Geo Pertea

That GVec error suggests an integer overflow happening (that value should never be negative). It is possible there is a specific, very large bundle causing this issue. If you run...

As it crashes please look at the last line of the log - if it starts with `^bundle` and has the word "done" following the genomic location it means the...

That's a monster bundle with 7 million alignments (4 million distinct) and 740k junctions. Processing such a bundle, with such a large number of junctions can also take a lot...

Can you clarify what the error message says exactly? If the GVec error message shows a negative value, that is a possible sign of integer overflow (bundles may be too...

@pratora, my apologies for the delay, I got the bundle data you shared (thank you!) and thanks to it, we were able to find the problem, we'll fix it in...

Fixed by commit 5f21416 Fix included in release v2.2.2. @pratarora let me know if that fully solves the problem on your data, which seem to have very large bundles.

Thank you so much for the confirmation. This still ties into a larger issue about 64bit conversion being needed for some internal data structures, that I have to address, but...

This is usually caused by read alignments spanning/bridging the two genes when they are very close to each other, and there is currently no easy solution for that - if...

interesting - thank you for these reports related to parsing failures of this viral annotation. In this particular case I can see that some CDSs are dropped when they are...

StringTie does not output any CDS features (only `exon` features), which are needed by `-x` -and `-y` options of gffread. You might want to run an ORF finder program (e.g....