Hello,
I don't know why I still have this problem..
I have run tophat2 with different dataset, sometimes it goes well but sometime
I have this error.
I run only one job at a time on a virtual machine with 8G memory without using
galaxy plateform. I tried --no-coverage-search option but it changes nothing.
Thanks.
Delong
________________________________
De : Delong, Zhou
Envoyé : 27 août 2013 9:36
À : galaxy-u...@bx.psu.edu
Objet : Tophat Error: segment-based junction search failed with err
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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