Hello,
I would start by confirming the SAMTools indexes and tool installs. Confirm
that you can execute SAMTools tool's successfully within Galaxy. If there
are problems, check to see if there is a PATH issue. Make sure the "galaxy
user" is accessing the correct version (and indexes for reference
Hello all,
I have a user who is getting the following error when analyzing a FASTQ
file using TopHat for Illumina.
TopHat v2.0.10
[bam_header_read] EOF marker is absent. The input is probably truncated.
[bam_header_read] invalid BAM binary header (this is not a BAM file).
[bam_index_core] Invalid
Am 24.02.2015 um 13:01 schrieb Nicola Soranzo:
> Il 24.02.2015 10:19 Björn Grüning ha scritto:
>
>> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>>
>>> On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
>>>
The main problem for me was that I was not aware that the tophat tool
had a dep
Il 24.02.2015 10:19 Björn Grüning ha scritto:
Am 24.02.2015 um 10:03 schrieb Peter Cock:
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
The main problem for me was that I was not aware that the tophat
tool
had a dependency on a command line tool outside of galaxy
installation. I see i
On Tue, Feb 24, 2015 at 9:19 AM, Björn Grüning
wrote:
> Am 24.02.2015 um 10:03 schrieb Peter Cock:
>> ... So far so good, but at that point Galaxy
>> tries to index the BAM file itself. This happens for any BAM file,
>> regardless of the tool which created it - and simply expects samtools
>> on th
Am 24.02.2015 um 10:03 schrieb Peter Cock:
> On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
>> The main problem for me was that I was not aware that the tophat
>> tool had a dependency on a command line tool outside of galaxy
>> installation. I see in the admin interface that tophat has a
On Tue, Feb 24, 2015 at 6:31 AM, Michael Thon wrote:
> The main problem for me was that I was not aware that the tophat
> tool had a dependency on a command line tool outside of galaxy
> installation. I see in the admin interface that tophat has a dependency
> on samtools of type package and I as
The main problem for me was that I was not aware that the tophat tool had a
dependency on a command line tool outside of galaxy installation. I see in the
admin interface that tophat has a dependency on samtools of type package and I
assumed that should provide the samtools binary. Of course I
Sorry for this messy situation. With the next release Galaxy will be
able to set metadata using any version of samtools due to an excellent
fix by Nate - so this hopefully will become less of an issue.
-John
On Mon, Feb 23, 2015 at 10:01 AM, Peter Cock wrote:
> On Mon, Feb 23, 2015 at 2:13 PM, M
On Mon, Feb 23, 2015 at 2:13 PM, Michael Thon wrote:
>
> I figured that galaxy must be finding a samtools v1.1 even though the tool
> was not installed, according to the admin page. I uninstalled the samtools
> that was installed system-wide on the server. Now I get this error:
>
> Traceback (mos
> On Feb 23, 2015, at 8:23 AM, Saket Choudhary wrote:
>
> On 22 February 2015 at 23:17, Michael Thon wrote:
>> bam_index_build2() not yet
>
> Hi Michael,
>
> This seems to be related to this:
> https://github.com/samtools/samtools/issues/199
>
> You should probably switch to samtools 0.1.19
Nope, it still isn't working. I deleted tophat2, package_tophat2 and
package_samtools and then reinstalled tophat2 from Galaxy main. Here are what I
think are the relevant installed packages:
tophat2
package_tophat2_2_0_9
package_samtools_0_1_18
Any other advice would be appreciated.
> On Feb
Hi - Thanks for the info. I had two versions of samtools installed so I
uninstalled one and left only samtools 0.1.19 however I still get the error.
I'm using the tophat2 tool and I'm still getting the error. I just reinstalled
the tophat2 tool and I'm running it again.
> On Feb 23, 2015, a
On 22 February 2015 at 23:17, Michael Thon wrote:
> bam_index_build2() not yet
Hi Michael,
This seems to be related to this:
https://github.com/samtools/samtools/issues/199
You should probably switch to samtools 0.1.19
Saket
___
Please ke
I have a local installation of galaxy on my server. When I run tophat2, the
job runs but then throws this error:
Traceback (most recent call last):
File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py", line 129,
in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
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