tophat 1.3.0(Beta) closure search failed

[bambootear]

I tried to run tophat 1.3.0(Beta) with 90*2 illumina RNA-seq

tophat -o tophat-output -F 0.1 -p 6 -r 10 --mate-std-dev 45 --solexa1.3-quals --library-type fr-firststrand -i 30 --min-closure-intron 30
--min-coverage-intron 30 --closure-search --coverage-search --segment-length 30 ref polyA.1.fq polyA.2.fq


The same data and parameters worked well with tophat 1.2.0

[Tue Jun 7 01:43:17 2011] Beginning TopHat run (v1.3.0)
-----------------------------------------------
[Tue Jun 7 01:43:17 2011] Preparing output location tophat-output/
[Tue Jun 7 01:43:17 2011] Checking for Bowtie index files
[Tue Jun 7 01:43:17 2011] Checking for reference FASTA file
[Tue Jun 7 01:43:17 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue Jun 7 01:43:17 2011] Checking for Samtools
Samtools Version: 0.1.12
[Tue Jun 7 01:43:17 2011] Generating SAM header for ref
[Tue Jun 7 01:43:17 2011] Preparing reads
format: fastq
quality scale: phred64 (reads generated with GA pipeline version >= 1.3)
Left reads: min. length=90, count=11331560
Right reads: min. length=90, count=11332998
[Tue Jun 7 01:59:21 2011] Mapping left_kept_reads against ref with Bowtie
[Tue Jun 7 02:08:18 2011] Processing bowtie hits
[Tue Jun 7 02:19:24 2011] Mapping left_kept_reads_seg1 against ref with Bowtie (1/3)
[Tue Jun 7 02:21:27 2011] Mapping left_kept_reads_seg2 against ref with Bowtie (2/3)
[Tue Jun 7 02:23:34 2011] Mapping left_kept_reads_seg3 against ref with Bowtie (3/3)
[Tue Jun 7 02:25:36 2011] Mapping right_kept_reads against ref with Bowtie
[Tue Jun 7 02:34:46 2011] Processing bowtie hits
[Tue Jun 7 02:45:21 2011] Mapping right_kept_reads_seg1 against ref with Bowtie (1/3)
[Tue Jun 7 02:47:13 2011] Mapping right_kept_reads_seg2 against ref with Bowtie (2/3)
[Tue Jun 7 02:49:07 2011] Mapping right_kept_reads_seg3 against ref with Bowtie (3/3)
[Tue Jun 7 02:51:00 2011] Searching for junctions via segment mapping
[Tue Jun 7 03:02:19 2011] Searching for junctions via mate-pair closures
[FAILED]
Error: closure-based junction search failed with err =-11