FreeBayes encountered a sudden error

Question

[emilydolivo97]

I'm used to run the same freebayes code on my BAM files. I tried today to rerun the same code on the same bam files using the same conda env but I have this error. I'm using these packages version :

• minimap2==2.26
• samtools==1.19.2
• freebayes==1.3.7

( in my script I combined minimap2 and freebayes)

/opt/conda/conda-bld/freebayes_1711687983774/_build_env/x86_64-conda-linux-gnu/include/c++/12.3.0/bits/stl_vector.h:1123: std::vector<_Tp, _Alloc>::reference std::vector<_Tp, _Alloc>::operator [with _Tp = Allele; _Alloc = std::allocator<Allele>; reference = Allele*&; size_type = long unsigned int]: Assertion '__n < this->size()' failed. Aborted (core dumped)

[Pierre Lindenbaum]

cross-posted;: https://github.com/freebayes/freebayes/issues/794

[emilydolivo97]

Yes Sir, because it's urgent. To increase my chances of receiving a response, I posted on both Biostars and GitHub

[Michael]

I think it will be best answered by the developer. However, I suspect that you are experiencing out-of-memory conditions. Your best bet to get this done quickly is to free some RAM or move it to a larger machine.

[emilydolivo97]

thank you Sir , I don't know , because I have 29G of RAM memory

[Michael]

You seemingly resolved your issue by downgrading. However, you wrote you used the same version before, so I doubt that this minor version change touches the core of the issue here. In the optimal case you would send the developer your core file for debugging. Anyway, 29GB isn't that much, just in case you encounter the same error in the future I'd simply try a larger VM.

[Pierre Lindenbaum]

you did not link between the two so no one knows that you're asking two sets of online volunteers to spend their time on your problem without telling them that you're also asking the other group.

[emilydolivo97]

I'm really sorry for that , but as I said it's something urgent

Answer 1

[emilydolivo97]

I downgraded the FreeBayes version to 1.3.6, and it resolved the issue.