Kallisto returns 'illegal instruction' when running commands

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Eleanor Ward

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Mar 10, 2024, 3:11:21 PMMar 10

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Hi,

I am using Kallisto through the conda package manager, using a a linux x86.64 WSL2 on windows. I have installed kallisto, fastqc and multiqc into an environment to use for rna-seq. I have checked that kallisto is update to date. I downloaded the mouse GRCm39 reference transcriptome from ensembl and unzipped it using gunzip.

I then tried to build the index using kallisto index -i Mus_musculus.GRCm39.cdna.all.index Mus_musculus.GRCm39.cdna.all.fa and the terminal returns 'Illegal instruction'. I know I can download an index to use instead but I'm really keen to know why this is happening.

This also happens when I try to quantify transcript counts with 'kallisto quant -i mouse_index.idx -o SRR1596111 -b 100 -t 8 SRR1596111_pass_1.fastq.gz SRR1596111_pass_2.fastq.gz' - the terminal returns '[quant] fragment length distribution will be estimated from the data Illegal instruction'

Any ideas as to how I can make kallisto work? I'm using the 0.50.1 version and have updated/ upgraded/ removed and reinstalled it etc.