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SpliceMap 3.3 Released - Improved long-read sensitivity

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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

          http://www.stanford.edu/group/wongla...p/contact.html

          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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