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  • end of file unexpected error when running splicemap

    Hi all,

    Nice to meet you, I am a newbie to this forum. Hopefully I am making post in the right forum.

    I am running splicemap to find splice-junction of a set of RNA-seq data but got the following error message:
    .
    .
    .
    .
    .
    Total Bowtie mapping section execution time: 5533.83 s.
    Generating .t file!...
    Total .t creation section execution time: 470.855 s.
    Removing mapping results!...
    Creating mapping index!...
    Generating mapping file!...
    Total mapping index creation section execution time: 445.987 s.
    Total Mapping section time: 6451.07 s.
    Running SpliceMap on gi|240254421|ref|NC_003070.9| ...
    sh: 1: Syntax error: end of file unexpected
    Running SpliceMap on gi|240254678|ref|NC_003071.7| ...
    sh: 1: Syntax error: end of file unexpected
    Running SpliceMap on gi|240255695|ref|NC_003074.8| ...
    sh: 1: Syntax error: end of file unexpected
    Running SpliceMap on gi|240256243|ref|NC_003075.7| ...
    sh: 1: Syntax error: end of file unexpected
    Running SpliceMap on gi|240256493|ref|NC_003076.8| ...
    sh: 1: Syntax error: end of file unexpected
    Total SpliceMap section time: 35.1471 s.
    Merging results and computing junctions...
    Reading SAM headers
    ERROR: could not open temp/NC_003070.fna_84.sam
    ERROR: Amalgamation failed = 512

    Does anyone know what it means? I tried running the same set of data using tophat but no error message was produced.
    Thank you for your help
    Last edited by kanewong; 04-11-2013, 07:00 AM.

  • #2
    Here is part of the original script(run.cfg) provided by the developers of spliceMap,

    ################################################################
    # These are the two lists of sequencer reads files.
    # "reads_list2" can be commeted out if reads are not paired-end.
    # Make sure the order of both lists are the same!
    # Also, "reads_list1" must be the first pair.
    # Note: pair-reads should be in the "forward-reverse" format.
    # (multiple values)

    > reads_list1
    data/long_reads_1_100K.txt.seq
    <

    > reads_list2
    data/long_reads_2_100K.txt.seq
    <
    ###################################################################

    Then I change the command according to my real situation
    ###################################################################


    > reads_list1
    data/SRR360147_1.fastq
    <

    > reads_list2
    data/SRR360147_2.fastq
    <
    ###################################################################



    My dataset is here: http://www.ncbi.nlm.nih.gov/sra/SRX103665
    Last edited by kanewong; 04-09-2013, 07:28 AM.

    Comment


    • #3
      Originally posted by kanewong View Post
      Here is part of the original script provided by the developers of spliceMap,


      ###################################################################
      Then I change the command according to my real situation

      > reads_list1
      data/SRR360147.fastq
      <

      #>
      #<
      ###################################################################

      Try to use "#" as shown above to comment out the read2 list. See example in red above. I am not completely sure what script you are referring to but see if that helps.

      Comment


      • #4
        (del).......
        Last edited by kanewong; 04-09-2013, 07:29 AM.

        Comment


        • #5
          Originally posted by kanewong View Post
          Hi, thanks for your advice, finally I download the same data from ebi(different file format for pair end reads), and modify my script as follows:


          ###################################################################
          > reads_list1
          data/SRR360147_1.fastq
          <

          > reads_list2
          data/SRR360147_2.fastq
          <
          ###################################################################

          Unfortunately an error still produced
          Was the error same as the one you originally posted or different?

          Comment


          • #6
            Originally posted by GenoMax View Post
            Was the error same as the one you originally posted or different?
            same..........

            Comment


            • #7
              Are there files in "temp/*" directory that the program is trying to access? Has the bowtie alignment worked?

              Comment


              • #8
                The temp directory is produced after I start running the program, but I am not sure if the program is accessing the files in temp when the error occurs.

                Bowtie alignment takes place before the error message appears, so I guess it works. But I am not sure if there is still any bowtie alignment steps afterwards.

                I learn that some programmers check the error logs to figure out which file produces error, but I am not sure how to do that.
                Last edited by kanewong; 04-08-2013, 08:49 AM.

                Comment


                • #9
                  Here is a sample page of how one can capture the standard error and output to file(s). The instructions are shell specific so depending on what shell (C-family or Bash) you are using you will need to choose the right directions.

                  If you can include the entire command line (along with the error logs or the relevant parts with errors) that would help.

                  Comment

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