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basilkhuder / Seurat-to-RNA-Velocity

A guide to using a Seurat object in conjunction with RNA Velocity
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Kallisto Bustools "Failed to find compatible kallisto binary." #17

Closed SimoniMD closed 2 years ago

SimoniMD commented 2 years ago

Hi! Thanks for this tutorial.

I'm stuck at the first part of the tutorial. I've managed to get the .gtf and .fa, and this is my code, but i'm getting an error with kb-bustools

kb ref -i index.idx -g t2g.txt -f1 cdna.fa -f2 intron.fa -c1 cdna_t2c.txt -c2 intron_t2c.txt --workflow lamanno -n 4 Homo_sapiens.GRCh38.cdna.all.fa Homo_sapiens.GRCh38.104.gtf

and my error generated is: Traceback (most recent call last): File "/home/simonim/anaconda2/envs/kb/bin/kb", line 8, in <module> sys.exit(main()) File "/home/simonim/anaconda2/envs/kb/lib/python3.8/site-packages/ngs_tools/logging.py", line 62, in inner return func(*args, **kwargs) File "/home/simonim/anaconda2/envs/kb/lib/python3.8/site-packages/kb_python/main.py", line 1346, in main raise UnsupportedOSError( kb_python.config.UnsupportedOSError: Failed to find compatible kallisto binary. Provide a compatible binary with the--kallistooption or runkb compile.

I thought this had something to do with the file path, but I'm running the command in the same folder as the .fa and .gtf, and have played around with that with no success. any thoughts?

SimoniMD commented 2 years ago

Nevermind, figured it out!

Jiangmeling commented 2 years ago

Hello, I have the same problem as above. How do you solve it?