dwgsim for single ends simulation

[kaile]

I want to use the dwgsim tool to do single end reads simulation, but i found
the tools can't do generate the single end reads. such as:
The input command is:
dwgsim -N 10000 -r 0.001 -1 100 ~/db/genome/hg18.fa r0.fq
The output file is:
r0.fq.bfast.fastq
r0.fq.bwa.read1.fastq
r0.fq.bwa.read2.fastq
I also checked the content of the fastq files:
r0.fq.bwa.read1.fastq
@chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/1
AGAGCAGAACTCTGTCTCAAAAAAAAAAAAAGAAAGAAAGAAGGTTTACAAATTTGTGTTGGGCCTCATTCAAAGCCGTCCTGGGCTGCGTGCGGCCGGT
### 100bp
r0.fq.bwa.read2.fastq
@chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/2
TCCTCTGTAATGGGAGAAAAAATGATAATCATGGCCATGAACAGAGGAGGACTGTGAAGTGTAAACTTAA
### default 70bp
Is there anyone tell me why the software gives two bwa reads which don't
like the single end reads and how I get the single end reads using the
dwgsim ?Thanks!

[nilshomer]

I want to use the dwgsim tool to do single end reads simulation, but i found
the tools can't do generate the single end reads. such as:
The input command is:
dwgsim -N 10000 -r 0.001 -1 100 ~/db/genome/hg18.fa r0.fq
The output file is:
r0.fq.bfast.fastq
r0.fq.bwa.read1.fastq
r0.fq.bwa.read2.fastq
I also checked the content of the fastq files:
r0.fq.bwa.read1.fastq
@chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/1
AGAGCAGAACTCTGTCTCAAAAAAAAAAAAAGAAAGAAAGAAGGTTTACAAATTTGTGTTGGGCCTCATTCAAAGCCGTCCTGGGCTGCGTGCGGCCGGT
### 100bp
r0.fq.bwa.read2.fastq
@chr1_203458592_203459164_0_1_0_0_3:0:0_2:0:0_0/2
TCCTCTGTAATGGGAGAAAAAATGATAATCATGGCCATGAACAGAGGAGGACTGTGAAGTGTAAACTTAA
### default 70bp
Is there anyone tell me why the software gives two bwa reads which don't
like the single end reads and how I get the single end reads using the
dwgsim ?Thanks!

Use "-2 0" to specify the second end should have length zero, since otherwise it uses the defaults.

[kaile]

Use "-2 0" to specify the second end should have length zero, since otherwise it uses the defaults.

Thanks! And I have already received your email on replying my question, you are so nice!