	13.142631	6	6
40.0	13.196985	9	9
41.0	13.247429	8	8
42.0	13.294244	7	7
43.0	13.337689	5	5
44.0	13.378009	7	7
45.0	13.415428	6	6
46.0	13.450154	8	8
47.0	13.482382	8	8
48.0	13.512291	5	5
49.0	13.540048	5	5
50.0	13.565807	3	3
51.0	13.589713	8	8
52.0	13.6119	7	7
53.0	13.632489	2	2
54.0	13.651598	4	4
55.0	13.669331	3	3
56.0	13.685788	3	3
57.0	13.701062	3	3
58.0	13.715236	3	3
59.0	13.72839	3	3
60.0	13.740598	2	2
61.0	13.751928	4	4
62.0	13.762442	1	1
63.0	13.7722	3	3
64.0	13.781256	1	1
65.0	13.78966	4	4
66.0	13.797459	3	3
67.0	13.804697	4	4
68.0	13.811415	1	1
69.0	13.817649	1	1
70.0	13.823434	1	1
71.0	13.828804	2	2
72.0	13.833787	3	3
73.0	13.838411	2	2
74.0	13.842703	2	2
75.0	13.846686	0	0
76.0	13.850382	3	3
77.0	13.853812	1	1
78.0	13.856996	0	0
79.0	13.85995	0	0
80.0	13.862692	1	1
81.0	13.865237	1	1
82.0	13.867598	2	2
83.0	13.86979	4	4
84.0	13.871824	0	0
85.0	13.873711	0	0
86.0	13.875463	1	1
87.0	13.877088	1	1
88.0	13.878597	2	2
89.0	13.879997	1	1
90.0	13.881297	1	1
91.0	13.882503	0	0
92.0	13.883622	1	1
93.0	13.88466	0	0
94.0	13.885624	1	1
95.0	13.886519	2	2
96.0	13.887349	0	0
97.0	13.88812	1	1
98.0	13.888835	0	0
99.0	13.889498	1	1
100.0	13.890114	0	0
102.0	0	1	1
103.0	0	1	1
104.0	0	3	3
105.0	0	1	1
107.0	0	1	1
108.0	0	1	1
111.0	0	1	1
112.0	0	1	1
113.0	0	2	2
116.0	0	2	2
117.0	0	2	2
118.0	0	1	1
119.0	0	1	1
121.0	0	1	1
127.0	0	1	1
129.0	0	2	2
130.0	0	1	1
132.0	0	1	1
135.0	0	1	1
136.0	0	1	1
146.0	0	1	1
147.0	0	1	1
151.0	0	1	1
152.0	0	1	1
154.0	0	1	1
157.0	0	1	1
159.0	0	2	2
172.0	0	1	1
176.0	0	2	2
181.0	0	1	1
188.0	0	1	1
201.0	0	1	1
205.0	0	1	1
213.0	0	1	1
222.0	0	1	1
229.0	0	1	1
239.0	0	2	2
242.0	0	1	1
248.0	0	1	1
250.0	0	2	2
254.0	0	1	1
257.0	0	1	1
260.0	0	1	1
264.0	0	1	1
270.0	0	1	1
271.0	0	1	1
275.0	0	1	1
278.0	0	1	1
282.0	0	1	1
283.0	0	1	1
318.0	0	1	1
331.0	0	1	1
355.0	0	1	1
367.0	0	1	1
370.0	0	1	1
372.0	0	1	1
373.0	0	1	1
404.0	0	1	1
409.0	0	1	1
425.0	0	1	1
444.0	0	1	1
462.0	0	1	1
508.0	0	1	1
523.0	0	1	1
549.0	0	1	1
559.0	0	1	1
595.0	0	1	1
607.0	0	1	1
612.0	0	1	1
643.0	0	1	1
784.0	0	1	1
807.0	0	1	1
836.0	0	1	1
864.0	0	1	1
942.0	0	1	1
958.0	0	1	1
979.0	0	1	1
1023.0	0	1	1
1040.0	0	1	1
1560.0	0	1	1
1733.0	0	1	1
1778.0	0	1	1
1851.0	0	1	1
1916.0	0	1	1
3314.0	0	1	1