Juan Montenegro Cabrera

Hello everyone, I am getting a similar error with this version of braker. This are the last 10 lines of the log: ``` [Wed Jul 20 18:08:55 2022] Alignment of...

Thank you Tomas, I tried as you suggested and got a warning when running the protein-based braker: ``` #********* # WARNING: # The hints file(s) for GeneMark-EX contain less than...

The assembly is nearly a chromosome-level assembly, 97% of the assembly is in 23 contigs (15 chromosomes expected), so I would say it's not really fragmented. In the RNAseq run,...

Thanks Thomas, and thank you for suggesting tsebra. It has worked quite nicely with my assemblies. Do you think tsebra can be used to merge braker runs with isoseq-derived annotations...

Dear Ivan, Thank you for your reply. I will give raptor a go. I currently have the gfa with the sequences embedded and also the contigs which should be the...

Hi Ivan, I am getting this issue trying to install raptor in my $HOME in my cluster: PermissionError: [Errno 13] Permission denied: '/usr/include/ncbi-vdb' make[1]: *** [Makefile:41: configure] Error 2 make[1]:...

Hi Ivan, thank you for your reply, I installed meson and ninja into my $HOME using pip pip install meson ninja --user then I moved to the the raptor root...

Well, finally got it to compile correctly. Perhaps I had some unmet dependency when trying to compile with bam compatibility. Thank you, I will give it a try now Cheers,...

I just tried So the compilation worked, but the tests failed: ``` $ make unit make install BDIR=meson-release-pb make[1]: Entering directory '/home/jmontenegro/soft/raptor' ninja -C meson-release-pb reconfigure ninja: Entering directory `meson-release-pb'...

Hi Ivan, Thank you for your reply. I think we finally got it installed in the cluster. I found a header in the GFA file: H VN:Z:1.0 is that a...