title: Why does fastx_trimmer think that my fastq file is an unknown file format?
body: <p>I have some .fastq files from an Illumina NextSeq run. Many of the sequences have poly-A tracts that complicate mapping them. I want to remove all sequences of ten consecutive A's and have been trying to do so using fastx_clipper as follows:</p>
  
  <pre><code>ha1c6n8$ fastx_clipper -l 32 -Q33 -n -v -a AAAAAAAAAA –i FR0826_S1_L004_R1_001.fastq –o FR0826_L004_trimmed.fastq
  </code></pre>
  
  <p>This has resulted in the following error message:</p>
  
  <pre><code>fastx_clipper: input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)
  </code></pre>
  
  <p>I'm not entirely sure what this means. I looked into the fastq file using head:</p>
  
  <pre><code>ha5c6n8$ head FR0826_S1_L004_R1_001.fastq
  
  @NS500289:18:H1237BGXX:4:11401:2791:1023 1:N:0:1
  NCTACATTGGTTCCTCAGCCAAGCACATACACCAAATGTCTGAACCTGCGGTACCTCTCGTACTGAGCAGGATT
  +
  #&lt;&lt;AAFAFFFAFFFFF7FF)FF.F&lt;FAFFFFF&lt;FF.AFFF7F.F.FFAFFFF)7AF7F&lt;FFF&lt;&lt;F7FFFFFF7F
  @NS500289:18:H1237BGXX:4:11401:19266:1023 1:N:0:1
  NAATGGGTCTGCGAGAGCGCCAGCTATCCTGAGGGAAACTTCGGAGGGGGCCGGCTACTAGATGGTTCGCTTAGT
  +
  #&lt;7AAFAFFFFFFFF7FFAA.AFF&lt;F...&lt;AFFFF7F..FA.A&lt;AA&lt;F7)FA7.FF.&lt;FA..F.A7AF..FFF.A
  @NS500289:18:H1237BGXX:4:11401:6297:1023 1:N:0:1
  NATAAGAGGGGTGTGGCTAGGCTAAGCGTTTTGAGCTGCATTGCTGCGTGCTTGATGCTTGTCCCTTTTGATCGT
  </code></pre>
  
  <p>As far as I can tell, this looks like a perfectly normal fastq-formatted file. Can anyone explain what's causing this error?
  Thanks!</p>