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  • some problem with tophat

    has anyone here used tophat ?
    when i map single-end solid sequences(fastq format) to hg18 as follow:
    ~/bin/tophat bowtie-0.11.3_index/hg18 query.fq -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4

    there is such error:
    Error: you must set the mean inner distance between mates with -r
    Traceback (most recent call last):
    File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1487, in ?
    sys.exit(main())
    File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1402, in main
    exit(1)
    TypeError: 'str' object is not callable

    what's going on ?
    can anyone help me? thanks in advance~~

  • #2
    Wrong forum

    removed...I was in the wrong forum
    Last edited by RockChalkJayhawk; 10-30-2009, 10:10 AM.

    Comment


    • #3
      Originally posted by zslee View Post
      has anyone here used tophat ?
      when i map single-end solid sequences(fastq format) to hg18 as follow:
      ~/bin/tophat bowtie-0.11.3_index/hg18 query.fq -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4

      there is such error:
      Error: you must set the mean inner distance between mates with -r
      Traceback (most recent call last):
      File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1487, in ?
      sys.exit(main())
      File "/picb/home55/zsli/Public/mapping/bin/tophat", line 1402, in main
      exit(1)
      TypeError: 'str' object is not callable

      what's going on ?
      can anyone help me? thanks in advance~~
      In the command above, you are placing the arguments (the index name and the FASTQ file of your reads) before the options. It should be:

      tophat -o mapre -a 5 -m 2 -i 70 -I 5000 --solexa1.3-quals -g 40 -p 4 bowtie-0.11.3_index/hg18 query.fq

      Comment


      • #4
        yes, that works, thanks a lot !

        Comment


        • #5
          Similiar sort of problem.

          Hi all,

          I am getting this error

          Traceback (most recent call last):
          File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2607, in ?
          sys.exit(main())
          File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2504, in main
          params.read_params = check_reads_format(params, reads_list)
          File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1234, in check_reads_format
          zf = ZReader(f_name, params.system_params)
          File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1185, in __init__
          self.file=open(filename)
          IOError: [Errno 2] No such file or directory: '-o'


          while running tophat

          tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &

          Please help me with this error.

          Thanking you in advance.

          Regards
          Deepak

          Comment


          • #6
            maybe try the last version of tophat 1.4.1

            Originally posted by oxydeepu View Post
            Hi all,

            I am getting this error

            Traceback (most recent call last):
            File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2607, in ?
            sys.exit(main())
            File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 2504, in main
            params.read_params = check_reads_format(params, reads_list)
            File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1234, in check_reads_format
            zf = ZReader(f_name, params.system_params)
            File "/home/deepak/bioTools/tophat-1.3.1.Linux_x86_64//tophat", line 1185, in __init__
            self.file=open(filename)
            IOError: [Errno 2] No such file or directory: '-o'


            while running tophat

            tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &

            Please help me with this error.

            Thanking you in advance.

            Regards
            Deepak

            Comment


            • #7
              Originally posted by oxydeepu View Post
              tophat -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq -o tophat_new &
              Aside from using a newer version, you might try "tophat -o tophat_new -r 200 -i 50 -I 250000 /home/deepak/bowtie-0.12.5/indexes/hs_genome 37_NoIndex_L001_R1_001.fastq" instead. Depending on how tophat parses how it's called, what you wrote as a command could cause an issue (the error suggests that it's trying to open a file called "-o", suggesting that it's not seeing that as an option but a file name).

              Comment

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