Francesco Cicconardi

I'll rerun it, no problem! ;) F

Hi @KatharinaHoff, I re-run everything wiht --UTR=off. It looks like everything went smooth with the `BRAKER RUN FINISHED` in the log file. Is the final result `augustus.hints.*` right? Cheers F...

I see a lot of inconsistencies in the GTF, I mean the exon feature in the 3rd column is missing. It's really hard to convert and handle the file. F

I don't kown @leleory, it seems very convoluted and prone to errors. I'm using mikado and it's very stringent, any single coordinate error makes it complain. F

Sorry, I think I was a bit grumpy HAHAHAH. I'm just fighting with these conversions for a few days, it's so frustrating. You're doing a great job!!! Seriously. Sorry again!...

Hi @Geraldene, I deleted all files and re-run the pipeline from scratch. It worked. Cheers F

It looks like I solved the problem, apparently, nucmer runs out of memory. You have to recompile it. @jokelley, google the actual error from the nucmer error log file, I...

@aganezov, The idea that I have, but honestly don't know if it is correct, is trying to merge two assemblies produced from the same set of reads but a different...

Make sense now, let's see if I understand it. I'll make a "graphical" description ``` Assembly1 CATCGATCGTACGTAGCTAGCTAGCTAGCTCGTACGTACGTACG ||||||||||||||||||||||||||||||| Assembly2 TACGTAGCTAGCTAGCTAGCTCGTACGTACGTACGATCGATCGCT Contigs.fasta -> TACGTAGCTAGCTAGCTAGCTCGTACGTACG Assembly1 -> CATCGATCGTACGTAGCTAGCTAGCTAGCTCGTACGTACGTACG Assembly2 -> TACGTAGCTAGCTAGCTAGCTCGTACGTACGTACGATCGATCGCT ```...

Not trivial, considering that there could be differences in the aligned portion. How would you do that? With a reciprocal blast search I would find homologous contigs, but the actual...