Path for .pheno file

[Melody Rynerson Palmer]

Hi Joe,

I'm working with Gail's group on the eMERGE CNV data and am stuck.

I have run plink with multiple quantitative phenotypes (--all-pheno) and your ALL... CNV files. Now I am trying to use InsertPlinkPvalues.pl. It's getting stuck after 

'Data-filter-advanced-unique records only'

and giving the error 

File not found! Pheno file: WeightTEST.pheno

How is it looking for the phenotype file? Should the --out option in my created ParseCNV.log direct it there with a path somehow? I have been trying different --out possibilities, like the prefix of the .assoc.linear files including the path, but nothing has worked so far. Below is the most recent (prefix)ParseCNV.log that I created for InsertPlinkPvalues to find, paths simplified so it's easier to read. 

Running Command: perl ParseCNV.pl {path1}PennCNV/eMERGE_660W_FinalReports_IntCsvPATHS.txt-ALL_CleanCNV.rawcnv {path2}ParseCNVRelease_18/NullControl_ForQuantitativeTrait.rawcnv {path1}PennCNV/ALLDEL.fam {path3}ALLDEL.map --keepTemp --out {path3}DUPcAllnoSite

Above with and without --includePed tried.

Will it be a problem that my plink.log files from the association analysis include all phenotypes because I did with --all-pheno? 

Please let me know if I can clarify my question. 

Thank you!

Melody Palmer