Question: Tophat Error: Segment-Based Junction Search Failed With Err
0
Delong, Zhou • 140 wrote:
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 aoűt 2013 9:36
Ŕ : galaxy-user@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_directo
ry/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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modified 5.2 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
5.2 years ago by
Delong, Zhou • 140
