Error in <TROOT::WriteTObject>

[elcortegano]

Hi,

I have been able to run steps of the cnvnator pipeline from read extraction to CNV calling without issue for several independent samples. When I want to merge the root files, however, I got the following error:

cnvnator -root out.root -chrom cpDNA -merge CC1952_L1.root CC1952_L2.root

Allocating memory ...
Merging trees for 'cpDNA' ...
Readng tree cpDNA from file 'CC1952_L1.root' ...
Readng tree cpDNA from file 'CC1952_L2.root' ...
Filling and saving tree for 'cpDNA' ...
Error in <TROOT::WriteTObject>: The current directory (root) is not associated with a file. The object (cpDNA) has not been written.

I assume this is an error coming from ROOT, but it is unclear to me how it could be misconfigured when other steps have worked (and when ROOT was installed via conda without problem).

Any ideas? thanks

[abyzov]

Hi, we are now advising users to switch to CNVpytor (https://github.com/abyzovlab/CNVpytor). We are still going to maintain main functionality of CNVnator for some time. Merging is NOT one of the main function. But you can bypass that step by parsing two bams when generating root file.

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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978

[elcortegano]

Oh, that's quite helpful, will try the alternative.

Just to clarify, parsing two BAMs would be done with cnvnator -root out.root -tree file1.bam file2.bam ..., right? I thought to have read in another issue here that only one sample was supported, but if I can use cnvnator with several BAMs from the beginning that'd be great.

[abyzov]

Yes, I believe that command will work.

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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978

On Mar 17, 2022, at 2:32 PM, elcortegano @.**@.>> wrote:

Oh, that's quite helpful, will try the alternative.

Just to clarify, parsing two BAMs would be done with cnvnator -root out.root -tree file1.bam file2.bam ..., right? I thought to have read in another issue here that only one sample was supported, but if I can use cnvnator with several BAMs from the beginning that'd be great.

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[elcortegano]

It works great, thanks for the support!