Closed hoeferjanka closed 4 months ago
Hi Janka, great work attempting to debug
Please see issue #420 for a possible solution
Illegal instruction is probably caused by the kallisto binary not being compitable with your cpu. Running previous version of kallisto solves the issue for most users
Hi Hadas,
Thanks for the help! Using a different version solved the issue for me.
Using kallisto version 0.46 worked for me in the end. I am leaving my solution steps here, in case someone else needs it!
Because there is no index.idx available for download for this kallisto version (index and version must be compatible), I had to create one. Here is the code I used:
wget ftp://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz wget ftp://ftp.ensembl.org/pub/release-108/gtf/mus_musculus/Mus_musculus.GRCm39.108.gtf.gz
gunzip Mus_musculus.GRCm39.dna.primary_assembly.fa.gz gunzip Mus_musculus.GRCm39.108.gtf.gz
conda install -c bioconda gffread
gffread Mus_musculus.GRCm39.108.gtf -g Mus_musculus.GRCm39.dna.primary_assembly.fa -w transcripts.fa
kallisto index -i mouse_index.idx transcripts.fa
with this mouse_index.idx I can now run the kallisto quant commands and i get the abundance.tsv files.
Hi,
I have an issue running kallisto quant. The command i am running to index files is as follows:
$ kallisto quant -i index.idx -o kallisto_output_SRR24163115 -t 12 SRR24163115_1P.fastq SRR24163115_2P.fastq
[quant] fragment length distribution will be estimated from the data Illegal instruction
I keep receiving the "Illegal instruction" message. From researching on this issue i found that i have to check out the following things, which could cause the problem: I made sure that my input files are intact fastq files. I made sure that I have enough RAM and the needed CPU compatibility. I made sure that the kallisto version i am using (0.50.1) is the version the index.idx was created with. I tried updating conda and after updating it restarting the computer. The issue is still there. I tried deinstalling and reinstalling both kallisto and the index files.
After all this did resolve the error, i tried to creat an index myslef by downloading the files from the kallisto GitHub site: Mus_musculus.GRCm39.108.gtf.gz and Mus_musculus.GRCm39.dna.primary_assembly.fa.gz
I created a fasta file from these two with this command: $ gffread Mus_musculus.GRCm39.108.gtf -g Mus_musculus.GRCm39.dna.primary_assembly.fa -w transcripts.fa
When trying to create the index with kallisto, i got the same error as earlier:
$ kallisto index -i mouse_index.idx transcripts.fa
Illegal instruction
My next step is to ask for advice here. I am not sure which other options i have to try out.
Thanks!
Janka