Tophat error: results more than one accepted_hits file

[setia]

Hi All,
I run Tophat and cufflink simultaneously in a batch file with the following command

tophat -o INBOX/BRCA/batch3/tophat.output.$1 -p 8 --library-type=fr-unstranded -G reference/genes.gtf reference/BowtieIndex/genome INBOX/BRCA/batch3/$1_1.fastq.gz INBOX/BRCA/batch3/$1_2.fastq.gz

cufflinks -o INBOX/BRCA/batch3/Cuffres.$1 -p 8 -g reference/genes.gtf -b reference/BowtieIndex/genome.fa INBOX/BRCA/batch3/tophat.output.$1/accepted_hits.bam

After around 17 node time, it failed and give the output log as follows:

gcc not loaded, will load default gcc
bowtie not loaded, will load default bowtie
samtools not loaded, will load default samtools

[Sun Nov 25 12:08:29 2012] Beginning TopHat run (v1.4.0)
-----------------------------------------------
[Sun Nov 25 12:08:29 2012] Preparing output location INBOX/BRCA/batch2/tophat.output.SRR327840/
[Sun Nov 25 12:08:29 2012] Checking for Bowtie index files
[Sun Nov 25 12:08:29 2012] Checking for reference FASTA file
[Sun Nov 25 12:08:29 2012] Checking for Bowtie
Bowtie version: 0.12.6.0
[Sun Nov 25 12:08:29 2012] Checking for Samtools
Samtools Version: 0.1.12
[Sun Nov 25 12:08:29 2012] Generating SAM header for reference/BowtieIndex/genome
format: fastq
quality scale: phred33 (default)
[Sun Nov 25 12:08:31 2012] Reading known junctions from GTF file
[Sun Nov 25 12:08:45 2012] Preparing reads
left reads: min. length=50, count=81275603
right reads: min. length=50, count=82295955
[Sun Nov 25 13:11:10 2012] Creating transcriptome data files..
[Sun Nov 25 13:12:18 2012] Building Bowtie index from genes.fa
[Sun Nov 25 13:45:04 2012] Mapping left_kept_reads against transcriptome genes with Bowtie
[Sun Nov 25 15:00:57 2012] Mapping right_kept_reads against transcriptome genes with Bowtie
[Sun Nov 25 16:16:26 2012] Converting left_kept_reads.m2g to genomic coordinates (map2gtf)
[Sun Nov 25 17:04:50 2012] Converting right_kept_reads.m2g to genomic coordinates (map2gtf)
[Sun Nov 25 17:52:54 2012] Resuming TopHat pipeline with unmapped reads
[Sun Nov 25 17:52:54 2012] Mapping left_kept_reads.m2g_um against genome with Bowtie
[Sun Nov 25 17:59:25 2012] Processing bowtie hits
[Sun Nov 25 18:06:59 2012] Mapping left_kept_reads.m2g_um_seg1 against genome with Bowtie (1/2)
[Sun Nov 25 18:13:58 2012] Mapping left_kept_reads.m2g_um_seg2 against genome with Bowtie (2/2)
[Sun Nov 25 18:20:54 2012] Mapping right_kept_reads.m2g_um against genome with Bowtie
[Sun Nov 25 18:27:40 2012] Processing bowtie hits
[Sun Nov 25 18:36:06 2012] Mapping right_kept_reads.m2g_um_seg1 against genome with Bowtie (1/2)
[Sun Nov 25 18:44:23 2012] Mapping right_kept_reads.m2g_um_seg2 against genome with Bowtie (2/2)
[Sun Nov 25 18:52:46 2012] Searching for junctions via segment mapping
[Sun Nov 25 21:15:22 2012] Retrieving sequences for splices
[Sun Nov 25 21:22:20 2012] Indexing splices
[Sun Nov 25 21:30:22 2012] Mapping left_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie (1/2)
[Sun Nov 25 23:20:53 2012] Mapping left_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie (2/2)
[Mon Nov 26 00:31:16 2012] Joining segment hits
[Mon Nov 26 00:57:57 2012] Mapping right_kept_reads.m2g_um_seg1 against segment_juncs with Bowtie (1/2)
[Mon Nov 26 02:48:13 2012] Mapping right_kept_reads.m2g_um_seg2 against segment_juncs with Bowtie (2/2)
[Mon Nov 26 03:58:50 2012] Joining segment hits
[Mon Nov 26 04:26:15 2012] Reporting output tracks
-----------------------------------------------
Run complete [17:52:23 elapsed]
cufflinks: /lib64/libz.so.1: no version information available (required by cufflinks)
You are using Cufflinks v2.0.2, which is the most recent release.
open: No such file or directory
File INBOX/BRCA/batch2/tophat.output.SRR327840/accepted_hits.bam doesn't appear to be a valid BAM file, trying SAM...
Error: cannot open alignment file INBOX/BRCA/batch2/tophat.output.SRR327840/accepted_hits.bam for reading

in the tophat result folder, instead of one accepted_hits.bam files, there are 46 files like shown below

accepted_hits.0000.bam
accepted_hits.0001.bam
…
accepted_hits.0046.bam

I do not see any error message from Tophat. Other samples work fine, only in some sample the same problem occurs. Does anyone have the same problem with me and please let me know what maybe the problem and also the trick to solve it. Thank you.

Setia