SEQanswers - yet another "Error: segment-based junction search failed with err = -9"

I have run into the same problem that are few people have encountered before when I am using TopHat to align 7 lanes of Illumina data to hg19. Since I am relatively new to tophat, can somebody give me a hint? Thanks!

here are the screen output and segment_juncs.log:

Code:

[Fri Aug 20 14:58:12 2010] Beginning TopHat run (v1.0.13)

-----------------------------------------------

[Fri Aug 20 14:58:12 2010] Preparing output location /home/haiti/tmpdata/all_brn/tophat/

[Fri Aug 20 14:58:12 2010] Checking for Bowtie index files

[Fri Aug 20 14:58:12 2010] Checking for reference FASTA file

[Fri Aug 20 14:58:12 2010] Checking for Bowtie

        Bowtie version:          0.12.5.0

[Fri Aug 20 14:58:12 2010] Checking reads

        seed length:     35bp

        format:          fastq

        quality scale:   phred33 (default)

[Fri Aug 20 15:31:58 2010] Reading known junctions from GFF file

        Warning: TopHat did not find any junctions in GFF file

[Fri Aug 20 15:53:49 2010] Mapping reads against hg19 with Bowtie

[Sat Aug 21 00:52:55 2010] Joining segment hits

[Sat Aug 21 01:22:40 2010] Searching for junctions via segment mapping

        [FAILED]

Error: segment-based junction search failed with err = -9

segment_juncs.log

Code:

segment_juncs v1.0.13

---------------------------

Loading reference sequences...

        Loading chr1...done

        Loading chr2...done

        Loading chr3...done

        Loading chr4...done

        Loading chr5...done

        Loading chr6...done

        Loading chr7...done

        Loading chr8...done

        Loading chr9...done

        Loading chr10...done

        Loading chr11...done

        Loading chr12...done

        Loading chr13...done

        Loading chr14...done

        Loading chr15...done

        Loading chr16...done

        Loading chr17...done

        Loading chr18...done

        Loading chr19...done

        Loading chr20...done

        Loading chr21...done

        Loading chr22...done

        Loading chrX...done

        Loading chrY...done

        Loading chrM...done

Found 0 potential split-segment junctions

Indexing extensions in /home/haiti/tmpdata/all_brn/tophat/tmp//left_kept_reads_missing.fq

Total extensions: 637479408

Looking for junctions by island end pairings

Adding hits from segment file 0 to coverage map

Map covers 325972654 bases

Map covers 320327918 bases in sufficiently long segments

Map contains 5580241 good islands

276495363 are left looking bases

276492492 are right looking bases

Collecting potential splice sites in islands