scripture problem

[zwzhu]

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?