Tobias Baril
Tobias Baril
Hey all! Just a quick update on this - we have tracked this to the memory-hungry EMBOSS `water` implementation, which also seems to be the root of #163. We are...
This has been pushed in release `5.1.0`. I will add more patch notes shortly, but the main change is a shift away from using `water` for alignments to using `matcher`...
Version 5.1.0 contains the changes that should solve these issues. It is currently waiting for approval in bioconda so should be live later this evening or tomorrow depending on when...
Thanks for sharing @gemmacol. This looks like TEstrainer finished as expected (@jamesdgalbraith could confirm for sure). The OOM is potentially happening during the file tidying steps of TEstrainer. In your...
Hi @gemmacol, Thanks for the update! In this case, I reckon the culprit might be the divergence calculator as this performs lots of alignments, which gets quite memory hungry on...
Hi, This looks like an issue with Bioconductor. I haven't been able to reproduce this issue - is there anything unusual about your system (permissions, OS, etc?). Sometimes these post-script...
closing due to lack of activity
In this case, the best solution is to use the prebuilt docker/singularity container - I am not responsible for and do not have the capacity to maintain bioconductor packages, they...
Hi @manwensu, any updates on the RepeatModeler run? Some of the solutions suggested in #145 might work for future runs, and at least prevent the eternal elongation of strange low...
Closing due to lack of activity. For more assistance, please open a new issue.