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BGS-Experiment.log
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BGS-Experiment.log
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>>New Entry<< ------------------------------------------------
Date : 17th April 2011
Author : Edward MK WU
Title : 3-Mismatch Occurrence
ACGT.35bp1M.1113.fa/ncbi.chr1.fa ---
ACGT.35bp1M.1113.fa/ncbi.genome.fa ---
ACGT.100bp1M.fa/ncbi.chr1.fa --- 2,954,989 ( 90,019) [2bwt-bio11: 29.3795s] [bgs-bio11: 10.4253s]
ACGT.100bp1M.fa/ncbi.genome.fa --- 41,747,986 (845,847) [2bwt-bio11:147.2918s] [bgs-bio11: 37.0406s]
>>New Entry<< ------------------------------------------------
Date : 16th April 2011
Author : Edward MK WU
Title : 2-Mismatch Occurrence
ACGT.35bp1M.1113.fa/ncbi.chr1.fa --- 103,353,567 (149,115) [2bwt-bio11: 78.7440s] [bgs-bio11: 32.1197s]
ACGT.35bp1M.1113.fa/ncbi.genome.fa --- 1,229,392,188 (655,999) [2bwt-bio11:282.9702s] [bgs-bio11:284.1945s]
ACGT.100bp1M.fa/ncbi.chr1.fa --- 1,474,653 ( 79,036)
ACGT.100bp1M.fa/ncbi.genome.fa --- 20,672,931 (794,513)
>>New Entry<< ------------------------------------------------
Date : 26th March 2011
Author : Edward MK WU
Title : 2-Mismatch Occurrence
Short read set = ACGT.100bp1M.fa
Index = NCBI Chromosome 1
[Thread:Case1] 330139 occurrences are found.
[Thread:Case2] 206054 occurrences are found.
[Thread:Case3] 222059 occurrences are found.
[Thread:Case0] 716401 occurrences are found.
>>New Entry<< ------------------------------------------------
Date : 1st March 2011
Author : Edward MK WU
Title : To note the occ distribution (Device handles at most 8 SA ranges)
Short read set = ACGT.100bp1M.fa
Index = NCBI Chromosome 1
Device 1-mismatch matching
+Strand 143,737 (in 40,906 reads)
BStrand 210,189 (in 72,373 reads)
All 1-mismatch matching
+Strand 735,727 (in 46,228 reads)
BStrand 1,474,653 (in 79,036 reads)
>>New Entry<< ------------------------------------------------
Date : 12th February 2011
Author : Edward MK WU
Title : To note the occ distribution (Device handles at most 8 SA ranges)
Short read set = ACGT.100bp1M.fa
Index = NCBI Chromosome 1
Device 1-mismatch matching
+Strand 131,574 (in 34,136 reads)
BStrand 229,797 (in 61,559 reads)
All 1-mismatch matching
+Strand 281,879 (in 35,777 reads)
BStrand 565,293 (in 63,734 reads)
>>New Entry<< ------------------------------------------------
Date : 24th January 2011
Author : Edward MK WU
Title : To note the occ distribution
Rev : 20
Short read set = ACGT.100bp1M.fa
Index = NCBI Chromosome 1
Strand = Positive
Exact matching
71,149 (in 20,477 reads)
Exactly 1-mismatch matching
210,730 (in ? reads)
Device 1-mismatch matching
115,656 (in 33,644 reads)
Host 1-mismatch matching
166,223 (in 2,133 reads)
>>New Entry<< ------------------------------------------------
Date : 24th January 2011
Author : Edward MK WU
Title : Performance benchmark
Rev : 20
Short read set = ACGT.100bp1M.fa
Index = NCBI Chromosome 1
Strand = Positive
Environment = bio11
Exact matching
------------------------------------
Device time = 97.048897 ms
Index loading time = 0.3139s
Short read loading = 0.3438s
Alignment time = 0.1274s
Text pos and disk = 0.1682s
1-mismatch matching
------------------------------------
Device time = 597.181641 ms
Index loading time = 0.6999s
Short read loading = 0.3665s
Alignment time = 0.6325s
Host alignment time = 0.2624s
Text pos and disk = 0.6910s
Summing up above 5 = 2.6523s (+170% comp to exact)