tophat rna-seq crash

[wokai001]

I'm using tophat for aligning Illumina rna-seq data. It crashed in one of the last steps:

[Tue Jan 10 08:26:56 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Tue Jan 10 08:26:56 2012] Preparing output location ./tophat_out_bwa/
[Tue Jan 10 08:26:56 2012] Checking for Bowtie index files
[Tue Jan 10 08:26:56 2012] Checking for reference FASTA file
[Tue Jan 10 08:26:56 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jan 10 08:26:56 2012] Checking for Samtools
Samtools Version: 0.1.17
[Tue Jan 10 08:26:56 2012] Generating SAM header for hshiv
format: fastq
quality scale: phred33 (default)
[Tue Jan 10 08:27:16 2012] Preparing reads
left reads: min. length=101, count=86332313
[Tue Jan 10 08:55:48 2012] Mapping left_kept_reads against hshiv with Bowtie
[Tue Jan 10 09:35:06 2012] Processing bowtie hits
[Tue Jan 10 10:30:04 2012] Mapping left_kept_reads_seg1 against hshiv with Bowtie (1/4)
[Tue Jan 10 12:41:18 2012] Mapping left_kept_reads_seg2 against hshiv with Bowtie (2/4)
[Tue Jan 10 14:54:35 2012] Mapping left_kept_reads_seg3 against hshiv with Bowtie (3/4)
[Tue Jan 10 17:08:07 2012] Mapping left_kept_reads_seg4 against hshiv with Bowtie (4/4)
[Tue Jan 10 18:56:53 2012] Searching for junctions via segment mapping
[FAILED]
Error: segment-based junction search failed with err =1
Error: could not get read# 839911731 from stream!

I used tophat on Ubuntu Linux (linux kernel 3.0.0-14-generic). Actually, I first aligned my reads with bwa (bwa aln, then bwa samse) and extracted the unmapped reads with samtools into bam. From there, I used the (tophat) bam2fastx tool to convert the unmapped reads back into fastq. The unmapped reads (about 30%) then go as Input into tophat.

Has someone any idea what's going on there?

Thanks for your help
Wolfgang