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dariober / cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing
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error in evaluating the argument 'con' in selecting a method for function 'isOpen': TabixFile: file(s) do not exist: #46

Closed asmlgkj closed 2 years ago

asmlgkj commented 2 years ago

thanks a lot for this great package, solid. can you have a lookof mine question?

conda install mamba mamba install cnv_facets mamba install 'r-facets>=0.6.1' 'r-data.table' 'r-ggplot2' 'r-argparse>=2' 'snp-pileup>=0.6.1' 'r-gridextra' 'bioconductor-rsamtools' 'samtools' 'bcftools >=1.9' git clone https://github.com/dariober/cnv_facets.git and get the cnv_facets.R

and use the Rscript in the absolute path of conda environment of cnv_facets

cnv_facets.R -t -n -vcf -o but gets an error

Error in h(simpleError(msg, call)) : error in evaluating the argument 'con' in selecting a method for function 'isOpen': TabixFile: file(s) do not exist: test.vcf.gz’ ‘test.vcf.gz.tbi’ Calls: exec_snp_pileup_parallel ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

dariober commented 2 years ago

Hi- Is your vcf file actually called test.vcf.gz? If so can you check if the argument -vcf is actually pointing to it? Maybe show the actual command you are executing.

asmlgkj commented 2 years ago

sorry, I misunderstand it as an output, so what kind of vcf it accepts, can vcf output by vardict it ?

dariober commented 2 years ago

Have a look at the documentation (admittedly quite terse). Basically, this is a vcf file of common polymorphic SNPs.Note also that cnv_facets.R is a command line wrapper for the R package facets. For more detail of the method look at the R package itself and its pubblication. I'm closing the issue now but feel free to re-open.

asmlgkj commented 2 years ago

@dariober thanks a lot. another errors wanted for help. the same as above, but a vcf from NCBI Rscript cnv_facets/bin/cnv_facets.R -t test1_CASE.sortdedup.bam -n test1.sort_dedup.bam -vcf human_9606_b151_GRCh37p13/00-commonall.vcf.gz -o test1 Error in makeCluster(nprocs, type = "FORK") : could not find function "makeCluster" Calls: exec_snp_pileup_parallel Execution halted