Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
One plot error about CNVpipeline stage5
I met another error about GenomeStrip2.0 CNVdiscoveryPipeline, and it stopped at stage5. Some parts of the error log are as following,
ERROR 09:59:48,040 FunctionEdge - Contents of /faststorage/home/siyang/USER/yeweijian/Project/DanishPanGenome/2015January_Task/20150110_GenomeStrip/result/4_CNVpip/X/cnv_stage5/logs/CNVDiscoveryStage5-2.out: Error in xy.coords(x, y, xlabel, ylabel, log) : 'x' and 'y' lengths differ Calls: plotVariantsPerSamplePDF ... plotVariantsPerSample -> plot -> plot.default -> xy.coords In addition: Warning message: In max(vpsData, na.rm = T) : no non-missing arguments to max; returning -Inf Execution halted
It is a little weird that this error only occured in chrX and chrY, and I think it may caused by R settings. However, I am not able to fix it by myself, could you help?