sung

Hi, Before I begin, thanks for the wonderful pipeline! Without Prokka I wouldn't be able to study half the things I'm doing right now. Prokka annotation of our lab's Haloarchaeal...

Error during processing, no result output - TypeError: expected str, bytes or os.PathLike object, not StringIO

2

Hello, PhisPy process errors out and doesn't produce results file - confirmed same behavior on both separate venv & pip installation and conda environment installation. Attaching error message (this one...

[Feedback] gtt-gen-SCG-HMMs vs SCG sets wiki instruction output

1

Hi, I thought you might like a feedback post for the SCG generator script vs the wiki instruction. I just finished running a test run of the gtt-gen-SCG-HMMs script versus...

gtt-gen-SCG-HMMs: Downloading the PFam HMM information file failed

3

I'm trying to build a custom SCG set using GToTree's built in SCG screening tool (which usually works wonderfully by the way). Right now I'm getting "Downloading the PFam HMM...

### Question I'm testing out ClipKIT on hmmalign output which contains '.' characters depicting insertion gaps (as for hmmalign's logic for what is an insertion gap relative to a reference,...

Yet another protein fasta formatting issue

2

I'm working with a genome where the standard Bakta database annotation returns about 4k of 4.5k predicted genes as hypothetical proteins. I have a large protein fasta file that's gotten...