Does anybody have any idea why I would be getting this error before the tool runs? -- Branden Timm Great Lakes Bioenergy Research Center btimm@wisc.edu On 4/19/2011 10:45 AM, Branden Timm wrote:
Hi All, I'm having issues running BWA for Illumina with the latest version of Galaxy (5433:c1aeb2f33b4a).
It seems that the error is a python list error while preparing the job:
Traceback (most recent call last): File "/home/galaxy/galaxy-central/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.prepare() File "/home/galaxy/galaxy-central/lib/galaxy/jobs/__init__.py", line 371, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/home/galaxy/galaxy-central/lib/galaxy/tools/__init__.py", line 1575, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/home/galaxy/galaxy-central/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 106, in respond IndexError: list index out of range I checked the bwa_index.loc file for errors, it seems that the line for the reference genome I'm trying to map against is correct (all whitespace is tab characters): synpcc7002 synpcc7002 Synechococcus /home/galaxy/galaxy-central/bwa_ indices/SYNPCC7002
I'm not sure what the next troubleshooting step is, any ideas?
-- Branden Timm btimm@glbrc.wisc.edu
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