Joanna Rifkin

Excellent, thanks! On Wed, Aug 9, 2023 at 3:51 PM Shujun Ou ***@***.***> wrote: > Yes, that's correct. Try something closer but with good gene annotation > quality, otherwise, Arabidopsis...

Hi again! I tried just using the Arabidopsis CDS seem to get the same issue: > Error: Error while loading sequence > perl make_bed_with_intact.pl EDTA.intact.fa > EDTA.intact.bed > > Wed...

Hi Shujun, Thanks, I'll give that a try. Cheers, Joanna On Tue, Aug 15, 2023 at 11:31 PM Shujun Ou ***@***.***> wrote: > Hi Joanna, > > The easiest "fix"...

Hi Shujun, I've tried submitting the job with "bash" rather than "sh" but it doesn't seem to change the main problem, where it's trying to annotate the CDS file. Here's...

Hi Shujun, Good news! It's not trying to annotate TEs in CDS any more. It doesn't seem to be able to locate CDS with a path outside of the directory...

Hi again, I think this is still possibly an issue: when I try to run panEDTA with symlinks to completed EDTA runs in other directories, it makes this non-functioning symlink...

Hi Shujun, Thanks! I'm just running panEDTA and doing everything de novo in sequence, and that seems to be working fine. I figured since everything needed to be redone with...

Great, thank you! On Mon, Mar 18, 2024 at 4:38 PM Shujun Ou ***@***.***> wrote: > If the issue is resolved, I will close this thread. Please reopen or open...

Hi again, Any sense of what's going on here? Thanks! Joanna

Hello again, Just wondering whether you had any thoughts about what might be wrong here. I tried running just the reannotation command (perl $path/EDTA.pl --genome $genome -t $threads --step final...