Error setting-up and running bowtie tasks
I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm But the xml doesn't match (it only has two columns): <!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table> What should there be in the 'columns' section? Thanks, Chris
Chris, The tool_data_table_conf.xml.sample file has been updated to the correct column values, so just copy that or the relevant sections over. Let us know if you have any problems getting things working. Regards, Kelly On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:
I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/ drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux- x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range
I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/ h_sapiens_37_asm
But the xml doesn't match (it only has two columns):
<!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table>
What should there be in the 'columns' section? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
Hi Kelly, Thanks. That solved the error. However, the job never ends in the UI despite there being a 'job finished normally' entry in the logs. Cheers, Chris On 06/12/10 15:30, Kelly Vincent wrote:
Chris,
The tool_data_table_conf.xml.sample file has been updated to the correct column values, so just copy that or the relevant sections over. Let us know if you have any problems getting things working.
Regards, Kelly
On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:
I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range
I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm
But the xml doesn't match (it only has two columns):
<!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table>
What should there be in the 'columns' section? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
Oh, and I should also add there was a small bug in the error output: galaxy.jobs.runners.drmaa ERROR 2010-12-06 14:39:51,555 Uncaught exception queueing job Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 112, in run_next self.queue_job( obj ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 128, in queue_job log.exception("failure running job %d" % job_wrapper.get_id_tag()) TypeError: %d format: a number is required, not str THis is fixable by changing the below: diff -r 8a4ff7b2c6e6 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py Tue Nov 30 13:05:42 2010 +0000 +++ b/lib/galaxy/jobs/runners/drmaa.py Mon Dec 06 14:47:45 2010 +0000 @@ -125,7 +125,7 @@ class DRMAAJobRunner( BaseJobRunner ): command_line = self.build_command_line( job_wrapper, include_metadata=True ) except: job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.get_id_tag()) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) return runner_url = job_wrapper.tool.job_runner On 06/12/10 15:30, Kelly Vincent wrote:
Chris,
The tool_data_table_conf.xml.sample file has been updated to the correct column values, so just copy that or the relevant sections over. Let us know if you have any problems getting things working.
Regards, Kelly
On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:
I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range
I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm
But the xml doesn't match (it only has two columns):
<!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table>
What should there be in the 'columns' section? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721 The University of Dundee is a registered Scottish charity, No: SC015096
Thanks for catching this. Fixed in galaxy-central. -Dannon On Dec 6, 2010, at 11:41 AM, Chris Cole wrote:
Oh, and I should also add there was a small bug in the error output:
galaxy.jobs.runners.drmaa ERROR 2010-12-06 14:39:51,555 Uncaught exception queueing job Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 112, in run_next self.queue_job( obj ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 128, in queue_job log.exception("failure running job %d" % job_wrapper.get_id_tag()) TypeError: %d format: a number is required, not str
THis is fixable by changing the below: diff -r 8a4ff7b2c6e6 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py Tue Nov 30 13:05:42 2010 +0000 +++ b/lib/galaxy/jobs/runners/drmaa.py Mon Dec 06 14:47:45 2010 +0000 @@ -125,7 +125,7 @@ class DRMAAJobRunner( BaseJobRunner ): command_line = self.build_command_line( job_wrapper, include_metadata=True ) except: job_wrapper.fail( "failure preparing job", exception=True ) - log.exception("failure running job %d" % job_wrapper.get_id_tag()) + log.exception("failure running job %s" % job_wrapper.get_id_tag()) return
runner_url = job_wrapper.tool.job_runner
On 06/12/10 15:30, Kelly Vincent wrote:
Chris,
The tool_data_table_conf.xml.sample file has been updated to the correct column values, so just copy that or the relevant sections over. Let us know if you have any problems getting things working.
Regards, Kelly
On Dec 6, 2010, at 10:20 AM, Chris Cole wrote:
I have previously been able to run bowtie jobs successfully, but now I get this error: galaxy.jobs.runners.drmaa ERROR 2010-12-06 15:09:44,068 failure running job 2248 Traceback (most recent call last): File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/runners/drmaa.py", line 124, in queue_job job_wrapper.prepare() File "/homes/www-galaxy/galaxy_devel/lib/galaxy/jobs/__init__.py", line 368, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/tools/__init__.py", line 1524, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/homes/www-galaxy/galaxy_devel/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/homes/www-galaxy/galaxy_devel/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs2.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 182, in respond IndexError: list index out of range
I've a feeling it has something to with the bowtie_indices.loc file and it's associated entry in tool_data_table_conf.xml. I can see that the format for the .loc file has changed (it now has four columns instead of two): h_sapiens37 NCBI37 Homo sapiens ncbi37 /db/bowtie/h_sapiens_37_asm
But the xml doesn't match (it only has two columns):
<!-- Locations of indexes in the Bowtie mapper format --> <table name="bowtie_indexes"> <columns>name, value</columns> <file path="tool-data/bowtie_indices.loc" /> </table>
What should there be in the 'columns' section? Thanks,
Chris _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
-- Dr Chris Cole Senior Bioinformatics Research Officer School of Life Sciences Research University of Dundee Dow Street Dundee DD1 5EH Scotland, UK
url: http://network.nature.com/profile/drchriscole e-mail: chris@compbio.dundee.ac.uk Tel: +44 (0)1382 388 721
The University of Dundee is a registered Scottish charity, No: SC015096 _______________________________________________ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev
participants (3)
-
Chris Cole -
Dannon Baker -
Kelly Vincent