I am trying do pseudoalignment for RNA-seq analysis using Kallisto. I am using Kallisto through the miniconda3 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 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
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.
I tried updating / upgrading kallisto in conda and removing then reinstalling the package. I've tried changing the names of the index / fasta file , using zipped and unzipped fasta files to create the index, using .index and .idx to specify the index file. I changed the directory where my files were and removed the package sra-tools from the conda environment before removing and reinstalling kallisto again. I have no idea what the problem is!
Thanks