Hi, thanks for this great tool!
I was running SCEVAN on a small cancer scRNA-seq dataset, when my calls to pipelineCNA kept running into errors. pipelineCNA ran successfully until the message
time classify tumor cells: 10.6155943870544"
However, after this message, my script threw an error. The traceback of calls shown was as below:
pipelineCNA -> plotCNclonal -> getScevanCNV -> read.table -> file
When I investigated the source code of plotCNclonal and getScevanCNV, it appears that when plotCNclonal internally calls getScevanCNV, it does not provide the value of its output_dir parameter to the parameter path of getScevanCNV. Hence, getScevanCNV uses its default value of "./output" instead, which causes the error, because it is attempting to read a file that does not exist.
I am using the latest version of SCEVAN.
Hi, thanks for this great tool!
I was running SCEVAN on a small cancer scRNA-seq dataset, when my calls to
pipelineCNAkept running into errors.pipelineCNAran successfully until the messageHowever, after this message, my script threw an error. The traceback of calls shown was as below:
When I investigated the source code of
plotCNclonalandgetScevanCNV, it appears that whenplotCNclonalinternally callsgetScevanCNV, it does not provide the value of itsoutput_dirparameter to the parameterpathofgetScevanCNV. Hence,getScevanCNVuses its default value of"./output"instead, which causes the error, because it is attempting to read a file that does not exist.I am using the latest version of SCEVAN.