Illegal Instruction creating Kallisto reference index

Technical Topics Data Science, ML & AI
1

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

2

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

3

I have fixed the issue by reinstalling it manually.

you can follow the steps here: Source

Good luck!

4

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 https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)”

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

5

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