an error with Tophat mapping

[zhyd9]

Hi,

I met a problem when mapped with Tophat. The detailed information is as follows:

tophat -o /nfs/users/nfs_y/yz4/transcriptome_analysis/cufflinks/mbuppf_tophat_out -r 180 --mate-std-dev 50 -i 30 /nfs/users/nfs_y/yz4/transcriptome_analysis/cufflinks/version1.EMU.fas.13-8-2010 /fuse/mpsafs/runs/3535/3535_3_1.fastq /fuse/mpsafs/runs/3535/3535_3_2.fastq

[Mon Oct 4 11:57:19 2010] Beginning TopHat run (v1.0.13)
-----------------------------------------------
[Mon Oct 4 11:57:19 2010] Preparing output location /nfs/users/nfs_y/yz4/transcriptome_analysis/cufflinks/mbuppf_tophat_out/
[Mon Oct 4 11:57:19 2010] Checking for Bowtie index files
[Mon Oct 4 11:57:19 2010] Checking for reference FASTA file
Warning: Could not find FASTA file /nfs/users/nfs_y/yz4/transcriptome_analysis/cufflinks/version1.EMU.fas.13-8-2010.fa
[Mon Oct 4 11:57:19 2010] Reconstituting reference FASTA file from Bowtie index
[Mon Oct 4 11:58:08 2010] Checking for Bowtie
Bowtie version: 0.12.3.0
[Mon Oct 4 11:58:08 2010] Checking reads
seed length: 37bp
format: fastq
quality scale: phred33 (default)
[Mon Oct 4 12:06:53 2010] Mapping reads against version1.EMU.fas.13-8-2010 with Bowtie
[Mon Oct 4 12:50:13 2010] Joining segment hits
[Mon Oct 4 12:52:10 2010] Mapping reads against version1.EMU.fas.13-8-2010 with Bowtie
[Mon Oct 4 13:35:28 2010] Joining segment hits
[Mon Oct 4 13:35:29 2010] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err = 1

Anybody has an idea to help me out.

Regards,
Yadong