ParseCNV outputfiles problems.

[vincent Ruan]

Dear Joseph Glessner:

    Hi!

    I tried to run the example command as tutorial said, while I got no entries in CNVR_ALL_ReviewedCNVRs_XXX (postfix) but column names in both CNVR-based analysis and gene-based analysis.However, CNVR_ALL_ReviewedCNVRs_ControlEnriched.txt was not blank like other outputfile. Even if I took your previous suggestion that InsertPlinkValues.pl should be corrected ,it didn't work at all. And the ERROR that "cannot execute system command R CMD BATCH OutputFiles/.AllRes.R "during process made me confused. Could you please tell me the problem and help me to fix them?

Thank you so much.

Sincerely, 

Vincent 

[ParseCNV]

Hi Vincent,

Sorry for the delayed reply, somehow I didn't see this one.

Based on the .log, you must be using a very old ParseCNV version (2015-05-14: ParseCNVRelease_17 or earlier)
Please download and use the latest version 2019-07-01: ParseCNVRelease_21
You should get outputs with these line counts:
   1 CNVR_ALL_ReviewedCNVRs_ControlEnriched.txt
   3 CNVR_ALL_ReviewedCNVRs.txt
   3 CNVR_ALL_ReviewedCNVRs_verbose.txt

The Error reported here is a bug, the actual process worked:  ERROR that "cannot execute system command R CMD BATCH OutputFiles/.AllRes.R "

Regards,

Joseph Glessner