Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hi Björn,

That’s right! It was quiet strange. I need to extend the memory and cores usage 
via command line.

Thank you so much!

Deepak


> On Aug 11, 2017, at 10:00, Björn Grüning  wrote:
> 
> Hi,
> 
> it seems that your Docker Box only gets 1GB :(
> 
> please re-check the configs.
> Sorry to be not more helpful!
> Bjoern
> 
> On 11.08.2017 15:55, Deepak Tanwar wrote:
>> Also, I am running this container on a Mac Pro using Kitematic and I
>> have docker preference set to use 12 cores and 64 GB RAM.
>> 
>> Thanks,
>> Deepak
>> 
>> 
>>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar >> > wrote:
>>> 
>>> Hi Björn,
>>> 
>>> If I do docker stats:
>>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>>>NET I/O BLOCK I/O   PIDS
>>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>>   158kB / 785kB   11.4GB / 81MB   106
>>> 
>>> And, after ssh into docker machine:
>>> 
>>> FilesystemSize  Used Available Use% Mounted on
>>> tmpfs   896.2M186.6M709.6M  21% /
>>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>>> Users   931.0G683.8G247.2G  73% /Users
>>> /dev/sda1   282.7G 14.9G253.2G   6%
>>> /mnt/sda1/var/lib/docker/aufs
>>> 
>>> Best regards,
>>> Deepak
>>> 
>>> 
 On Aug 11, 2017, at 9:39 AM, Björn Grüning >>> > wrote:
 
 Hi Deepak,
 
 how are you running this Container?
 Can you check how many memory you have inside the container?
 
 Cheers,
 Bjoern
 
 On 11.08.2017 15:35, Deepak Tanwar wrote:
> Hello,
> 
> I am trying to build Bowtie2 index for hg19.
> I a using Docker image of Galaxy.
> 
> Computer I am using have 12 cores and 64 GB of RAM.
> 
> Error I am getting is:
> 
> Fatal error: Exit code 1 ()
> Building a SMALL index
> Could not allocate space for a joined string of 2897310462 elements.
> Switching to a packed string representation.
> Building a SMALL index
> Could not find approrpiate bmax/dcv settings for building this index.
> Already tried a packed string representation.
> Please try indexing this reference on a computer with more memory.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build --wrapper basic-0
> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
> fa.fa hg19 fa
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Error building index.
> 
> Please help!
> 
> Thank you,
> Deepak
> 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
> https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
> http://galaxyproject.org/search/
> 
>>> 
>>> ___
>>> Please keep all replies on the list by using "reply all"
>>> in your mail client.  To manage your subscriptions to this
>>> and other Galaxy lists, please use the interface at:
>>> https://lists.galaxyproject.org/
>>> 
>>> To search Galaxy mailing lists use the unified search at:
>>> http://galaxyproject.org/search/
>> 

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] Bowtie2 index building

[Björn Grüning]

Hi,

it seems that your Docker Box only gets 1GB :(

please re-check the configs.
Sorry to be not more helpful!
Bjoern

On 11.08.2017 15:55, Deepak Tanwar wrote:
> Also, I am running this container on a Mac Pro using Kitematic and I
> have docker preference set to use 12 cores and 64 GB RAM.
> 
> Thanks,
> Deepak
> 
> 
>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar > > wrote:
>>
>> Hi Björn,
>>
>> If I do docker stats:
>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>> NET I/O BLOCK I/O   PIDS
>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>158kB / 785kB   11.4GB / 81MB   106
>>
>> And, after ssh into docker machine:
>>
>> FilesystemSize  Used Available Use% Mounted on
>> tmpfs   896.2M186.6M709.6M  21% /
>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>> Users   931.0G683.8G247.2G  73% /Users
>> /dev/sda1   282.7G 14.9G253.2G   6%
>> /mnt/sda1/var/lib/docker/aufs
>>
>> Best regards,
>> Deepak
>>
>>
>>> On Aug 11, 2017, at 9:39 AM, Björn Grüning >> > wrote:
>>>
>>> Hi Deepak,
>>>
>>> how are you running this Container?
>>> Can you check how many memory you have inside the container?
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> On 11.08.2017 15:35, Deepak Tanwar wrote:
 Hello,

 I am trying to build Bowtie2 index for hg19.
 I a using Docker image of Galaxy.

 Computer I am using have 12 cores and 64 GB of RAM.

 Error I am getting is:

 Fatal error: Exit code 1 ()
 Building a SMALL index
 Could not allocate space for a joined string of 2897310462 elements.
 Switching to a packed string representation.
 Building a SMALL index
 Could not find approrpiate bmax/dcv settings for building this index.
 Already tried a packed string representation.
 Please try indexing this reference on a computer with more memory.
 Error: Encountered internal Bowtie 2 exception (#1)
 Command: bowtie2-build --wrapper basic-0
 /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
 fa.fa hg19 fa
 Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
 Error building index.

 Please help!

 Thank you,
 Deepak



 ___
 Please keep all replies on the list by using "reply all"
 in your mail client.  To manage your subscriptions to this
 and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

 To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

>>
>> ___
>> Please keep all replies on the list by using "reply all"
>> in your mail client.  To manage your subscriptions to this
>> and other Galaxy lists, please use the interface at:
>>  https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>  http://galaxyproject.org/search/
> 
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Also, I am running this container on a Mac Pro using Kitematic and I have 
docker preference set to use 12 cores and 64 GB RAM.

Thanks,
Deepak


On Aug 11, 2017, at 9:54 AM, Deepak Tanwar 
mailto:dktan...@hotmail.com>> wrote:

Hi Björn,

If I do docker stats:
CONTAINER   CPU %   MEM USAGE / LIMIT MEM % 
  NET I/O BLOCK I/O   PIDS
dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%
  158kB / 785kB   11.4GB / 81MB   106

And, after ssh into docker machine:

FilesystemSize  Used Available Use% Mounted on
tmpfs   896.2M186.6M709.6M  21% /
tmpfs   497.9M476.0K497.4M   0% /dev/shm
/dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
Users   931.0G683.8G247.2G  73% /Users
/dev/sda1   282.7G 14.9G253.2G   6% 
/mnt/sda1/var/lib/docker/aufs

Best regards,
Deepak


On Aug 11, 2017, at 9:39 AM, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hi Björn,

If I do docker stats:
CONTAINER   CPU %   MEM USAGE / LIMIT MEM % 
  NET I/O BLOCK I/O   PIDS
dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%
  158kB / 785kB   11.4GB / 81MB   106

And, after ssh into docker machine:

FilesystemSize  Used Available Use% Mounted on
tmpfs   896.2M186.6M709.6M  21% /
tmpfs   497.9M476.0K497.4M   0% /dev/shm
/dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
Users   931.0G683.8G247.2G  73% /Users
/dev/sda1   282.7G 14.9G253.2G   6% 
/mnt/sda1/var/lib/docker/aufs

Best regards,
Deepak


On Aug 11, 2017, at 9:39 AM, Björn Grüning 
mailto:bjoern.gruen...@gmail.com>> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
 https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
 http://galaxyproject.org/search/


___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

Re: [galaxy-dev] Bowtie2 index building

[Björn Grüning]

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
> Hello,
> 
> I am trying to build Bowtie2 index for hg19.
> I a using Docker image of Galaxy.
> 
> Computer I am using have 12 cores and 64 GB of RAM.
> 
> Error I am getting is:
> 
> Fatal error: Exit code 1 ()
> Building a SMALL index
> Could not allocate space for a joined string of 2897310462 elements.
> Switching to a packed string representation.
> Building a SMALL index
> Could not find approrpiate bmax/dcv settings for building this index.
> Already tried a packed string representation.
> Please try indexing this reference on a computer with more memory.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build --wrapper basic-0
> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
> fa.fa hg19 fa 
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Error building index. 
> 
> Please help!
> 
> Thank you,
> Deepak
> 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
> 
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[galaxy-dev] Bowtie2 index building

[Deepak Tanwar]

Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
 fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[galaxy-dev] bowtie2 indexes & errors

[Nikolaos Tur]

Hi,

I observe next error:

[2017-03-21 10:30:56] Beginning TopHat run (v2.1.0)
---
[2017-03-21 10:30:56] Checking for Bowtie
 Bowtie version:2.2.5.0
[2017-03-21 10:30:56] Checking for Bowtie index files (genome)..
Error: Could not find Bowtie 2 index files
(/home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84.*.bt2)

And this error is clear: no index files with *.bt2. But we have for
GRCm38_84:
../GRCm38_84/GRCm38_84.3.bt2l
../GRCm38_84/GRCm38_84.rev.1.bt2l
../GRCm38_84/GRCm38_84.1.bt2l
../GRCm38_84/GRCm38_84.rev.2.bt2l
../GRCm38_84/GRCm38_84.2.bt2l
../GRCm38_84/GRCm38_84.4.bt2l
../GRCm38_84/GRCm38_84.fa

as I understand from the manual for bowtie2 "l" at the end of files means
that indexes were created for large file. If it is correct way then why
Galaxy tools do not understand this extension and how it should be solve?

Okay I have simply created symbolic links to them with *.bt2 extensions (I
don't know if *.tb2 and *.tb2l have the same format) and run job again:

[2017-03-21 11:40:41] Beginning TopHat run (v2.1.0)
---
[2017-03-21 11:40:41] Checking for Bowtie
 Bowtie version:2.2.5.0
[2017-03-21 11:40:41] Checking for Bowtie index files (genome)..
[2017-03-21 11:40:41] Checking for reference FASTA file
[2017-03-21 11:40:41] Generating SAM header for
/home/galaxy/tool-data/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84
[2017-03-21 11:40:50] Preparing reads
left reads: min. length=101, max. length=101, 37099122 kept reads
(11326 discarded)
   right reads: min. length=101, max. length=101, 36957824 kept reads
(152624 discarded)
[2017-03-21 12:11:25] Mapping left_kept_reads to genome GRCm38_84 with
Bowtie2
   [FAILED]
Error running bowtie:
Error reading _plen[] array: 895748346, 4294967292
Error: Encountered internal Bowtie 2 exception (#1)
Command:
/home/galaxy/tools/dependencies/bowtie2/2.2.5/iuc/package_bowtie_2_2_5/30bd7eaeddbf/bin/bowtie2-align-s
--wrapper basic-0 -k 20 -D 15 -R 2 -N 0 -L 20 -i S,1,1.25 --gbar 4 --mp 6,2
--np 1 --rdg 5,3 --rfg 5,3 --score-min C,-14,0 -p 8 --sam-no-hd -x
/home/galaxy/tooldata/GRCm38_84/bowtie2_index/GRCm38_84/GRCm38_84 -
(ERR): bowtie2-align exited with value 1

If this is not an extension problem then what is an origin of this error
and how to solve it?

Thanx,
Nikolaos
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/

[galaxy-dev] bowtie2 data_manager issue

[Joseph Sarro]

I am indexing reference genomes for bowtie2/tophat2, using the
corresponding data manager. I am getting some successful indexes and others
are giving an error. For the successful ones I see the genomes are
appearing in the "built in index" drop down for both bowtie2 and tophat2.
For the unsuccessful ones I am seeing them in the bowtie2 drop down but not
tophat2. Any ideas on what could be causing this issue?

The error message is as follows

Thanks in advance.

Traceback (most recent call last):
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/runners/local.py",
line 128, in queue_job
job_wrapper.finish( stdout, stderr, exit_code )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py",
line 1375, in finish
self.tool.exec_after_process( self.queue.app, inp_data, out_data,
param_dict, job=job )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/tools/__init__.py",
line 2107, in exec_after_process
data_manager.process_result( out_data )
  File 
"/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/tools/data_manager/manager.py",
line 303, in process_result
self.process_move( data_table_name, name, output_ref_values[ name
].extra_files_path, **data_table_value )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py",
line 1891, in extra_files_path
return self.dataset.extra_files_path
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/model/__init__.py",
line 1707, in get_extra_files_path
return self.object_store.get_filename( self, dir_only=True,
extra_dir=self._extra_files_path or "dataset_%d_files" % self.id )
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
line 487, in get_filename
return self._call_method('get_filename', obj, ObjectNotFound,
True, **kwargs)
  File "/vectorbase/web/Galaxy/galaxy-dist/lib/galaxy/objectstore/__init__.py",
line 508, in _call_method
% ( method, str( obj ), str( kwargs ) ) )
ObjectNotFound: objectstore, _call_method failed: get_filename on
, kwargs: {'dir_only':
True, 'extra_dir': 'dataset_19568_files'}
Tool execution generated the following error message:
Unable to finish job
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Bowtie2

[Björn Grüning]

Awesome!

Glad you got it to work.

Am 13.01.2016 um 21:19 schrieb Laforest, Martin:
> Seems to work after server reboot...
> 
> Thanks
> 
> Martin
> 
> De : Laforest, Martin
> Envoyé : 13 janvier 2016 10:00
> À : 'galaxy-dev@lists.galaxyproject.org'
> Objet : RE: Bowtie2
> 
> Oups I made a mistake I have problems with the tophat wrapper, not 
> bowtie. Bowtie runs fine...
> 
> Tophat - fast splice junction mapper for RNA-Seq reads
> 4eb3c3beb9c7
> Devteam
> 
> Packages package_bowtie_2_2_5 and package_2_0_14 are installed...
> 
> Thanks
> 
> Martin
> 
> De : Laforest, Martin
> Envoyé : 13 janvier 2016 09:43
> À : 'galaxy-dev@lists.galaxyproject.org'
> Objet : Bowtie2
> 
> Hello,
> 
> Please excuse my simple question since I'm a newbie... I've searched the 
> mailing list but did not find the appropriate answer...
> 
> I have a new Galaxy installation. I installed the tool  "Bowtie2: Fast and 
> sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool 
> apparently runs fine and I can download the BAM file at the end and see its 
> content (with IGV for example).
> 
> The problem is that my dataset is red and when I check the error, I get 
> "OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy 
> tries to set the data type, I don't know.
> 
> Many thanks for your help.
> 
> Martin
> 
> 
> 
> 
> ___
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
> 
___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Bowtie2

[Laforest, Martin]

Seems to work after server reboot...

Thanks

Martin

De : Laforest, Martin
Envoyé : 13 janvier 2016 10:00
À : 'galaxy-dev@lists.galaxyproject.org'
Objet : RE: Bowtie2

Oups I made a mistake I have problems with the tophat wrapper, not bowtie. 
Bowtie runs fine...

Tophat - fast splice junction mapper for RNA-Seq reads
4eb3c3beb9c7
Devteam

Packages package_bowtie_2_2_5 and package_2_0_14 are installed...

Thanks

Martin

De : Laforest, Martin
Envoyé : 13 janvier 2016 09:43
À : 'galaxy-dev@lists.galaxyproject.org'
Objet : Bowtie2

Hello,

Please excuse my simple question since I'm a newbie... I've searched the 
mailing list but did not find the appropriate answer...

I have a new Galaxy installation. I installed the tool  "Bowtie2: Fast and 
sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool 
apparently runs fine and I can download the BAM file at the end and see its 
content (with IGV for example).

The problem is that my dataset is red and when I check the error, I get 
"OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries 
to set the data type, I don't know.

Many thanks for your help.

Martin

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

Re: [galaxy-dev] Bowtie2

[Laforest, Martin]

Oups I made a mistake I have problems with the tophat wrapper, not bowtie. 
Bowtie runs fine...

Tophat - fast splice junction mapper for RNA-Seq reads
4eb3c3beb9c7
Devteam

Packages package_bowtie_2_2_5 and package_2_0_14 are installed...

Thanks

Martin

De : Laforest, Martin
Envoyé : 13 janvier 2016 09:43
À : 'galaxy-dev@lists.galaxyproject.org'
Objet : Bowtie2

Hello,

Please excuse my simple question since I'm a newbie... I've searched the 
mailing list but did not find the appropriate answer...

I have a new Galaxy installation. I installed the tool  "Bowtie2: Fast and 
sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool 
apparently runs fine and I can download the BAM file at the end and see its 
content (with IGV for example).

The problem is that my dataset is red and when I check the error, I get 
"OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries 
to set the data type, I don't know.

Many thanks for your help.

Martin

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/

[galaxy-dev] Bowtie2

[Laforest, Martin]

Hello,

Please excuse my simple question since I'm a newbie... I've searched the 
mailing list but did not find the appropriate answer...

I have a new Galaxy installation. I installed the tool  "Bowtie2: Fast and 
sensitive read alignment" (Revision 019c2a81547a, Owner: devteam). The tool 
apparently runs fine and I can download the BAM file at the end and see its 
content (with IGV for example).

The problem is that my dataset is red and when I check the error, I get 
"OSError: [Errno 2] No such file or directory"... Maybe it is when Galaxy tries 
to set the data type, I don't know.

Many thanks for your help.

Martin

___
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/