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  • Tophat Error: Report generation failed with err = 1

    Hi,
    I am new to the bioinformatics field but want to map my RNA-Seq data using TopHat. I've installed bowtie and tophat and the sample test on bowtie ran successfully (old powermac G5, 2GB RAM).

    However, when I test Tophat with the test_data set I get the error message: Error: Report generation failed with err = 1.

    Without knowing much about programing it seems to me that the -k parameter could be wrong. I suspect it should be "-k 1" whereas Tophat has it as "-k 1,1n". Anyone encountered this or have any ideas?

    This is the output I get after the command line:

    -----

    Macintosh:~/test_data darwin$ tophat -r 20 test_ref reads_1.fq reads_2.fq

    [Thu Feb 18 20:02:21 2010] Beginning TopHat run (v1.0.13)
    -----------------------------------------------
    [Thu Feb 18 20:02:21 2010] Preparing output location ./tophat_out/
    [Thu Feb 18 20:02:21 2010] Checking for Bowtie index files
    [Thu Feb 18 20:02:21 2010] Checking for reference FASTA file
    [Thu Feb 18 20:02:21 2010] Checking for Bowtie
    Bowtie version: 0.12.3.0
    [Thu Feb 18 20:02:21 2010] Checking reads
    seed length: 75bp
    format: fastq
    quality scale: phred33 (default)
    [Thu Feb 18 20:02:21 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:02:32 2010] Joining segment hits
    Splitting reads into 3 segments
    [Thu Feb 18 20:02:32 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:02:44 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:02:55 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:03:06 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:03:17 2010] Joining segment hits
    Splitting reads into 3 segments
    [Thu Feb 18 20:03:17 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:03:29 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:03:40 2010] Mapping reads against test_ref with Bowtie
    [Thu Feb 18 20:03:51 2010] Searching for junctions via segment mapping
    [Thu Feb 18 20:03:51 2010] Retrieving sequences for splices
    [Thu Feb 18 20:03:51 2010] Indexing splices
    [Thu Feb 18 20:03:53 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:53 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:53 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:53 2010] Joining segment hits
    sort: invalid field specification `-k 1,1n'
    [Thu Feb 18 20:03:53 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:53 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:54 2010] Mapping reads against segment_juncs with Bowtie
    [Thu Feb 18 20:03:54 2010] Joining segment hits
    sort: invalid field specification `-k 1,1n'
    [Thu Feb 18 20:03:54 2010] Reporting output tracks
    [FAILED]
    Error: Report generation failed with err = 1

    ------------

    Cheers,
    Darwin
    Last edited by Darwin; 02-19-2010, 10:53 AM.

  • #2
    I meet the same err message, can anybody help us?

    tophat -p 10 -o ORYwthDEF -r -70 -G input.gff

    Comment


    • #3
      Hello,
      Did you ever found the cause of the error?
      Thank you,
      Mariam.

      Comment


      • #4
        I also receive this error message with TopHat 1.0.14. I, however, get it for the first time and my read-config is somewhat unusual, because i have "very few" reads that poorly align to the reference genome. Console output looks like this:

        Code:
        ~$ tophat --num-threads 8 --solexa1.3-quals Provirus reads.fq
        
        [Wed Sep 15 22:37:15 2010] Beginning TopHat run (v1.0.14)
        -----------------------------------------------
        [Wed Sep 15 22:37:15 2010] Preparing output location ./tophat_out/
        [Wed Sep 15 22:37:15 2010] Checking for Bowtie index files
        [Wed Sep 15 22:37:15 2010] Checking for reference FASTA file
        [Wed Sep 15 22:37:15 2010] Checking for Bowtie
            Bowtie version:         0.12.5.0
        [Wed Sep 15 22:37:15 2010] Checking reads
            seed length:     50bp
            format:         fastq
            quality scale:     phred64 (reads generated with GA pipeline version >= 1.3)
        [Wed Sep 15 22:37:56 2010] Mapping reads against Provirus with Bowtie
        [Wed Sep 15 22:38:01 2010] Joining segment hits
        [Wed Sep 15 22:38:01 2010] Searching for junctions via segment mapping
        Warning: junction database is empty!
        [Wed Sep 15 22:38:28 2010] Joining segment hits
        [Wed Sep 15 22:38:28 2010] Reporting output tracks
        [B]    [FAILED]
        Error: Report generation failed with err = 1[/B]


        I thought it's probably related to (underlying Bowtie) not finding any mappable reads, but thats not the case, because:

        Code:
        ~$ bowtie -t --threads 8 --solexa1.3-quals Provirus reads.fq reads.bout.txt
        
        Time loading forward index: 00:00:00
        Time loading mirror index: 00:00:00
        Seeded quality full-index search: 00:00:02
        # reads processed: 651981
        [B]# reads with at least one reported alignment: 315 (0.05%)[/B]
        # reads that failed to align: 651666 (99.95%)
        Reported 315 alignments to 1 output stream(s)
        Time searching: 00:00:02
        Overall time: 00:00:02
        Any suggestions appreciated! Thanks in advance & Cheers
        Uwe

        Comment


        • #5
          I get the same error message as Uwe, but have been unable to find the cause, despite trying many different things. I have tried TopHat versions 1.0.14, 1.0.13, 1.0.12, and 1.0.11 and Bowtie versions 0.12.7.0, 0.12.5.0 and 0.12.3.0. I compiled TopHat and Bowtie myself but also tried the precompiled 64-bit linux binaries of the most recent versions. I ran TopHat on human 37 bp paired-end reads (with a mean separation argument [-r] of 100, 200, 300 bp) and on human 46 bp single reads. I tried with or without the butterfly-search argument. I set the segment-length argument 10 or 20. I modified the code so that the seed length is 10, 20 or 25 rather than choosing the minimum read length, which is what the TopHat code does by default. I verified that the quality scores are in phred33 format, which is also what TopHat chooses by default. I built my own hg18 bowtie indexes using the make_hg18.sh script and used the prebuilt indexes from the website. In all cases I get the same result: no junctions appear to be found. A typical result looks like:

          Code:
          tophat $BOWTIE_INDEXES/hg18 data/test_nb/NA19119_argonne.fastq 
          
          [Fri Sep 17 09:13:00 2010] Beginning TopHat run (v1.0.14)
          -----------------------------------------------
          [Fri Sep 17 09:13:00 2010] Preparing output location ./tophat_out/
          [Fri Sep 17 09:13:00 2010] Checking for Bowtie index files
          [Fri Sep 17 09:13:00 2010] Checking for reference FASTA file
          [Fri Sep 17 09:13:00 2010] Checking for Bowtie
              Bowtie version:         0.12.7.0
          [Fri Sep 17 09:13:00 2010] Checking reads
              seed length:     46bp
              format:         fastq
              quality scale:     phred33 (default)
          [Fri Sep 17 09:13:46 2010] Mapping reads against hg18 with Bowtie
          [Fri Sep 17 09:13:59 2010] Joining segment hits
          [Fri Sep 17 09:13:59 2010] Searching for junctions via segment mapping
          Warning: junction database is empty!
          [Fri Sep 17 09:16:12 2010] Joining segment hits
          [Fri Sep 17 09:16:12 2010] Reporting output tracks
              [FAILED]
          Error: Report generation failed with err = 1
          Any help would be appreciated!

          Comment


          • #6
            Hello grahammcv,

            I too have just experienced this problem. Have you found a resolution?

            I noticed a thread on here entitled "Running ~35 bp and >=50 RNASeq reads" that might be a clue to a solution.

            I am in the process of trying it out and will try to post results for everyone who might be having this same problem.
            Last edited by jdanderson; 09-23-2010, 08:07 PM. Reason: Misspelling

            Comment


            • #7
              Hi,everyone

              I also got the same error as you all.
              I doubted the index files or reads,but the cause was so simple in my case.

              I saw the report.log and it says 'cant open BED file'.
              I run tophat as root the other day,so junction.bed file was ownd by root.
              That's why I got the error when running tophat as not root.

              After changing owner of junction.bed , I got correct result.

              Maybe you all don't make an elementary mistake like me
              I would be glad this thread would help you.

              Comment


              • #8
                Oops, my mistake had to do with permissions on the annotation files as well.

                Comment


                • #9
                  Because Tmp directory too big

                  I am getting this error too. I believe (atleast in my case) that it is due to disk getting full with the tmp directory. Errors I get are:
                  Code:
                  Reporting output tracks
                          [FAILED]Report generation failed with err = -11
                  or
                  Code:
                  Error: Report generation failed with err = 1
                  Just before giving this error, tophat says:

                  Code:
                  sort: close failed: -: No space left on device

                  Comment


                  • #10
                    Hi flobpf,

                    How you solve the problem about the sort error?
                    I'm facing the same error as well
                    Thanks for advice.
                    Originally posted by flobpf View Post
                    I am getting this error too. I believe (atleast in my case) that it is due to disk getting full with the tmp directory. Errors I get are:
                    Code:
                    Reporting output tracks
                            [FAILED]Report generation failed with err = -11
                    or
                    Code:
                    Error: Report generation failed with err = 1
                    Just before giving this error, tophat says:

                    Code:
                    sort: close failed: -: No space left on device

                    Comment

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