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Niinleslie / MesKit

A tool kit for dissecting cancer evolution from multi-region derived tumor biopsies via somatic mutations
GNU General Public License v3.0
35 stars 9 forks source link

example data analysis failed! #248

Open weizhiting opened 3 years ago

weizhiting commented 3 years ago

Hi, i used the docker version of meskit and shiny-server. I can successfully open the browser, but when i follow the example data analysis, I can not draw the mutation profile. error message "An error has occurred. Check your logs or contact the app author for clarification.". Other function such as CNV profile seems work well. So, can you help me check the reasons? By the way, the docker name not allowed lowercase, so the Meskit should be meskit.

likelet commented 3 years ago

@weizhiting thanks for point this out. @Niinleslie plz check the issue ASAP

weizhiting commented 3 years ago

Thanks for your response! Another issue I noticed when i use the docker version of meskit. The 105th rows of "compareCCF.R" "tidyr::drop_na()" should be wrong. This will drop private mutation if the mutation reads in all the metastasis sites or primary sites is 0. Or you can change your "validMaf" function not to remove the mutation with vaf=0. Point out if I am wrong!

Niinleslie commented 3 years ago

@weizhiting Hi, we have updated the docker version of MesKit and it should work fine now! It was indeed a bug with the function "compareCCF" and it has beed fixed. We greatly appreciate your feedback and suggestions!

weizhiting commented 3 years ago

Hi, i update the docker to the latest version. But the compareCCF did not update, and still will drop the private mutation. Please check it. What is more, the shiny website will failed when i choose "use the indel ccf".