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abyzovlab / AGE

a tools that implements an algorithm for optimal alignment of sequences with structural variants (SVs)
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Error #3

Open CGNAT opened 5 years ago

CGNAT commented 5 years ago

Hi I get the following error when submitting directly on the command line on our HPC server. terminate called after throwing an instance of 'std::bad_alloc' what(): std::bad_alloc Aborted

This error also leads me to believe that the program will hang if it doesnt have enough memory or, it cannot run the program on such large files.

Is this due to the file size being too large? The program will run with large files of the same sequence but crashes if I try to run it on smaller 10Mb (Bytes) chunks of the reference sequence. Looking around has led me to believe that this is a memory issue. Is this correct?

Ideally, I want to look for breakpoints across the entire genome. Is this possible using AGE?

Thank you!

abyzov commented 5 years ago

Hi, the current implementation does not allow to align against large genomic regions as it indeed allocates to much memory. Overall, AGE is not aimed at aligning against entire genome as it is not fast. Its purpose is to realign contigs/reads around SV breakpoints. These breakpoints should be known with some rough resolution.

Alexej Abyzov, Ph.D. Senior Associate Consultant, Assistant 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