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| galaxy.tools ERROR 2017-11-10 16:44:17,027 Exception caught while attempting tool execution: | |
| Traceback (most recent call last): | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1311, in handle_single_execution | |
| job, out_data = self.execute(trans, incoming=params, history=history, rerun_remap_job_id=rerun_remap_job_id, mapping_over_collection=mapping_over_collection, execution_cache=execution_cache) | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1391, in execute | |
| return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs) | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/actions/__init__.py", line 244, in execute | |
| (chrom_info, db_dataset) = app.genome_builds.get_chrom_info(input_dbkey, trans=trans, custom_build_hack_get_len_from_fasta_conversion=tool.id != 'CONVERTER_fasta_to_len') | |
| File "/galaxy/galaxy-app/lib/galaxy/util/dbkeys.py", line 79, in get_chrom_info | |
| chrom_info = build_fasta_dataset.get_converted_dataset(trans, 'len').file_name | |
| File "/galaxy/galaxy-app/lib/galaxy/model/__init__.py", line 2158, in get_converted_dataset | |
| new_dataset = next(iter(self.datatype.convert_dataset(trans, self, target_ext, return_output=True, visible=False, deps=deps, target_context=target_context, history=history).values())) | |
| File "/galaxy/galaxy-app/lib/galaxy/datatypes/data.py", line 612, in convert_dataset | |
| converted_dataset = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)[1] | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 1391, in execute | |
| return self.tool_action.execute(self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs) | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/actions/__init__.py", line 209, in execute | |
| history, inp_data, inp_dataset_collections = self._collect_inputs(tool, trans, incoming, history, current_user_roles) | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/actions/__init__.py", line 186, in _collect_inputs | |
| history = tool.get_default_history_by_trans(trans, create=True) | |
| File "/galaxy/galaxy-app/lib/galaxy/tools/__init__.py", line 2023, in get_default_history_by_trans | |
| return trans.get_history(create=create) | |
| File "/galaxy/galaxy-app/lib/galaxy/work/context.py", line 32, in get_history | |
| raise NotImplementedError("Cannot create histories from a work request context.") | |
| NotImplementedError: Cannot create histories from a work request context. | |
| galaxy.tools.execute WARNING 2017-11-10 16:44:17,027 There was a failure executing a job for tool [toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1] - Error executing tool: Cannot create histories from a work request context. | |
| galaxy.tools.execute DEBUG 2017-11-10 16:44:17,027 Executed 19 job(s) for tool toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.5.2b-1 request: (362.973 ms) | |
| galaxy.workflow.run ERROR 2017-11-10 16:44:17,039 Failed to schedule Workflow[id=2814,name=Copy of bwiner: RNA-Seq workflow - TopHat], problem occurred on WorkflowStep[index=5,type=tool]. | |
| Traceback (most recent call last): | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 173, in invoke | |
| jobs = self._invoke_step(step) | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 245, in _invoke_step | |
| jobs = step.module.execute(self.trans, self.progress, self.workflow_invocation, step) | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/modules.py", line 885, in execute | |
| raise Exception(message) | |
| Exception: Failed to create 19 out of 19 job(s) for workflow step. | |
| galaxy.workflow.run ERROR 2017-11-10 16:44:17,040 Failed to execute scheduled workflow. | |
| Traceback (most recent call last): | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 80, in __invoke | |
| outputs = invoker.invoke() | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 173, in invoke | |
| jobs = self._invoke_step(step) | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/run.py", line 245, in _invoke_step | |
| jobs = step.module.execute(self.trans, self.progress, self.workflow_invocation, step) | |
| File "/galaxy/galaxy-app/lib/galaxy/workflow/modules.py", line 885, in execute | |
| raise Exception(message) | |
| Exception: Failed to create 19 out of 19 job(s) for workflow step. |
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