cnvnator genotype 'TSystem' error

[skittikun]

Hello,

I am trying to run genotype of the root file via

cnvnator
-root GENONAME.root
-genotype
1000 \

GENONAME.g.cnvcall

However, I got this error

" input_line_13:2:9: error: member access into incomplete type 'TSystem'
gSystem->ProcessEvents();
/usr/local/root/6.22.02/include/TInetAddress.h:38:14: note: forward declaration of 'TSystem'
friend class TSystem; "

I tried to look around but can't find the TSystem error anywhere.

Thank you in advance,

Chris

[abyzov]

Hi, not sure what is wrong with this. Are you able to start root? Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, 200 1st street SW, Harwick 7-91 Rochester, MN 55905 www.abyzovlab.org tel: +1-(507)-538-0978

[skittikun]

Hello Alexej,

I can run all of prior steps including create root, histo, calculate stat, partition, and cnv call.

Best,
Chris

[abyzov]

Hi, sorry. Not sure why software does not works. We are not maintaining CNVnator anymore. Perhaps, it is better to switch to CNVpytor https://github.com/abyzovlab/CNVpytor Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, 200 1st street SW, Harwick 7-91 Rochester, MN 55905 www.abyzovlab.org tel: +1-(507)-538-0978

[skittikun]

Thank you so much, Chris

…

On Aug 13, 2023, at 5:18 PM, abyzov ***@***.***> wrote: Hi, sorry. Not sure why software does not works. We are not maintaining CNVnator anymore. Perhaps, it is better to switch to CNVpytor https://github.com/abyzovlab/CNVpytor Alexej Abyzov, Ph.D. Senior Associate Consultant, Associate Professor of Biomedical Informatics, Department of Health Sciences Research, Center for Individualized Medicine, Mayo Clinic ----------------------------- Mayo Clinic, 200 1st street SW, Harwick 7-91 Rochester, MN 55905 www.abyzovlab.org tel: +1-(507)-538-0978 — Reply to this email directly, view it on GitHub <#282 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABYYKNPDIBNELP24C7JSQK3XVB5WBANCNFSM6AAAAAA2NZCDGI>. You are receiving this because you authored the thread.