I'm trying to run tkgwv2 and I'm stuck at the plink2tkrelated step, where I get this error:
# Arguments used:
--freqFile /home/jkimsis/install/tkgwv2-master/support/1000GP3_EUR_22M_noFixed.frq
# Estimating coefficient of relatedness Rxy for VL10 VL11 awk: cannot open "VL10____VL11.tped" (No such file or directory)
wc: VL10____VL11.tped: No such file or directory
Error in strsplit(system(comm10b, intern = T), " ")[[1]] :
subscript out of bounds
In addition: Warning message:
In system(comm10b, intern = T) :
running command 'wc -l VL10____VL11.tped' had status 1 and error message 'Function not implemented'
Execution halted
Looking in to it, I've found that the ped files created in the bam2plink step contain far too many characters, for example, file VL10.bim contains 560087 lines, which means VL10.ped should contain (560087 x 2) + 6 = 1120180 characters, but it contains 22147110 characters, which is about 20 times too many. The ratio is similar for all other samples. Does anyone know what might be causing this? I have run tkgw2 successfully on the same computer before, but with a different set of files.
Hello,
I'm trying to run tkgwv2 and I'm stuck at the plink2tkrelated step, where I get this error:
Looking in to it, I've found that the ped files created in the bam2plink step contain far too many characters, for example, file VL10.bim contains 560087 lines, which means VL10.ped should contain (560087 x 2) + 6 = 1120180 characters, but it contains 22147110 characters, which is about 20 times too many. The ratio is similar for all other samples. Does anyone know what might be causing this? I have run tkgw2 successfully on the same computer before, but with a different set of files.