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  • TOPHAT ,Error locating program: prep_reads

    Dear all,

    I have a problem of using TOPHAT:


    [Fri Jul 22 17:37:28 2011] Beginning TopHat run (v1.3.1)
    -----------------------------------------------
    [Fri Jul 22 17:37:28 2011] Preparing output location ./tophat_out/
    [Fri Jul 22 17:37:28 2011] Checking for Bowtie index files
    [Fri Jul 22 17:37:28 2011] Checking for reference FASTA file
    [Fri Jul 22 17:37:28 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Fri Jul 22 17:37:28 2011] Checking for Samtools
    Samtools Version: 0.1.17
    [Fri Jul 22 17:37:28 2011] Generating SAM header for test_ref
    [Fri Jul 22 17:37:28 2011] Preparing reads
    format: fastq
    quality scale: phred33 (default)
    Error locating program: prep_reads

  • #2
    I also have the same error! Can anyone help?

    [Wed Aug 17 19:41:10 2011] Beginning TopHat run (v1.3.1)
    -----------------------------------------------
    [Wed Aug 17 19:41:10 2011] Preparing output location /d/RNAseq/Tophat/
    [Wed Aug 17 19:41:10 2011] Checking for Bowtie index files
    [Wed Aug 17 19:41:10 2011] Checking for reference FASTA file
    Warning: Could not find FASTA file /d/database/hg19/hg19_c.fa
    [Wed Aug 17 19:41:10 2011] Reconstituting reference FASTA file from Bowtie index
    Executing: /d/bowtie-0.12.7/bowtie-inspect /d/database/hg19/hg19_c > /d/RNAseq/Tophat/tmp/hg19_c.fa
    [Wed Aug 17 19:45:47 2011] Checking for Bowtie
    Bowtie version: 0.12.7.0
    [Wed Aug 17 19:45:47 2011] Checking for Samtools
    Samtools Version: 0.1.17
    [Wed Aug 17 19:45:47 2011] Generating SAM header for /d/database/hg19/hg19_c
    [Wed Aug 17 19:45:51 2011] Preparing reads
    format: fasta
    Error locating program: prep_reads

    Comment


    • #3
      Originally posted by disciple View Post
      I also have the same error! Can anyone help?

      [Wed Aug 17 19:41:10 2011] Beginning TopHat run (v1.3.1)
      -----------------------------------------------
      [Wed Aug 17 19:41:10 2011] Preparing output location /d/RNAseq/Tophat/
      [Wed Aug 17 19:41:10 2011] Checking for Bowtie index files
      [Wed Aug 17 19:41:10 2011] Checking for reference FASTA file
      Warning: Could not find FASTA file /d/database/hg19/hg19_c.fa
      [Wed Aug 17 19:41:10 2011] Reconstituting reference FASTA file from Bowtie index
      Executing: /d/bowtie-0.12.7/bowtie-inspect /d/database/hg19/hg19_c > /d/RNAseq/Tophat/tmp/hg19_c.fa
      [Wed Aug 17 19:45:47 2011] Checking for Bowtie
      Bowtie version: 0.12.7.0
      [Wed Aug 17 19:45:47 2011] Checking for Samtools
      Samtools Version: 0.1.17
      [Wed Aug 17 19:45:47 2011] Generating SAM header for /d/database/hg19/hg19_c
      [Wed Aug 17 19:45:51 2011] Preparing reads
      format: fasta
      Error locating program: prep_reads
      I fix this error by Add samtools “/path/to/install/directory/bin” into shell PATH.

      or you can export your tophat path into PATH

      Check this post http://seqanswers.com/forums/showthread.php?t=12688
      Last edited by chenyao; 08-17-2011, 04:37 AM. Reason: typo

      Comment

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