Kallisto returns 'illegal instruction' when running commands

Question

[Eleanor]

Hi,

I am trying do pseudoalignment for RNA-seq analysis using Kallisto. 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.

However, 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.

Thanks

[GenoMax]

Are you able to run kallisto version? Does that print version information?

[Eleanor]

Yes, I'm using version 0.50.1 !

[GenoMax]

Not clear if are you able to run the command I mentioned above and get this version information? If you are then the answer given by @bioinfoguy may not apply.

[bioinfoguy]

That's not quite true. The illegal instruction is triggered at the point the CPU attempts to execute the illegal machine instruction (i.e. an instruction not supported in its microcode), not when the program is loaded. This means this error will only arise in execution paths that trigger it, like indexing or quantification, and not necessarily all commands, like printing the version.

[GenoMax]

Sure. If one are using a different OS on an identical underlying CPU architecture or if one is using an older Intel/AMD CPU that lacks specific instruction sets like SSE2 etc that the software is compiled for. Since OP is running WSL2 I am going guess that they are using a reasonably new CPU.

I just wanted to confirm if OP is able to run the executable they got i.e. there was no obvious architecture mismatch. e.g. trying to run macOS kallisto on linux results in an immediate error.

$ ./kallisto
-bash: ./kallisto: cannot execute binary file: Exec format error

Answer 1

[bioinfoguy]

This likely means that you are using a version of the executable compiled making use of CPU instructions that your CPU doesn't have. You could try to obtain the executable in another way, compile it yourself, or run it on another computer if you have access to one.