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abyzovlab / CNVnator

a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
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*** Break *** segmentation violation #245

Open Saeideh-Ashouri opened 3 years ago

Saeideh-Ashouri commented 3 years ago

Hello @abyzov

I am using CNVnator on WGS data of human genome with the reference genome hg38. It runs successfully until the step for calling CNVs. However, in the step to get the support reads for CNV calls, I get " Break segmentation violation" error. I run CNVnator using singularity and this is my command:

singularity exec -B /path/to/data/ cnvnator.sif cnvnator -pe /path/to/bam/file -qual 20 -over 0.8 -root /path/to/root/file -f /path/to/CNV/calls

The error message is:

Error in : error reading all requested bytes from file null, got 204 of 300 Error in : null failed to read the file type data. Can't open file 'null'.

Break segmentation violation Generating stack trace... 0x00005555555e3eb0 in from /CNVnator_v0.4.1/src/cnvnator 0x00005555555d7a91 in from /CNVnator_v0.4.1/src/cnvnator 0x00005555555a04a6 in from /CNVnator_v0.4.1/src/cnvnator 0x00005555555a1868 in from /CNVnator_v0.4.1/src/cnvnator 0x000055555556a0c5 in from /CNVnator_v0.4.1/src/cnvnator 0x00002aaaac2bd0b3 in __libc_start_main + 0xf3 from /lib/x86_64-linux-gnu/libc.so.6 0x000055555556c54e in from /CNVnator_v0.4.1/src/cnvnator

Any ideas why this happens? And any recommendation to get it solved?

Thank you in advance, Saeideh

abyzov commented 3 years ago

Hi, the error message is not that informative. My guess is that it can’t find some input file. Please check.

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