Illegal Instruction creating Kallisto reference index

Hi everyone! I am new to data sciences. I need to train to analyze scRNAseq data by myself. To do so, I need to first create an index using reference human genome (dowloaded on Ensembl as FASTA file: Homo_sapiens.GRCh38.cdna.all.fa ). I follow online lectures and he recommands us to use kallisto (0.50.0) in conda environment. I got the line of code to create this index which is: kallisto index -i Homo_sapiens.GRCh38.cdna.all.index Homo_sapiens.GRCh38.cdna.all.fa but after any try I got the error message “Illegal instruction”. I can not find any similar topic so I looking for some help with this.

Thank you

Having the exact same issue right now, what CPU are you using?, are you running from native linux or in Windows Subsystem for Linux? I have tried both options on a Ryzen 5 5500 I do not think my CPU is incompatible with kallisto

I have fixed the issue by reinstalling it manually.

you can follow the steps here: Source

Good luck!

I had the same problem but fix it reinstalling Kallisto through Homebrew insted of Conda.

I intalled Homebrew with this command:
/bin/bash -c “$(curl -fsSL”

Then you have to have to run 2 more commands:
(echo; echo ‘eval “$(/opt/homebrew/bin/brew shellenv)”’) >> /Users/emanuelmuruaga/.zprofile

eval “$(/opt/homebrew/bin/brew shellenv)”

And then you can instal kallisto with this command
brew install kallisto

That’s all! Good luck

Hello! I also encountered this issue, and was able to identify it: Kallisto 0.50.0 was built on a machine with support for AVX-512 CPU instructions. If you run it on a machine that does not have AVX-512 (which is many CPUs), you’ll get the “Illegal Instruction” error.

Here’s the bioconda-recipes bug report: kallisto 0.50.0 fails with "Illegal instruction" · Issue #42633 · bioconda/bioconda-recipes · GitHub

Here’s the kallisto bug report: Illegal instruction error when running kallisto index · Issue #399 · pachterlab/kallisto · GitHub