I have searched throughout the site and I still can't find an answer. I have ref genome hg38.fa and bwa index files in the same directory/folder I am trying to align a fastq file but it keeps returning this
[M::bwa_idx_load_from_disk] read 0 ALT contigs [fread] Unexpected end of file
I have tried re-indexing, and re-downloading the fastq files. Still the same error. Is it a problem of directory?