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  • #16
    Hi,

    I was doing on trial run for SpliceMap on my data and got this error message after Bowtie mapping:

    Genereating mapping file!...
    Total mapping index creation section execution time: 541.607 s.
    Total Mapping section time: 11970.7 s.
    Running SpliceMap on /home/bowtie/chr1.fa ...
    COMMAND: ./bin/SpliceMap test.cfg /home/bowtie/chr1.fa
    ERROR: fork failed

    Has anyone else had this problem / knows of a fix?

    Thank you.

    Comment


    • #17
      Originally posted by SolexaNewbie View Post
      Hi,

      I was doing on trial run for SpliceMap on my data and got this error message after Bowtie mapping:

      Genereating mapping file!...
      Total mapping index creation section execution time: 541.607 s.
      Total Mapping section time: 11970.7 s.
      Running SpliceMap on /home/bowtie/chr1.fa ...
      COMMAND: ./bin/SpliceMap test.cfg /home/bowtie/chr1.fa
      ERROR: fork failed

      Has anyone else had this problem / knows of a fix?

      Thank you.
      Hi,

      Does the example data set in the tutorial work?
      SpliceMap: De novo detection of splice junctions from RNA-seq
      Download SpliceMap Comment here

      Comment


      • #18
        Hi John,

        Thank you very much for your prompt reply. Yes, I've just run the tutorial and all went well. I will try moving the chr1.fa (downloaded from UCSC) to the genome folder used in the tutorial.

        Comment


        • #19
          Originally posted by SolexaNewbie View Post
          Hi John,

          Thank you very much for your prompt reply. Yes, I've just run the tutorial and all went well. I will try moving the chr1.fa (downloaded from UCSC) to the genome folder used in the tutorial.
          I hope that works.

          I'm trying to think why that might be the case.. If it still doesn't work
          could you email me the log files as described in



          You can directly send to me at johnmu (at) stanford.edu

          Sorry for the trouble!

          John Mu
          SpliceMap: De novo detection of splice junctions from RNA-seq
          Download SpliceMap Comment here

          Comment


          • #20
            Hi I am very new to RNA-seq analysis. But I need to complete the mapping of my data using SpliceMap. I am not able to edit the run.cfg file and I am getting the following error
            ""ls: cannot access /cluster/rnaseq/genome/hg18/chr*.fa: No such file or directory
            ERROR: I found no chromosomes, please check the genome_dir (/cluster/rnaseq/genome/hg18/) and the chromosome_wildcard (chr*.fa)"".
            Could anyone tell me how to correct the same? I put the index files like hg18_c.1.ebwt
            etc and the .fa files in different folders in the working directory.

            Comment

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