Hello,
I have run several analysis with Tophat 2 on my local instance of galaxy and I 
get this error for all of them..

segment-based junction search failed with err = 1 or -9

Here is an example of full error report:


Error in tophat:

[2013-08-23 11:56:58] Beginning TopHat run (v2.0.6)
-----------------------------------------------
[2013-08-23 11:56:58] Checking for Bowtie
                  Bowtie version:        2.0.2.0
[2013-08-23 11:56:58] Checking for Samtools
                Samtools version:        0.1.18.0
[2013-08-23 11:56:58] Checking for Bowtie index files
[2013-08-23 11:56:58] Checking for reference FASTA file
[2013-08-23 11:56:58] Generating SAM header for 
/usr/local/data/bowtie2/hg19/hg19
        format:          fastq
        quality scale:   phred33 (default)
[2013-08-23 11:58:04] Preparing reads
         left reads: min. length=50, max. length=50, 145339247 kept reads 
(34946 discarded)
        right reads: min. length=50, max. length=50, 145340153 kept reads 
(34040 discarded)
[2013-08-23 14:16:21] Mapping left_kept_reads to genome hg19 with Bowtie2
[2013-08-24 01:04:37] Mapping left_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 03:38:22] Mapping left_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-24 05:29:58] Mapping right_kept_reads to genome hg19 with Bowtie2
[2013-08-24 19:50:22] Mapping right_kept_reads_seg1 to genome hg19 with Bowtie2 
(1/2)
[2013-08-24 22:36:38] Mapping right_kept_reads_seg2 to genome hg19 with Bowtie2 
(2/2)
[2013-08-25 01:40:37] Searching for junctions via segment mapping
        Coverage-search algorithm is turned on, making this step very slow
        Please try running TopHat again with the option (--no-coverage-search) 
if this step takes too much time or memory.
        [FAILED]
Error: segment-based junction search failed with err =-9
Collecting potential splice sites in islands


cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/deletions.bed':
 No such file or directory
cp: cannot stat 
`/home/galaxy/galaxy-dist/database/job_working_directory/000/515/tophat_out/insertions.bed':
 No such file or directory

I did some research on the internet and it seems to be a memory problem to me, 
is there any solution other than rerun these jobs on a more powerful machine?

And why has Bowtie/Tophat discard different numbers of reads? What will be the 
impact? Does it means that if I don't have exact matches between the paired end 
input, it is still be possible to run the job?

Thanks,
Delong
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