Hi there,
I have downloaded fasta assembly from hamster:
and paired end raw reads:
I aligned the using bowtie2 aligner. my commands are as follows:
bowtie2 -x hamster_index -1 SRR40216_1.fastq -2 SRR40216_2.fastq -S hamster.sam
samtools view -bS hamster.sam > hamster.bam
samtools sort hamster.bam hamster.sorted
samtools mpileup -C50 -uf GCF_000349665.1_MesAur1.0_genomic.fna hamster.sorted.bam | bcftools call -c - | vcfutils.pl vcf2fq -d 10 -D 100 | gzip > hamster.diploid.fq.gz
fq2psmcfa -q20 hamster.diploid.fq.gz > hamster.diploid.psmcfa
psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc hamster.diploid.psmcfa
psmc2history.pl diploid.psmc | history2ms.pl > ms-cmd.sh (here problem arises: ** Illegal division by zero at /usr/bin/history2ms.pl line 48, <> line 31.)
then I checked my diploid.psmc file and found there are two columns with values only 0. (attached)
Any idea why I am getting this??? I followed same pipeline for other organisms like horse, dog etc. and got good results.
Best Regards
Zillur
I have downloaded fasta assembly from hamster:
and paired end raw reads:
I aligned the using bowtie2 aligner. my commands are as follows:
bowtie2 -x hamster_index -1 SRR40216_1.fastq -2 SRR40216_2.fastq -S hamster.sam
samtools view -bS hamster.sam > hamster.bam
samtools sort hamster.bam hamster.sorted
samtools mpileup -C50 -uf GCF_000349665.1_MesAur1.0_genomic.fna hamster.sorted.bam | bcftools call -c - | vcfutils.pl vcf2fq -d 10 -D 100 | gzip > hamster.diploid.fq.gz
fq2psmcfa -q20 hamster.diploid.fq.gz > hamster.diploid.psmcfa
psmc -N25 -t15 -r5 -p "4+25*2+4+6" -o diploid.psmc hamster.diploid.psmcfa
psmc2history.pl diploid.psmc | history2ms.pl > ms-cmd.sh (here problem arises: ** Illegal division by zero at /usr/bin/history2ms.pl line 48, <> line 31.)
then I checked my diploid.psmc file and found there are two columns with values only 0. (attached)
Any idea why I am getting this??? I followed same pipeline for other organisms like horse, dog etc. and got good results.
Best Regards
Zillur