Originally posted by wilflugo
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C:\temp\ecoli>java -ea -Xmx1g align2.RandomReads3 maxsnps=0 maxinss=0 maxdels=0 maxsubs=0 adderrors=false out=reads.fastq reads=1000 minlength=18 maxlength=55 seed=-1
snpRate=0.0, max=0, unique=true
insRate=0.0, max=0, len=(0-0)
delRate=0.0, max=0, len=(0-0)
subRate=0.0, max=0, len=(0-0)
nRate =0.0, max=0, len=(0-0)
genome=1
PERFECT_READ_RATIO=0.0
ADD_ERRORS_FROM_QUALITY=false
REPLACE_NOREF=false
paired=false
read length=18-55
Wrote reads.fastq
Time: 0.344 seconds.
C:\temp\ecoli>java -ea -Xmx1g align2.BBMap in=reads.fastq
Executing align2.BBMap [in=reads.fastq]
BBMap version 34.94
Retaining first best site only for ambiguous mappings.
No output file.
Set genome to 1
Loaded Reference: 0.057 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 0.924 seconds.
Analyzed Index: 1.860 seconds.
Cleared Memory: 0.188 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 1000 (36146 bases)
Mapping: 0.275 seconds.
Reads/sec: 3630.35
kBases/sec: 131.22
Read 1 data: pct reads num reads pct bases num bases
mapped: 100.0000% 1000 100.0000% 36146
unambiguous: 96.8000% 968 96.9181% 35032
ambiguous: 3.2000% 32 3.0819% 1114
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 100.0000% 1000 100.0000% 36146
semiperfect site: 100.0000% 1000 100.0000% 36146
Match Rate: NA NA 100.0000% 36146
Error Rate: 0.0000% 0 0.0000% 0
Sub Rate: 0.0000% 0 0.0000% 0
Del Rate: 0.0000% 0 0.0000% 0
Ins Rate: 0.0000% 0 0.0000% 0
N Rate: 0.0000% 0 0.0000% 0
Total time: 3.521 seconds.
snpRate=0.0, max=0, unique=true
insRate=0.0, max=0, len=(0-0)
delRate=0.0, max=0, len=(0-0)
subRate=0.0, max=0, len=(0-0)
nRate =0.0, max=0, len=(0-0)
genome=1
PERFECT_READ_RATIO=0.0
ADD_ERRORS_FROM_QUALITY=false
REPLACE_NOREF=false
paired=false
read length=18-55
Wrote reads.fastq
Time: 0.344 seconds.
C:\temp\ecoli>java -ea -Xmx1g align2.BBMap in=reads.fastq
Executing align2.BBMap [in=reads.fastq]
BBMap version 34.94
Retaining first best site only for ambiguous mappings.
No output file.
Set genome to 1
Loaded Reference: 0.057 seconds.
Loading index for chunk 1-1, build 1
Generated Index: 0.924 seconds.
Analyzed Index: 1.860 seconds.
Cleared Memory: 0.188 seconds.
Processing reads in single-ended mode.
Started read stream.
Started 8 mapping threads.
Detecting finished threads: 0, 1, 2, 3, 4, 5, 6, 7
------------------ Results ------------------
Genome: 1
Key Length: 13
Max Indel: 16000
Minimum Score Ratio: 0.56
Mapping Mode: normal
Reads Used: 1000 (36146 bases)
Mapping: 0.275 seconds.
Reads/sec: 3630.35
kBases/sec: 131.22
Read 1 data: pct reads num reads pct bases num bases
mapped: 100.0000% 1000 100.0000% 36146
unambiguous: 96.8000% 968 96.9181% 35032
ambiguous: 3.2000% 32 3.0819% 1114
low-Q discards: 0.0000% 0 0.0000% 0
perfect best site: 100.0000% 1000 100.0000% 36146
semiperfect site: 100.0000% 1000 100.0000% 36146
Match Rate: NA NA 100.0000% 36146
Error Rate: 0.0000% 0 0.0000% 0
Sub Rate: 0.0000% 0 0.0000% 0
Del Rate: 0.0000% 0 0.0000% 0
Ins Rate: 0.0000% 0 0.0000% 0
N Rate: 0.0000% 0 0.0000% 0
Total time: 3.521 seconds.
You can generate the same set of reads with and without SNPs by fixing the seed to a positive number, like this:
randomreads.sh maxsnps=0 adderrors=false out=perfect.fastq reads=1000 minlength=18 maxlength=55 seed=5
randomreads.sh maxsnps=2 snprate=1 adderrors=false out=2snps.fastq reads=1000 minlength=18 maxlength=55 seed=5
The RNG for the SNPs and positions are independent.
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