title: Commands are not executed when running code through system in a for loop
body: <p>This is my first time creating a for loop with two variables. I have a bunch of DNA sequencing samples that I want to run through. Each set of data has two files that needs to be run at the same time. </p>
  
  <p>When I just run the system(paste()) in R without the for loop variables, it works just fine. So I know that the issue is with the loop itself. When I run the script below, I don't get an error, it runs but nothing happens. </p>
  
  <p>I obviously messed something up. I just don't know where to go from here. </p>
  
  <pre><code>for (j in list.files(pattern = "R1_001.trim.paired.fastq.gz")) {
    for (h in list.files(pattern = "R2_001.trim.paired.fastq.gz")) {
      outname=paste(substr(j, start=1, stop=7), sep= "")
      system(paste("docker run -v /path/:/path/ -w /path/ combinelab/salmon salmon quant -i /path/CanFam3.1_index -l A -1 ",j,"-2 ",h,"-o ",outname, ,sep="")
      )
    }
  }
  </code></pre>