schmigle

Patch error: "Tuple Index out of Range"

2

I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching long-read sections. The RagTag "patch"...

VOGDB issue--extra enclosing folder

4

After repeatedly running into the following error when trying to extract the VOG databases: ``` The subcommand ['hmmpress', '-f', 'DRAM_data/vog_latest_hmms.txt'] experienced an error: Error: File format problem in trying to...

Empty Array During Refinement

9

During `rosella recover`, encountered the following error immediately following attempted refinement: ``` Traceback (most recent call last): File "/opt/miniconda/envs/rosella/bin/flight", line 10, in sys.exit(main()) File "/opt/miniconda/envs/rosella/lib/python3.10/site-packages/flight/flight.py", line 465, in main args.func(args)...

makepaddedseqdb issue

3

I'm trying to make a pipeline using foldseek easy-search, and I'd like it to be GPU-compatible, both to generate structures with prostt5 and to run rapid comparisons. However, the padding...