This question has been asked previously, but unfortunately for me the solutions posted did not resolve my issue. I am trying to use BWA to align my ddradseq paired end reads to a reference genome, and keep running into the issue of the program throwing the error [E::bwa_idx_load_from_disk] fail to locate the index files.
This is the code I am using:
# Load the BWA module:
module load bwa
bwa mem -t 2 genome/genome.fasta \ processrad_out/sample1.1.fq.gz processrad_out/sample1.2.fq.gz \
>bwa_out/sample1.sam
My data it stored in the 'processrad_out' directory, indexed genome in the 'genome' directory, and I want the output to be stored in the 'bwa_out' directory.
I have already indexed the genome, and have tried running my script in the indexed genome directly, but still seem to have the same issue. These are the indexed files I have:
LeachsGenome.fasta
LeachsGenome.fasta.ann
LeachsGenome.fasta.fai
LeachsGenome.fasta.sa
LeachsGenome.fasta.amb
LeachsGenome.fasta.bwt
LeachsGenome.fasta.pac
Previously when I indexed I was missing the .fai file but managed to correct that issue. Despite, the program is still having difficulty locating the indexed files. I have also tried re-indexing as that seems to have worked for some people but no such luck. I know my paths are correct and I can quite figure out what the correct solution is.
I am fairly new to bioinformatics and am trying to learn as much as I can. Any suggestions are welcome and highly appriciated!