Hi I have created the index files for my reference genome following the guidelines and had no errors.
This is what I wrote:
$PICARD CreateSequenceDictionary \
REFERENCE=Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa \
OUTPUT=Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.dict
samtools faidx Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
bwa index -a bwtsw Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
When I try to use the command:
bwa mem -M -t 1 -p Path/to/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa \
HEX-50_samtofastq_interleaved.fq > HEX-50_bwa_mem.sam
I get this error:
[E::bwa_idx_load_from_disk] fail to locate the index files
Everything is within the same directory, so what have I done wrong here?