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Algorithm to implement Fraction and Copy number Estimate from Tumor/normal Sequencing.
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run cnv_facets error for some samples, hope someone for help!! #191

Closed edceeyuchen closed 1 year ago

edceeyuchen commented 1 year ago

Hello, thank you for very nice tools for CNV analysis! Mostly, it works well, but I met some samples run error:

  1. Loading file /share/home/luoylLab/zengyuchen/PROJECT/chromothripsis/25.Facets/results/UBC/246/246T.csv.gz... [2023-05-18 15:59:39] Plotting histogram of coverage... [2023-05-18 16:03:10] Preprocessing sample... [2023-05-18 16:05:49] Processing sample... Error in abs(lorclust[[jhi]]$valor) : non-numeric argument to mathematical function Calls: run_facets -> procSample -> clustersegs -> wilcox.test Execution halted

  2. [2023-05-17 16:53:12] Loading file /share/home/luoylLab/zengyuchen/PROJECT/chromothripsis/25.Facets/results/UBC/65/65T.csv.gz... [2023-05-17 16:53:43] Plotting histogram of coverage... [2023-05-17 16:56:46] Preprocessing sample... [2023-05-17 16:57:46] Processing sample... [2023-05-17 17:04:19] Fitting model... [2023-05-17 17:17:37] Writing output [E::hts_idx_push] Unsorted positions on sequence #1: 229241292 followed by 2 Error in value[3L] : index build failed file: /share/home/luoylLab/zengyuchen/PROJECT/chromothripsis/25.Facets/results/UBC/65/65T.vcf.gz Calls: indexTabix ... tryCatch -> tryCatchList -> tryCatchOne -> Execution halted

And most error are the first one, i don't find the same problem in the issues, Hope for help! Thank you~

edceeyuchen commented 1 year ago

My version is 0.5.14