matheuscburger / excavator2 Goto Github PK

Hello,

I tried running the following command and got the error. Please do check and let me know how to fix this
Command
sudo perl EXCAVATORDataPrepare.pl ExperimentalFilePrepare.window.txt --processors 2 --target xgen_50000 --assembly hg19
And the ExperimentalFilePrepare.windows.txt looks like :

/home/Tumor-TO.bam /home/Tumor Tmor-TO
/home/Normal-NO.bam /home/Normal Normal-NO

Error
Program folder is: /home/EXCAVATOR2_Package_v1.1.2
Preparing Multiprocessor Analysis...
Error in [.data.frame(ExperimentalTable, , 2) :
undefined columns selected
Calls: [ -> [.data.frame
Execution halted
Starting Multiprocessor Analysis!
Couldn't open the input file /home/EXCAVATOR2_Package_v1.1.2/.tmp.68712/ParallelReadPerla.sh. at EXCAVATORDataPrepare.pl line 79.

Thanks
Arshiya