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  • fastx_quality_stats error : input file (-) has unknown file format

    Hi.
    I was trying to check qualities of my fastq files from RNA-seq using fastx-toolkit, but I kept getting a following error.

    Code:
    $ fastx_quality_stats -Q 33 4.1.fastq
    
    fastx_quality_stats error : input file (-) has unknown file format (not FASTA or FASTQ), first character = (10)
    RNA-seq was performed in Hiseq2000 (paired-end), and the guy who ran the sequencing gave me these files when I asked the raw sequencing data. I merged all the fastq files in each sample into one file using 'cat' command since I wated to map them as singe-ends.

    Has anyone expreinced this?

    Thanks!

  • #2
    The error means that the first line of the file is blank. If that's true, then the file is screwed up. What does
    Code:
    head 4.1.fastq
    show?

    Comment


    • #3
      The file doesn't seem to have blank at the start.

      Code:
      $ head 4.1.fastq 
      @HWI-ST908R:191:D27LWACXX:7:1101:4446:2397 2:N:0:CGATGT
      NNNNNNCNTCTTCNNNTGNGNNNNGNNCNTNGGGGAGACCNNGNNAANNNNNTTANNNGNNNANTNCCNNNNNNNNNGNNCNCTNNNNNNNNNNNNNNNNN
      +
      #####################################################################################################
      @HWI-ST908R:191:D27LWACXX:7:1101:4422:2401 2:N:0:CGATGT
      NNNNNNTNAGCTTNNNAANCCNNTANNCAACTCATCCGAGNNTNNTTNNNNNGGCNNNGNNNCNGTCCNNNNNNNNNTGNCNCGGNNNNTNNNNNNNNNNN
      +
      #####################################################################################################
      @HWI-ST908R:191:D27LWACXX:7:1101:4557:2387 2:N:0:CGATGT
      NNNNNNANTNTCNNNNCGNANNNNCNNNNCNNGNCGCTNCNNNNNNNNNNNNNTANNNNNNNGNNNTNNNNNNNNNNNNNNNNANNNNNNNNNNNNNNNNN
      As I mentioned earlier, I used 'cat' command to merge four files.
      Could that cause the problem?

      Comment


      • #4
        Oh, I actually missed the "input file (-)" part of the error. An input file of "-" typically means stdin, which is the default for that command. Also, there is no "-Q" parameter, so that's likely ignored. The command should be:

        Code:
        fastx_quality_stats -i 4.1.fastq

        Comment


        • #5
          Thanks, dpryan!
          It worked!!!
          I didn't add '-i' in front of the input file, so the program couldn't find a input file.
          Am I understanding right?

          Comment


          • #6
            That is correct. Some programs require an explicit "-i" to signify input.

            Comment

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