title: BWA fails to locate index genome
body: <p>I know this question has been asked before. I have searched through the threads and nothing has made a ton of sense to me. Admittedly, I am a newbie at bioinformatics so maybe the answer is clear to someone with more experience.</p>
  
  <p>I am trying to use BWA to align reads to a reference genome and keep the discarded reads, as I am looking for potential pathogen DNA (RNA, really) that could have been infecting the host.</p>
  
  <p>I have created, I think correctly, an index of the reference genome. I have the following files:</p>
  
  <p><code>_genome.fa</code></p>
  
  <p><code>_genome.fa.amb</code></p>
  
  <p><code>_genome.fa.ann</code></p>
  
  <p><code>_genome.fa.bwt</code></p>
  
  <p><code>_genome.fa.pac</code></p>
  
  <p><code>_genome.fa.sa</code></p>
  
  <p>I wanted to align paired-end reads to that index and keep the discards. That code is:</p>
  
  <p><code>module load swset/2018.05</code></p>
  
  <p><code>module load gcc/7.3.0</code></p>
  
  <p><code>module load bwa</code></p>
  
  <p><code>bwa mem ~/correctpath/_genome.fa correctfilename_R1_001.fastq correctfilename_R2_001.fastq -a &gt; sample_bwa.sam</code></p>
  
  <p>I continue to get the error:</p>
  
  <p><code>[E::bwa_idx_load_from_disk] fail to locate the index files</code></p>
  
  <p>I'm 99.% sure I have the file paths correct. I may have loaded the wrong BWA version. I may have created indexes incorrectly. Or maybe there is something obviously wrong in my bwa mem code.</p>
  
  <p>Again, I've tried to read through other similar posts, but nothing has made a ton of sense to me. Which is probably my fault.</p>
  
  <p>Can someone help?</p>
  
  <p>Thanks!</p>