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  • #16
    Thank you, I have removed the spaces in the read names and re-running MapSplice now. There is hope!

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    • #17
      I'm having the same error.

      I am using Ensembl Chromosomes, and they have "false" spaces in their name (which actually correspond to the description of the fasta).
      eg. >Uextra dna:chromosome chromosome:BDGP5:Uextra:1:29004656:1

      I've removed that extra part... let's hope it works now.

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      • #18
        I run into the same problem as repinementer. It gives an error in which it states that in needs the islands.gff file in the output folder. However, I cannot find this file in the output folder. Have more people encountered this problem?

        Input:
        python ~/MapSplice_1.15.2_macos/bin/mapsplice_segments.py -u ~/read1.fastq,~/read2.fastq -c ~/database/human_per_chromosome -B ~/MapSplice_1.15.2_macos/bowtie-0.12.7/index/h_sapiens_37_asm -Q fq —paired

        Output:
        [Tue Apr 5 11:49:10 2016] Beginning Mapsplice run (v1.15.2)
        ------------------------------------------------------
        bin directory: [/Users/kmaassen/projects/mapsplice/MapSplice_1.15.2_macos_2/bin/]
        [Tue Apr 5 11:49:10 2016] Checking for chromosomes files or directory
        [Tue Apr 5 11:49:10 2016] Checking for chromosomes files or directory passed
        [Tue Apr 5 11:49:10 2016] Checking for Bowtie index files
        [Tue Apr 5 11:49:10 2016] check reads format
        [Tue Apr 5 11:49:16 2016] merge paired end reads remove short
        [Tue Apr 5 11:49:40 2016] Converting bowtie mapped to SAM format
        [Tue Apr 5 11:49:40 2016] divide reads
        [Tue Apr 5 11:52:07 2016] Mapping reads against h_sapiens_37_asm with Bowtie
        [Tue Apr 5 12:00:36 2016] reads all chromo sizes
        [Tue Apr 5 12:00:52 2016] map splice_search
        [Tue Apr 5 12:00:58 2016] Aligning spliced reads
        cannot open input file mapsplice_out/tmp/islands.gff
        [FAILED]
        Error: Spliced read alignment failed

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