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  • an error when using tophat

    [wgf@world SRA_shortreads]$ tophat.py ../ws190_index/C.elegans.ws190.dna SRR019978.fastq

    [Fri Oct 29 15:26:03 2010] Beginning TopHat run (v1.1.1)
    -----------------------------------------------
    [Fri Oct 29 15:26:03 2010] Preparing output location ./tophat_out/
    [Fri Oct 29 15:26:03 2010] Checking for Bowtie index files
    [Fri Oct 29 15:26:03 2010] Checking for reference FASTA file
    [Fri Oct 29 15:26:03 2010] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Fri Oct 29 15:26:03 2010] Checking for Samtools
    Samtools version: 0.1.8.0
    [Fri Oct 29 15:26:05 2010] Checking reads
    min read length: 37bp, max read length: 37bp
    format: fastq
    quality scale: phred33 (default)
    Error locating program: prep_reads


    what is the problem?

  • #2
    how did you setup bowtie and tophat

    Comment


    • #3
      Originally posted by repinementer View Post
      how did you setup bowtie and tophat
      i download the bowtie and use this program to map the short reads successfully.

      i also download the tophat (v1.1.1) and make install according to the manual.

      In the /src directory, there is tophat.py to run.First time, i have run the tophat successfully, and the result is in the /tophat_out directory.

      after that, i change a larger fastq file, the error occurs.

      [wgf@world src]$ tophat.py ~/bowtie/ws190_index/C.elegans.ws190.dna ~/bowtie/SRA_shortreads/SRR019978.fastq

      [Fri Oct 29 18:16:05 2010] Beginning TopHat run (v1.1.1)
      -----------------------------------------------
      [Fri Oct 29 18:16:05 2010] Preparing output location ./tophat_out/
      [Fri Oct 29 18:16:05 2010] Checking for Bowtie index files
      [Fri Oct 29 18:16:05 2010] Checking for reference FASTA file
      [Fri Oct 29 18:16:05 2010] Checking for Bowtie
      Bowtie version: 0.12.7.0
      [Fri Oct 29 18:16:05 2010] Checking for Samtools
      Samtools version: 0.1.8.0
      [Fri Oct 29 18:16:07 2010] Checking reads
      min read length: 37bp, max read length: 37bp
      format: fastq
      quality scale: phred33 (default)
      Error locating program: prep_reads

      Comment


      • #4
        Did you run "make install"? If yes, you can run tophat using your_tophat_directory/bin/tophat.

        Otherwise, there should be some problem regarding TopHat installation.

        Comment


        • #5
          Originally posted by Daehwan View Post
          Did you run "make install"? If yes, you can run tophat using your_tophat_directory/bin/tophat.

          Otherwise, there should be some problem regarding TopHat installation.
          thank you. i have solved this problem.

          Comment


          • #6
            error

            Hi masylichu,
            how did you solve the problem? I have the same error.

            Luigi

            Comment


            • #7
              hello, Luigi

              That may be the problem of samtools installation.

              please you check your installation of samtools, meanwhile, follow the instruction of tophat software.

              Comment

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