Tool Error: Failure Preparing Job
Hi all, I'm working on a local Galaxy instance and I want to integrate TASSEL's GLM pipeline into it. But when I run the tool, it prompts: "tool error An error occurred running this job:* failure preparing job*" This is how the log looks like: galaxy.jobs.handler INFO 2013-07-08 16:00:47,648 (73) Job dispatched galaxy.jobs.runners.local DEBUG 2013-07-08 16:00:47,735 Local runner: starting job 73 galaxy.jobs.runners.local ERROR 2013-07-08 16:00:47,939 failure running job 73 Traceback (most recent call last): File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/__init__.py", line 184, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/tools/__init__.py", line 2435, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) galaxy.datatypes.metadata DEBUG 2013-07-08 16:00:48,206 Cleaning up external metadata files 127.0.0.1 - - [08/Jul/2013:16:00:50 +0800] "GET /api/histories/846c4efa2e1f970a HTTP/1.1" 200 - " http://localhost:8081/history?status=done&show_deleted=False&filename=None&dataset_id=b89568d7c4cc60f1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0" I figured the problem is that UnicodeEncodeError but I don't have an idea how to fix this or where to begin. I do hope you can help me. Thanks and Best Regards, Venice Margarette B. Juanillas
Unicode isn't handled nicely yet AFAIK so UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) might mean a http://www.fileformat.info/info/unicode/char/2013/index.htm - overtyping these in an ascii text editor will remove them but this is a wart for sure IMHO. You can follow our progress at fixing this on the trello card at https://trello.com/c/couxOih6 On Mon, Jul 8, 2013 at 6:28 PM, Venice Margarette Juanillas < venicemargarettejuanillas@gmail.com> wrote:
Hi all,
I'm working on a local Galaxy instance and I want to integrate TASSEL's GLM pipeline into it. But when I run the tool, it prompts:
"tool error An error occurred running this job:* failure preparing job*"
This is how the log looks like:
galaxy.jobs.handler INFO 2013-07-08 16:00:47,648 (73) Job dispatched galaxy.jobs.runners.local DEBUG 2013-07-08 16:00:47,735 Local runner: starting job 73 galaxy.jobs.runners.local ERROR 2013-07-08 16:00:47,939 failure running job 73 Traceback (most recent call last): File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/runners/local.py", line 72, in run_job job_wrapper.prepare() File "/storage/irri-gsl-galaxy/lib/galaxy/jobs/__init__.py", line 184, in prepare self.command_line = self.tool.build_command_line( param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/tools/__init__.py", line 2435, in build_command_line command_line = fill_template( self.command, context=param_dict ) File "/storage/irri-gsl-galaxy/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) UnicodeEncodeError: 'ascii' codec can't encode character u'\u2013' in position 23: ordinal not in range(128) galaxy.datatypes.metadata DEBUG 2013-07-08 16:00:48,206 Cleaning up external metadata files 127.0.0.1 - - [08/Jul/2013:16:00:50 +0800] "GET /api/histories/846c4efa2e1f970a HTTP/1.1" 200 - " http://localhost:8081/history?status=done&show_deleted=False&filename=None&dataset_id=b89568d7c4cc60f1" "Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:18.0) Gecko/20100101 Firefox/18.0"
I figured the problem is that UnicodeEncodeError but I don't have an idea how to fix this or where to begin. I do hope you can help me.
Thanks and Best Regards, Venice Margarette B. Juanillas
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Venice Margarette Juanillas