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imgag / ClinCNV

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
MIT License
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Running clinCNV reports an error #27

Closed heweihuang closed 2 years ago

heweihuang commented 2 years ago

please help，thank`s . run script : Rscript ./clinCNV.R --bed ./samples/bed_file.bed --normal ./samples/coverages_normal.cov --out result the error is as follows： ...... Loading required package: sandwich [1] "We start to estimate covariances between neighboring regions in germline data - may take some time 2022-03-10 17:22:41" [1] "Tree of covariances (using 2 predictors - sum of regions' lengths and log2 of distance between regions) plotted in result 2022-03-10 17:23:28" [1] "Calling started 2022-03-10 17:23:28" [1] "Working with germline sample 0 2022-03-10 17:23:28" [1] "Working with germline sample 1 2022-03-10 17:23:28" Error in writeLines(c("#type=GENE_EXPRESSION", paste0("#track graphtype=points name=\"", : cannot open the connection Calls: source ... outputSegmentsAndDotsFromListOfCNVs -> makeTrackAnnotation -> writeLines Execution halted

GermanDemidov commented 2 years ago

Hi,

I think there is something wrong with the data access permission. I think you should set chmod 755 to the results folder. ClinCNV can not write results to the file which means there is not enough permission.