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  • New version of MapSplice error

    I just tested new version of Mapsplice and it throwed the following error

    Code:
    ]$ python bin/mapsplice_segments.py MapSplice.cfg 
    
    [Fri Aug 20 17:29:24 2010] Beginning Mapsplice run (v1.13.6.1)
    -----------------------------------------------
    bin directory: [/home/bogugk/rnaseq/software/MapSplice_1.13.6.1/bin/] 
    [Fri Aug 20 17:29:24 2010] Preparing output location /home/bogugk/rnaseq/Human_CD4TCell_RNASEQ_data/MapSplice_Outputs/
    [Fri Aug 20 17:29:24 2010] Checking for chromosomes files or directory
    [Fri Aug 20 17:29:24 2010] Checking for Bowtie index files
    [Fri Aug 20 17:29:24 2010] merge paired end reads
    [Fri Aug 20 17:29:24 2010] Converting bowtie mapped to SAM format
    [Fri Aug 20 17:29:24 2010] divide reads
    [Fri Aug 20 17:31:30 2010] Mapping reads against hg18 with Bowtie
    [Fri Aug 20 19:29:10 2010] reads all chromo sizes
    [Fri Aug 20 19:29:44 2010] mapsplice_search
    [Fri Aug 20 19:32:13 2010] Aligning spliced reads
    cannot open input file /home/bogugk/rnaseq/Human_CD4TCell_RNASEQ_data/MapSplice_Outputs/tmp/islands.gff
            [FAILED]
    Error: Spliced read alignment failed
    Traceback (most recent call last):
      File "bin/mapsplice_segments.py", line 5823, in ?
        sys.exit(main())
      File "bin/mapsplice_segments.py", line 5278, in main
        search_whole_chromo)
      File "bin/mapsplice_segments.py", line 1023, in call_mapsplice_segment
        exit(1)
    TypeError: 'str' object is not callable

  • #2
    I am getting the same error from my attempt to use this software. It appears the islands.gff file is not being created in the output directory. Please help.

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    • #3
      bumpbumpbump

      Comment


      • #4
        Originally posted by mendl7 View Post
        bumpbumpbump
        Warning #2 on "the bumping".

        Comment


        • #5
          Chromosome file name and first line of fasta line not consistent might cause mapsplice_search to fail to generate island file. For example if the chromosome file name is "chr1.fa" the first line in fasta file should be >chr1.

          Please contact mapsplice (at) netlab.uky.edu for bug reports.
          Last edited by greenshell; 09-16-2010, 04:28 PM.

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          • #6
            I had the same problem, it was solved by moving all the other .fa files from the directory

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            • #7
              i mean the ones that are not fasta files corresponding to a chromosome

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              • #8
                Hi there!
                I'm getting the same error message and I tried all the suggestions that have been mentioned but nothing worked. The first line within my chromosome files is the name of the file, in my chromosome folder are the chromosome files and nothing else. I work with the D. melaogaster genome so I thought that I may have got another release than the bowtie's reference sequence. But again it didn't work. Please help me

                Comment


                • #9
                  Are there any other warning in the log file?

                  Can you send
                  unspliced_mapped_segments|unspliced_mapped_segments.sorted
                  unspliced_mapped_reads
                  divided_reads.fa
                  chrom_sizes

                  to
                  mapsplice (at) netlab.uky.edu?

                  Originally posted by cat View Post
                  Hi there!
                  I'm getting the same error message and I tried all the suggestions that have been mentioned but nothing worked. The first line within my chromosome files is the name of the file, in my chromosome folder are the chromosome files and nothing else. I work with the D. melaogaster genome so I thought that I may have got another release than the bowtie's reference sequence. But again it didn't work. Please help me

                  Comment


                  • #10
                    I'm having the same problem too.

                    Comment


                    • #11
                      Can you send first 10K line of

                      unspliced_mapped_segments|unspliced_mapped_segments.sorted
                      unspliced_mapped_reads
                      divided_reads.fa
                      chrom_sizes

                      to
                      mapsplice (at) netlab.uky.edu?

                      Most of the error is because the input file format is not correct, e.g. read name contain blank space, etc.

                      In the latest version of MapSplice, input file format checking is added.
                      If chromosome file format is not correct, warning message will be printed and it will try to convert chromosome file to correct format
                      If read file format is not correct, error message will be printed and exit
                      Last edited by greenshell; 04-13-2011, 06:18 AM.

                      Comment


                      • #12
                        I have the same problem. I run the latest version of MapSplice (v1.15.1), but still get the same error message: "cannot open input file mapsplice_Mm666_75bp_noribo/tmp/islands.gff [FAILED]" . Does anyone have a solution?

                        Comment


                        • #13
                          Originally posted by genomicist View Post
                          I have the same problem. I run the latest version of MapSplice (v1.15.1), but still get the same error message: "cannot open input file mapsplice_Mm666_75bp_noribo/tmp/islands.gff [FAILED]" . Does anyone have a solution?
                          Can you send first 10K line of

                          unspliced_mapped_segments|unspliced_mapped_segments.sorted
                          unspliced_mapped_reads
                          divided_reads.fa
                          chrom_sizes

                          to
                          mapsplice (at) netlab.uky.edu?

                          1.15.2 added checking of blank space in read name
                          Last edited by greenshell; 04-14-2011, 08:21 AM.

                          Comment


                          • #14
                            I do have a blank in my read names - is it what is causing this problem?

                            Comment


                            • #15
                              Yes, the format constraint is required in manual
                              Last edited by greenshell; 04-14-2011, 10:13 AM.

                              Comment

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