Question: Illegal instruction (core dumped) - Indexing a reference genome with STAR
0
gravatar for compuTE
2.5 years ago by
compuTE50
compuTE50 wrote:

Hello,

As the title suggests, I'm trying to index a reference genome (.fna and .gff of hg38 from the latest major release of https://www.ncbi.nlm.nih.gov/grc/human) with STAR aligner.

This is my script

#!/bin/bash
#SBATCH -A $group_name
#SBATCH -n 16
#SBATCH -N 1
#SBATCH -t 03:00:00
#SBATCH -J reference_genome_STAR_hg38
#SBATCH -o %j.STAR_reference.out
#SBATCH -e %j.STAR_reference.err

ml GCC/4.9.3-binutils-2.25
ml STAR/2.5.0a

STAR --runThreadN 16 --runMode genomeGenerate --genomeFastaFiles genome.fna --sjdbGTFfile annotation.gff --genomeDir ./reference_genome/ --sjdbOverhang 101

For some reason the job fails and I get

Illegal instruction     (core dumped) STAR --runThreadN 16 --runMode genomeGenerate --genomeFastaFiles genome.fna --sjdbGTFfile annotation.gff --genomeDir ./reference_genome/ --sjdbOverhang 101

On my stderr file.

Any help would be well appreciated, this is the first time I use this software and I'm pretty lost.

Note: I tested it with a smaller genome and annotation file and the problem persists.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by compuTE50
1

@Alex Dobin also makes pre-made indexes available here, if that works for you.

ADD REPLYlink written 2.5 years ago by genomax90k

I will get it from here. Thank you! :)

ADD REPLYlink written 2.5 years ago by compuTE50

How much memory are you assigning to the job? You would need at least 30+GB.

ADD REPLYlink written 2.5 years ago by genomax90k

I'm not sure how they installed STAR, so try providing your own version (you can download a binary from bioconda). Perhaps they installed it in an odd way.

ADD REPLYlink written 2.5 years ago by Devon Ryan96k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1940 users visited in the last hour