clincnv runs an error about family samples
heweihuang opened this issue · 2 comments
Hello, clincnv analyzed 3 family samples, and an error occurred. Although I set the parameter minimumNumOfElemsInCluster to 1, how can I solve the error? The error content is as follows:
[1] "We run script located in folder /fuer2/03.Soft/01.Soft_project/ClinCNV-1.17.2 . All the paths will be calculated realtive to this one. If everything crashes, please, check the correctness of this path first."
[1] "START cluster allocation."
[1] "Cluster allocated."
[1] "END cluster allocation."
[1] "We are started with reading the coverage files and bed files 2022-03-14 17:20:48"
[1] "Started basic quality filtering. 2022-03-14 17:20:49"
[1] "Amount of regions after filtering of 0-covered regions 99.528"
[1] "Normalization with GC and length starts. 2022-03-14 17:21:00"
[1] "Percentage of regions remained after GC correction: 0.997975235573553"
[1] "Amount of regions after GC-extreme filtering 99.327"
[1] "Amount of regions after Systematically Low Covered regions filtering 99.327"
[1] "We start to cluster your data (you will find a plot if clustering is possible in your output directory) ./result 2022-03-14 17:21:16"
Error: umap: number of neighbors must be smaller than number of items
Execution halted
Hi, it means the number of samples too small so a standard UMAP funciton does not work on them. I guess if you reduce the parameter n_neighbors in umap function which is used to depict the cohort. However, ClinCNV does not work well for small number of samples, so I don't know if it worth to do.
可以添加这个参数 --noPlot