Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • tophat error

    Hi all,
    First post here. I am trying to familiarize myself with tophat, so I'm trying to use some test data. I'm getting the following error.

    [2012-05-30 19:34:46] Beginning TopHat run (v2.0.0)
    -----------------------------------------------
    [2012-05-30 19:34:46] Checking for Bowtie
    Bowtie 2 not found, checking for older version..
    Bowtie version: 0.12.7.0
    [2012-05-30 19:34:46] Checking for Samtools
    Samtools version: 0.1.14.0
    [2012-05-30 19:34:46] Checking for Bowtie index files
    [2012-05-30 19:34:46] Checking for reference FASTA file
    Warning: Could not find FASTA file /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62.fa
    [2012-05-30 19:34:46] Reconstituting reference FASTA file from Bowtie index
    Executing: /home/solexa/bowtie-0.12.7/bowtie-inspect /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62 > ./tophat_out/tmp/scEF2.62.fa
    [2012-05-30 19:34:47] Generating SAM header for /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62
    format: fastq
    quality scale: phred33 (default)
    [2012-05-30 19:34:47] Reading known junctions from GTF file
    [2012-05-30 19:34:47] Preparing reads
    [FAILED]
    Error running 'prep_reads'
    Error: beginning of quality values record not found! (@SRR122141.331699 HWUSI-EAS1656_0002:8:2:8841:14981 length=38)

    Any help is appreciated.

    Thanks,

    E

  • #2
    Originally posted by licensed2skill84 View Post
    Error: beginning of quality values record not found! (@SRR122141.331699 HWUSI-EAS1656_0002:8:2:8841:14981 length=38)

    Any help is appreciated.

    Thanks,

    E
    I have the same error. Any ideas what's the problem?

    Comment


    • #3
      Hi. For whatever reason, converting the .sra file to .fastq with fastq-dump on our research cluster resulted in a corrupted fastq file. When I ran fastq-dump on my laptop, then transferred the resulting fastq file back to the cluster, all downstream analysis proceeded error free. Hope this helps.

      E

      Comment


      • #4
        Originally posted by rebrendi View Post
        I have the same error. Any ideas what's the problem?
        Same error with me too........Any idea of how to fix this

        Error: beginning of quality values record not found! (@HWI-ST611_0203:5:1101:2446:2180#0/2)

        Comment


        • #5
          Originally posted by licensed2skill84 View Post
          Hi. For whatever reason, converting the .sra file to .fastq with fastq-dump on our research cluster resulted in a corrupted fastq file. When I ran fastq-dump on my laptop, then transferred the resulting fastq file back to the cluster, all downstream analysis proceeded error free. Hope this helps.

          E
          We've had a few problems with fastq dump producing corrupted files whilst generating no errors. It's really important to check that you're using the latest version of the NCBI toolkit as some older versions seemed to have some nasty bugs in them.

          Comment


          • #6
            Originally posted by licensed2skill84 View Post
            Hi all,
            First post here. I am trying to familiarize myself with tophat, so I'm trying to use some test data. I'm getting the following error.

            [2012-05-30 19:34:46] Beginning TopHat run (v2.0.0)
            -----------------------------------------------
            [2012-05-30 19:34:46] Checking for Bowtie
            Bowtie 2 not found, checking for older version..
            Bowtie version: 0.12.7.0
            [2012-05-30 19:34:46] Checking for Samtools
            Samtools version: 0.1.14.0
            [2012-05-30 19:34:46] Checking for Bowtie index files
            [2012-05-30 19:34:46] Checking for reference FASTA file
            Warning: Could not find FASTA file /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62.fa
            [2012-05-30 19:34:46] Reconstituting reference FASTA file from Bowtie index
            Executing: /home/solexa/bowtie-0.12.7/bowtie-inspect /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62 > ./tophat_out/tmp/scEF2.62.fa
            [2012-05-30 19:34:47] Generating SAM header for /shared/solexa/solexa/Genomes/ELAND/sacCer/scEF2.62/bowtie/scEF2.62
            format: fastq
            quality scale: phred33 (default)
            [2012-05-30 19:34:47] Reading known junctions from GTF file
            [2012-05-30 19:34:47] Preparing reads
            [FAILED]
            Error running 'prep_reads'
            Error: beginning of quality values record not found! (@SRR122141.331699 HWUSI-EAS1656_0002:8:2:8841:14981 length=38)

            Any help is appreciated.

            Thanks,

            E
            I got the same problem.
            Do you fix this problem now?

            Comment


            • #7
              I had this issue, I think it was a corrupted file issue.

              My file was concatenated from multiple fastq files (all which ran individually no problem). When I redid the concatenation it worked fine.

              Comment

              Latest Articles

              Collapse

              • seqadmin
                Strategies for Sequencing Challenging Samples
                by seqadmin


                Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
                03-22-2024, 06:39 AM
              • seqadmin
                Techniques and Challenges in Conservation Genomics
                by seqadmin



                The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

                Avian Conservation
                Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
                03-08-2024, 10:41 AM

              ad_right_rmr

              Collapse

              News

              Collapse

              Topics Statistics Last Post
              Started by seqadmin, Yesterday, 06:37 PM
              0 responses
              7 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, Yesterday, 06:07 PM
              0 responses
              7 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-22-2024, 10:03 AM
              0 responses
              49 views
              0 likes
              Last Post seqadmin  
              Started by seqadmin, 03-21-2024, 07:32 AM
              0 responses
              66 views
              0 likes
              Last Post seqadmin  
              Working...
              X