Joanna Rifkin

Hi! I think I'm getting a similar error to this series, and was wondering if cooketho's steps solved the problem or if there's something else I should do. I'm trying...

Hi Shujun, Thanks for getting back to me so quickly! I've been using version 2.0.0. I'm working on several plant genomes in the Brassicaceae, some small, some large and TE-rich....

Hi again Shujun, Any thoughts about running panEDTA via Singularity? Thanks so much for all your help! Joanna On Wed, May 24, 2023 at 3:34 PM Joanna R. ***@***.***> wrote:...

Hi again, Thanks again for your awesome program! Any sense on whether panEDTA is likely to be working with Singularity soon or whether I should find a workaround? I can...

Hi Shujun, Thanks, that's very helpful! I'll do that. Thank you again! Joanna On Tue, Jun 27, 2023 at 5:21 PM Shujun Ou ***@***.***> wrote: > Hi Joanna, > >...

Thanks so much! I ended up just solving this by switching to the conda install, which seems to be working well. Thanks again! Joanna On Tue, Sep 12, 2023 at...

Hi Shujun, Thanks! I have the new version running, and I'm getting the following error: > ERROR: Raw LTR results not found in Crubella_474_v1_names_shortened.1.cds.fa.mod.EDTA.raw/Crubella_474_v1_names_shortened.1.cds.fa.mod.LTR.raw.fa > If you believe the program...

Hi Shujun, Thanks! I know it's not supposed to be trying to annotate the TEs in the CDS - I don't understand why it is trying to do so. When...

Hi again! I tried rerunning it with the genomes + CDS list in a different order and got this error: > Wed Aug 9 15:24:54 EDT 2023 ERROR: Fail to...

Hi Shujun, Gotcha. So instead of: genome genome cds genome cds I should have genome [related cds] genome cds genome cds Right? Would it be better to just fill in...