galaxy - velvet devteam revision 08256557922f

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galaxy - velvet devteam revision 08256557922f

fernandez Edgar

Hey Guys,

 

I need your help understanding what’s happening with velvet  devteam revision 08256557922f.

 

After installing it, velvet was giving me the following error:

galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness

 

I realized velvet needed that galaxy was restarted.

 

Now, velvet finishes his jobs (becomes green) however, the following message is on galaxy’s

Job output not returned from cluster

 

And you can see in the logs of the handler:

galaxy.jobs DEBUG 2016-10-31 10:17:08,548 (1669) Working directory for job is: /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669

galaxy.jobs.handler DEBUG 2016-10-31 10:17:08,567 (1669) Dispatching to drmaa runner

galaxy.jobs DEBUG 2016-10-31 10:17:08,621 (1669) Persisting job destination (destination id: torque)

galaxy.jobs.runners DEBUG 2016-10-31 10:17:08,630 Job [1669] queued (63.397 ms)

galaxy.jobs.handler INFO 2016-10-31 10:17:08,652 (1669) Job dispatched

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Building dependency shell command for dependency 'velvet'

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Find dependency velvet version 1.2.10

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,896 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7f80f807bd50> (isnull? False)

galaxy.jobs.command_factory INFO 2016-10-31 10:17:08,945 Built script [/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh] for tool command[PACKAGE_BASE=/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f; export PACKAGE_BASE; . /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f/env.sh; velveth 2>&1 | grep "Version" | sed -e 's/Version //' > /home/galaxy/galaxy-prod/database/tmp/GALAXY_VERSION_STRING_1669 2>&1; python /home/galaxy/galaxy-prod/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/velvet/08256557922f/velvet/velveth_wrapper.py '/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat' '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/dataset_4306_files' 21  -fasta -short /home/galaxy/galaxy-prod/database/files/003/dataset_3537.dat]

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Building dependency shell command for dependency 'samtools'

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Find dependency samtools version None

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps WARNING 2016-10-31 10:17:09,145 Failed to resolve dependency on 'samtools', ignoring

galaxy.jobs.runners DEBUG 2016-10-31 10:17:09,153 (1669) command is: mkdir -p working; cd working; /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh; return_code=$?; cd '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669'; python "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/set_metadata_KQTExg.py" "/home/galaxy/galaxy-prod/database/tmp/tmpLU0HQy" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/working/galaxy.json" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_in_HistoryDatasetAssociation_4437_kIYXWa,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_kwds_HistoryDatasetAssociation_4437_ArCXyb,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_out_HistoryDatasetAssociation_4437_l28qWr,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_results_HistoryDatasetAssociation_4437_oTDjOd,/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_override_HistoryDatasetAssociation_4437_8VzdJw" 5242880; sh -c "exit $return_code"

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,202 (1669) submitting file /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.sh

galaxy.jobs.runners.drmaa INFO 2016-10-31 10:17:09,210 (1669) queued as 1573.esilbac3a.esi.umontreal.ca

galaxy.jobs DEBUG 2016-10-31 10:17:09,214 (1669) Persisting job destination (destination id: torque)

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,642 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job is running

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:14,848 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job finished normally

galaxy.jobs.runners ERROR 2016-10-31 10:17:24,906 (1669/1573.esilbac3a.esi.umontreal.ca) Job output not returned from cluster: [Errno 2] No such file or directory: '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.o'

galaxy.model.metadata DEBUG 2016-10-31 10:17:25,314 loading metadata from file for: HistoryDatasetAssociation 4437

galaxy.jobs INFO 2016-10-31 10:17:25,541 Collecting metrics for Job 1669

galaxy.jobs DEBUG 2016-10-31 10:17:25,554 job 1669 ended (finish() executed in (636.363 ms))

galaxy.model.metadata DEBUG 2016-10-31 10:17:25,560 Cleaning up external metadata files

 

Do you have an  idea why I’m getting this problem?

 

Best regards,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 


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Re: galaxy - velvet devteam revision 08256557922f

fernandez Edgar

Hey everyone,

 

I haven’t got a feedback from you.

If you have any suggestions, I’m a little bit confused with this problem.

 

Thank you very much!

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 

 

From: Fernandez Edgar
Sent: October-31-16 11:40 AM
To: [hidden email]
Subject: [galaxy-dev] galaxy - velvet devteam revision 08256557922f

 

Hey Guys,

 

I need your help understanding what’s happening with velvet  devteam revision 08256557922f.

 

After installing it, velvet was giving me the following error:

galaxy.jobs.handler WARNING 2016-10-20 12:15:11,986 (1599) Tool 'toolshed.g2.bx.psu.edu/repos/devteam/velvet/velveth/1.2.10.0' removed from tool config, unable to run job galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness

galaxy.jobs.handler ERROR 2016-10-20 12:15:12,165 (1599) Error checking job readiness

 

I realized velvet needed that galaxy was restarted.

 

Now, velvet finishes his jobs (becomes green) however, the following message is on galaxy’s

Job output not returned from cluster

 

And you can see in the logs of the handler:

galaxy.jobs DEBUG 2016-10-31 10:17:08,548 (1669) Working directory for job is: /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669

galaxy.jobs.handler DEBUG 2016-10-31 10:17:08,567 (1669) Dispatching to drmaa runner

galaxy.jobs DEBUG 2016-10-31 10:17:08,621 (1669) Persisting job destination (destination id: torque)

galaxy.jobs.runners DEBUG 2016-10-31 10:17:08,630 Job [1669] queued (63.397 ms)

galaxy.jobs.handler INFO 2016-10-31 10:17:08,652 (1669) Job dispatched

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Building dependency shell command for dependency 'velvet'

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,891 Find dependency velvet version 1.2.10

galaxy.tools.deps DEBUG 2016-10-31 10:17:08,896 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.galaxy_packages.GalaxyPackageDependency object at 0x7f80f807bd50> (isnull? False)

galaxy.jobs.command_factory INFO 2016-10-31 10:17:08,945 Built script [/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh] for tool command[PACKAGE_BASE=/home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f; export PACKAGE_BASE; . /home/galaxy/galaxy-prod/tool-data/toolshed.dependency.dir/velvet/1.2.10/devteam/velvet/08256557922f/env.sh; velveth 2>&1 | grep "Version" | sed -e 's/Version //' > /home/galaxy/galaxy-prod/database/tmp/GALAXY_VERSION_STRING_1669 2>&1; python /home/galaxy/galaxy-prod/shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/velvet/08256557922f/velvet/velveth_wrapper.py '/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat' '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/dataset_4306_files' 21  -fasta -short /home/galaxy/galaxy-prod/database/files/003/dataset_3537.dat]

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Building dependency shell command for dependency 'samtools'

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Find dependency samtools version None

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver tool_shed_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,144 Resolver galaxy_packages returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps DEBUG 2016-10-31 10:17:09,145 Resolver conda returned <galaxy.tools.deps.resolvers.NullDependency object at 0x7f812d147d90> (isnull? True)

galaxy.tools.deps WARNING 2016-10-31 10:17:09,145 Failed to resolve dependency on 'samtools', ignoring

galaxy.jobs.runners DEBUG 2016-10-31 10:17:09,153 (1669) command is: mkdir -p working; cd working; /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/tool_script.sh; return_code=$?; cd '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669'; python "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/set_metadata_KQTExg.py" "/home/galaxy/galaxy-prod/database/tmp/tmpLU0HQy" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/working/galaxy.json" "/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_in_HistoryDatasetAssociation_4437_kIYXWa,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_kwds_HistoryDatasetAssociation_4437_ArCXyb,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_out_HistoryDatasetAssociation_4437_l28qWr,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_results_HistoryDatasetAssociation_4437_oTDjOd,/home/galaxy/galaxy-prod/database/files/004/dataset_4306.dat,/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/metadata_override_HistoryDatasetAssociation_4437_8VzdJw" 5242880; sh -c "exit $return_code"

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,202 (1669) submitting file /home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.sh

galaxy.jobs.runners.drmaa INFO 2016-10-31 10:17:09,210 (1669) queued as 1573.esilbac3a.esi.umontreal.ca

galaxy.jobs DEBUG 2016-10-31 10:17:09,214 (1669) Persisting job destination (destination id: torque)

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:09,642 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job is running

galaxy.jobs.runners.drmaa DEBUG 2016-10-31 10:17:14,848 (1669/1573.esilbac3a.esi.umontreal.ca) state change: job finished normally

galaxy.jobs.runners ERROR 2016-10-31 10:17:24,906 (1669/1573.esilbac3a.esi.umontreal.ca) Job output not returned from cluster: [Errno 2] No such file or directory: '/home/galaxy/galaxy-16.04/database/jobs_directory/001/1669/galaxy_1669.o'

galaxy.model.metadata DEBUG 2016-10-31 10:17:25,314 loading metadata from file for: HistoryDatasetAssociation 4437

galaxy.jobs INFO 2016-10-31 10:17:25,541 Collecting metrics for Job 1669

galaxy.jobs DEBUG 2016-10-31 10:17:25,554 job 1669 ended (finish() executed in (636.363 ms))

galaxy.model.metadata DEBUG 2016-10-31 10:17:25,560 Cleaning up external metadata files

 

Do you have an  idea why I’m getting this problem?

 

Best regards,

 

Edgar Fernandez

System Administrator (Linux)

Direction Générale des Technologies de l'Information et de la Communication

Université de Montréal

 

PAVILLON ROGER-GAUDRY, bureau X-210

(  Bur. : 1-514-343-6111 poste 16568

 


___________________________________________________________
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/