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Old 01-25-2016, 10:52 AM   #1
zillur
Senior Member
 
Location: Puerto Rico

Join Date: Sep 2014
Posts: 106
Default PSMC, having to generate diploid.psmc file

Hi there,
I have downloaded fasta assembly from hamster:
http://mirrors.vbi.vt.edu/mirrors/ft...5.1_MesAur1.0/

and paired end raw reads:
http://sra.dbcls.jp/search/view/SRP010049

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
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