[UPDATE] So sorry to update this so late, this turned out to be an error due to a hardware issue and was fixed when the hard disk was replaced.
I'm trying to align paired-end read files to the reference genome using the following command (bwa version: 0.7.17-r1188):
bwa mem $ref_genome_fasta Sample_R1_001.fastq.gz Sample_R2_001.fastq.gz
I get the following error after a few seconds:
[fread] Input/output error
[UPDATE] I was thinking it might be because of an issue with the input fastq.gz files but I checked them using fqtools -validate and they seem valid.
Has anyone encountered this issue or can help me to resolve it?