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Error in prepare_files #4

Closed sqreb closed 2 weeks ago

sqreb commented 5 years ago

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 commented 5 years ago

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 notifications@github.com 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

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