"Error in <ROOT::Math::FitResult>: FitConfiguration and Minimizer result are not consistent" in the step of stat

[heixiong1990]

my root version: root_v6.22.00 cnvnator: the latest version my command: step1: cnvnator -root AWS007C5.root -chrom chr1 chr2 chr3 chr4 -tree AWS007C5.bam
step2: cnvnator -root AWS007C5.root -chrom chr1 chr2 chr3 chr4 -d contig_dir/ -his 100 step3: cnvnator -root AWS007C5.root -chrom chr1 chr2 chr3 chr4 -stat 100 step4: cnvnator -root AWS007C5.root -chrom chr1 chr2 chr3 chr4 -partition 100 step5: cnvnator -root AWS007C5.root -chrom chr1 chr2 chr3 chr4 -call 100

Error log: The error in step3: "Error in : FitConfiguration and Minimizer result are not consistent". The log in step4: "Partitioning RD signal for 'chr1' with bin size of 100 ... Number of free parameters from FitConfig = 3 Number of free parameters from Minimizer = 2 Average RD per bin is 0 +- 0 Bin band is 2 BIn band is 3 Bin band is 4 ... Bin band is 128 Partitioning RD signal for 'chr2' with bin size of 100 ... ..." The err in step4: "Error in : FitConfiguration and Minimizer result are not consistent Abnormal range (0, -1) Abnormal range (1, 0) Abnormal range (2, 1) ..." Is it because of my parameters or my environment?

[abyzov]

Hi, most likely it is because the tools can determine robustly average RD. If you have shallow coverage you may try to run the tool with large bin size.

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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

[heixiong1990]

Hi, most likely it is because the tools can determine robustly average RD. If you have shallow coverage you may try to run the tool with large bin size. 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 3-12 Rochester, MN 55905 www.abyzovlab.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

Thanks. I have try other bin size, 200 and 1000, but the same error occured. My data is wgs, covering a depth of about 40X. could you give me some advice?

[abyzov]

Hi, sorry for slow response. Could you try doing that for all chromosomes, i.e., without specifying chr1, chr2, etc.

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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

On Jul 24, 2020, at 1:51 AM, heixiong1990 notifications@github.com<mailto:notifications@github.com> wrote:

Hi, most likely it is because the tools can determine robustly average RD. If you have shallow coverage you may try to run the tool with large bin size. 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 3-12 Rochester, MN 55905 www.abyzovlab.orghttp://www.abyzovlab.org<http://www.abyzovlab.org%3Chttp://www.abyzovlab.org> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745

Thanks. I have try other bin size, 200 and 1000, but the same error occured. My data is wgs, covering a depth of about 40X. could you give me some advice?

— You are receiving this because you commented. Reply to this email directly, view it on GitHubhttps://github.com/abyzovlab/CNVnator/issues/214#issuecomment-663373631, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLKGOPHAEQJSQH6GS66DZ3R5EVNZANCNFSM4PFKE57A.

[tamadezhenshiyuncai]

Hi, sorry for slow response. Could you try doing that for all chromosomes, i.e., without specifying chr1, chr2, etc. 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 3-12 Rochester, MN 55905 www.abyzovlab.org<http://www.abyzovlab.org> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745 On Jul 24, 2020, at 1:51 AM, heixiong1990 notifications@github.com<mailto:notifications@github.com> wrote: Hi, most likely it is because the tools can determine robustly average RD. If you have shallow coverage you may try to run the tool with large bin size. 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 3-12 Rochester, MN 55905 www.abyzovlab.org<http://www.abyzovlab.org<http://www.abyzovlab.org%3Chttp://www.abyzovlab.org>> tel: +1-(507)-538-0978 fax: +1-(507)-284-0745 Thanks. I have try other bin size, 200 and 1000, but the same error occured. My data is wgs, covering a depth of about 40X. could you give me some advice? — You are receiving this because you commented. Reply to this email directly, view it on GitHub<#214 (comment)>, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ACLKGOPHAEQJSQH6GS66DZ3R5EVNZANCNFSM4PFKE57A.

the same error occured without specifying chr1, chr2, etc.

[abyzov]

Could you please provide the command that you executed and the output you got from CNVnator.

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 fax: +1-(507)-284-0745