Error in prepare_files

[sqreb]

I am trying to use MARGE to analyze ChIP-seq data. When I ran into the steps of prepare_files, I ran into a problem. In this step , I want to be able to generate personal mutations and genomic information. But when I run MARGE as follow, the mutation filename is like "chrchr1_allele_1.mut", and can not generate personal genome files.
MMARGE.pl prepare_files -files Chip/MMARGE/ind_variation/SAMN01731493.sort.vcf -core 28 -ind SAMN01731493 -dir Chip/MMARGE/ind_mutation/SAMN01731493 -genome_dir Chip/MMARGE/ind_genome/SAMN01731493 -genome /home/wangdehe/common/UCSC/genome/split/hg19 -force

Error information
Generating chromosome 1
Done
Chip/MMARGE/ind_mutation/SAMN01731493/SAMN01731493/chr1_allele_1.mut does not exist - go to next strain

[vlink]

Hi Dehe, does your vcf file name the chromosomes chr1 in the very first column of the file? Thanks, Verena

…

On Dec 29, 2018, at 3:35 AM, Dehe Wang ***@***.***> wrote: I am trying to use MARGE to analyze ChIP-seq data. When I ran into the steps of prepare_files, I ran into a problem. In this step , I want to be able to generate personal mutations and genomic information. But when I run MARGE as follow, the mutation filename is like "chrchr1_allele_1.mut", and can not generate personal genome files. MMARGE.pl prepare_files -files Chip/MMARGE/ind_variation/SAMN01731493.sort.vcf -core 28 -ind SAMN01731493 -dir Chip/MMARGE/ind_mutation/SAMN01731493 -genome_dir Chip/MMARGE/ind_genome/SAMN01731493 -genome /home/wangdehe/common/UCSC/genome/split/hg19 -force Error information Generating chromosome 1 Done Chip/MMARGE/ind_mutation/SAMN01731493/SAMN01731493/chr1_allele_1.mut does not exist - go to next strain — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AD8p6Hyj4oCLGumLdbiR0i93KtiXLVRUks5u9ylDgaJpZM4ZkebF>.