Collapesed reads in Scripture for transcript assembly

[zwzhu]

I hava run Tophat for RNA-seq reads mapping, and want to using Scripture for transcripts assembly. the commands are
tophat -o ./tophat_out_YPD_1 ./Chr1 ../YPD_l1_1.fq
tophat -o ./tophat_out_YPD_2 ./Chr1 ../YPD_l1_2.fq
sed '1,2d' tophat_out_YPD_1/accepted_hits.sam | sort > tophat_out_YPD_1/accepted
_hits.sorted.sam
sed '1,2d' tophat_out_YPD_2/accepted_hits.sam | sort > tophat_out_YPD_2/accepted
_hits.sorted.sam
java -jar ./scripture-beta.jar -task makePairedFile -pair1 tophat_out_YPD_1/accepted_
hits.sorted.sam -pair2 tophat_out_YPD/accepted_hits.sorted.sam -out YPD.paired.s
am -sorted
cat tophat_out_YPD_1/accepted_hits.sorted.sam tophat_out_YPD_2/accepted_hits.sor
ted.sam > YPD_all_alignments.sam
java -jar ./igvtools.jar sort YPD_all_alignments.sam YPD_all_alignments.sorted.s
am
java -jar ./igvtools.jar index YPD_all_alignments.sorted.sam
java -jar ./igvtools.jar sort YPD.paired.sam YPD.paired.sorted.sam
java -jar ./igvtools.jar index YPD.paired.sorted.sam

so I got some files like these:
-rw-r--r-- 1 root root 69219776 11-02 19:31 YPD_all_alignments.sam
-rw-r--r-- 1 root root 69475267 11-02 19:32 YPD_all_alignments.sorted.sam
-rw-r--r-- 1 root root 613 11-02 19:33 YPD_all_alignments.sorted.sam.sai
-rw-r--r-- 1 root root 395434 11-02 19:35 YPD.paired.sam
-rw-r--r-- 1 root root 398912 11-02 19:36 YPD.paired.sorted.sam
-rw-r--r-- 1 root root 613 11-02 19:36 YPD.paired.sorted.sam.sai

I create a file "chromosome.sizes" as
[root@localhost rna-seq]# more chromosome.sizes
chr7 906452
chr6 1297466
chr5 643605
chr4 733397
chr3 1521169
chr2 1534814
chr1 782162

and a sequence file "chr1.fa" in the same directory
then execute the follow command
java -jar ./scripture-beta.jar -alignment YPD_all_alignments.sorted.sam -out chr1.scr
iptureESTest.segments -sizeFile chromosome.sizes -chr chr1 -chrSequence chr1.fa -pairedEnd YPD.paired.sorted.sam

and got the following infomation:
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: 177830504
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.

How can I solve this problem?
thanks!