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scripture problem

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  • scripture problem

    i have one lane of Paired-end reads with the length of 90nt from RNA-seq. These reads were aligned to reference genome sequence with tophat (v 1.0.13) as described in the documentation of Scripture, all left process was according to the instruction. but no result output.
    Here is a snippit of output I see on my screen.

    java -jar scripture.jar -alignment Chromosome1_YPD.all.alignments.sorted.sam
    -out chr1.scriptureESTest.segments_1 -sizeFile chromosome1.sizes -chr chr1
    -chrSequence Chromosome1.fa -pairedEnd Chromosome1_YPD.paired.sorted.sam

    Using Version VPaperR3
    Computing weights..... upweighting? false weight: 1.0
    Computing alignment global stats for chromosome chr1
    Has pairs: true
    Has upweighting turned on: false
    Computing weights..... upweighting? false weight: 1.0
    AlignmentDataModel loaded, initializing model stats
    Computing alignment global stats for chromosome chr1
    model stats loaded, initializing model
    Built the model: 0.0 free memory: 12112784
    Loaded chromosome Sequence
    Segmenting accross graph
    Going to get read iterator to make graph with counts
    Got read iterator
    Made it through all reads
    Collapsed reads
    Decollapsed by introns
    Made first graph
    Got extended pieces
    Made second graph
    Done making spliced graph
    Got Simple paths...
    Estimated distribution
    Made path trees
    Done adding paired ends (if available)
    Done getting paths. Total: 0
    Done with local segmentation
    Done setting local rate in graph
    Done scoring paths.

    "Collapsed reads"
    "Decollapsed by introns"
    what these mean?