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  • Tophat error

    I am new to RNAseq, I am trying to map my reads to my reference genome. It generates this error
    Generating SAM header for /path/ref
    Traceback (most recent call last):
    File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 4107, in <module>
    sys.exit(main())
    File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 3961, in main
    params.read_params = check_reads_format(params, reads_list)
    File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1856, in check_reads_format
    zf = ZReader(f_name, params)
    File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1809, in __init__
    self.file=open(filename)
    IOError: [Errno 2] No such file or directory: ''

    Any ideas how to fix this?

  • #2
    IOError: [Errno 2] No such file or directory: ''
    This is the critical piece. TopHat is not finding some file/directory that you specified in your command. Since you have not included your full command you will need to investigate which it may be.

    Comment


    • #3
      The following is my command.
      tophat2 -p 8 -r 300 -N 1 -o tophat_out /path/ref read1 read2
      And I have ref.fa and Bowtie built reference in this folder.
      The last line in log file is 'Generating SAM header for /path/ref'
      [2019-02-18 20:27:51] Beginning TopHat run (v2.1.2)
      -----------------------------------------------
      [2019-02-18 20:27:51] Checking for Bowtie
      Bowtie version: 2.3.4.3
      [2019-02-18 20:27:51] Checking for Bowtie index files (genome)..
      [2019-02-18 20:27:51] Checking for reference FASTA file
      [2019-02-18 20:27:51] Generating SAM header for /path/ref

      Comment


      • #4
        error same

        Originally posted by fanzhen View Post
        I am new to RNAseq, I am trying to map my reads to my reference genome. It generates this error
        Generating SAM header for /path/ref
        Traceback (most recent call last):
        File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 4107, in <module>
        sys.exit(main())
        File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 3961, in main
        params.read_params = check_reads_format(params, reads_list)
        File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1856, in check_reads_format
        zf = ZReader(f_name, params)
        File "/apps/tuxedo/tophat/2.1.2/bin/tophat", line 1809, in __init__
        self.file=open(filename)
        IOError: [Errno 2] No such file or directory: ''

        Any ideas how to fix this?


        Have you solved this problems?

        Comment

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