Hi Delong,
If you are mapping against a large reference genome and your datasets
are large, 8G of memory may simply not be enough, even with omitting
this paramater. Also, if you have set other TopHat parameters to be
sensitive, then those can also be contributing to memory usage.
Splitting t
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
Hi -
Pls see below
On 8/27/13 6:36 AM, Delong, Zhou wrote:
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
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)
Hello Humberto,
Are you using the public Main Galaxy instance at
http://main.g2.bx.psu.edu (http://usegalaxy.org)? If so, and a re-run of
the job still fails, please submit a bug report so that we can provide
feedback.
http://wiki.galaxyproject.org/Support#Reporting_tool_errors
There was a s
Hi Everyone.
Somebody knows what this error message means:
An error occurred running this job:Settings: Output files:
"/tmp/3010855.cyberstar.psu.edu/tmpU4RslD/tmpNmgc_h.*.ebwt" Line rate: 6 (line
is 64 bytes) Lines per side: 1 (side is 64 bytes) Offset rate: 5 (one in 32)
FTable chars: 10 Str
Hi,
Thanks for the reply, sorry about the multiple posts - it kept getting bounced
so I resubmitted the question. We seem to be having real problems with our
local install so I'll add it to the list...!
Cheers
David
On 14 Mar 2012, at 18:10, Jennifer Jackson wrote:
> Hi David,
>
> You ques
Hi David,
You question has posted to the list now and we will be getting back to
you. It didn't post immediately due to some mail mailman server issues here.
This looks like a problem that came up on a local instance. Because of
that, I am going to send this over to the galaxy-...@bx.psu.edu
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect
/local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect
/local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue
Hi,
JUst running a TopHat job which returned the following error:
Executing: /gpfs/cluster/isys/galaxy/Software/bin/bowtie-inspect
/local/tmp5Ywx45/dataset_942 > ./tophat_out/tmp/dataset_942.fa
[Tue Mar 13 12:45:08 2012] Checking for Bowtie
Bowtie version: 0.12.7.0
[Tue
Thanks Jen for your answer
Zohra
> Date: Tue, 11 Oct 2011 13:01:37 -0400
> From: j...@bx.psu.edu
> To: saci...@live.fr
> CC: galaxy-user@lists.bx.psu.edu
> Subject: Re: [galaxy-user] tophat error
>
> Hi Zohra,
>
> One more bit of help: in the past our team has notice
Hi Zohra,
One more bit of help: in the past our team has noticed that Color Space
files from NCBI's SRA database have a "placeholder" adapter base quality
score added in (for an unknown reason).
If you choose to use Galaxy, when passing the file through the FASTQ
Groomer tool (with input and
Hello Zohra,
For command line (not Galaxy) use of this tool, questions would be best
directed to the tool authors at tophat.cuffli...@gmail.com. That said,
there appears to be a mismatch between the quality scores in your fastq
file and what was expected (integer, linked to the -C option).
S
Hello,
I was trying to run tophat v1.3.2 on SOLID data and I have this error:
zohra@bart:~/Bureau/cancer$ tophat -o /tmp/tophat_SRR036752/ -g 1 -p 4 -C
/home/zohra/indexes_bowtie/humain_ SRR036752.fastq
[Tue Oct 11 13:23:53 2011] Beginning TopHat run (v1.3.2)
---
Hi Song,
We have alpha support for Tophat v1.3.0 and it appears to work fine with
Galaxy's Tophat wrappers. We'll upgrade and start full testing near term.
For now, when running in a local instances, we do encourage users to try
it and see if it meets their needs. Perhaps try with an uncompre
Hello Song Li,
The file extension seems to be a mismatch.
file.gz <- "gzip" utility
Exploring the use of gunzip or zcat are options to restore a "file.z".
Hopefully this helps,
Jen
Galaxy team
On 7/19/11 11:52 AM, Song Li wrote:
Hello everyone,
I was trying to run tophat in a local version
Hello everyone,
I was trying to run tophat in a local version of galaxy, but I got the
following error:
gzip: stdout: Broken pipe
[Tue Jul 19 14:10:36 2011] Processing bowtie hits
Error: could not open pipe gzip -cd <
./tophat_out/tmp/left_kept_reads_missing.fq.z
It seems that when tophat is cal
Hi. Newbie here. I'm trying to setup tophat for our local install. I'm
getting the following error when I try to run it. Has anyone seen this
before or have any ideas what I can try to fix it.
Thanks,
Simon
Error in tophat:
[Wed Jun 29 11:54:09 2011] Beginning TopHat run (v1.3.1)
--
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