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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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cnvnator genotype 'TSystem' error #282

Open skittikun opened 1 year ago

skittikun commented 1 year ago

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 commented 1 year ago

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 commented 1 year ago

Hello Alexej,

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

Best, Chris

abyzov commented 1 year ago

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 commented 1 year ago

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 https://github.com/abyzovlab/CNVnator/issues/282#issuecomment-1676261205, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABYYKNPDIBNELP24C7JSQK3XVB5WBANCNFSM6AAAAAA2NZCDGI. You are receiving this because you authored the thread.