Meme gives me UnicodeDecodeError. Is this an error from parsing the OUTPUT?
Hi, I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?). Thanks Thon Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view return template.render( **data ) Module mako.template:296 in render view return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)
Hi, I am hitting the same issue. meme itself runs fine on commandline. I suspected the html or xml generated by meme contains non-ascii, thus galaxy throw this error. Have you been able to fix that? MEME is not on the public galaxy server either.. Regards, Derrick On Thu, May 31, 2012 at 4:37 AM, Anthonius deBoer <thondeboer@me.com> wrote:
Hi,
I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?).
Thanks
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view return template.render( **data ) Module mako.template:296 in render view return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)
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I guess I know what the issue is (at least for my case). I checked the stdout, it contains: MEME — Multiple EM for Motif Elicitation USAGE: meme <dataset> [optional arguments] <dataset> file containing sequences in FASTA format [-h] print this message [-o <output dir>] name of directory for output files will not replace existing directory [-oc <output dir>] name of directory for output files will replace existing directory [-text] output in text format (default is HTML) [-dna] sequences use DNA alphabet [-protein] sequences use protein alphabet [-mod oops|zoops|anr] distribution of motifs ....... Then I checked the stderr, it has: mv: cannot stat `/misc/NFS/app/galaxy/galaxy_dist/dev/database/job_working_directory/000/973/dataset_2527_files/meme.html': No such file or directory Seems to me, the meme was ran but return its help page and didn't return any result. Still investigating why. Derrick On Wed, Jun 6, 2012 at 9:47 AM, Derrick Lin <klin938@gmail.com> wrote:
Hi,
I am hitting the same issue. meme itself runs fine on commandline.
I suspected the html or xml generated by meme contains non-ascii, thus galaxy throw this error.
Have you been able to fix that?
MEME is not on the public galaxy server either..
Regards, Derrick
On Thu, May 31, 2012 at 4:37 AM, Anthonius deBoer <thondeboer@me.com>wrote:
Hi,
I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?).
Thanks
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view return template.render( **data ) Module mako.template:296 in render view return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)
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Okay, it turned out to be my execution hosts on the cluster didn't have the required packages installed. I then install libxslt-devel and ImageMagick<http://www.imagemagick.org/>-devel, everything now works as expected. Hope this help, Derrick On Wed, Jun 6, 2012 at 10:03 AM, Derrick Lin <klin938@gmail.com> wrote:
I guess I know what the issue is (at least for my case). I checked the stdout, it contains:
MEME — Multiple EM for Motif Elicitation
USAGE:
meme <dataset> [optional arguments]
<dataset> file containing sequences in FASTA format [-h] print this message [-o <output dir>] name of directory for output files will not replace existing directory [-oc <output dir>] name of directory for output files will replace existing directory [-text] output in text format (default is HTML) [-dna] sequences use DNA alphabet [-protein] sequences use protein alphabet [-mod oops|zoops|anr] distribution of motifs
.......
Then I checked the stderr, it has:
mv: cannot stat `/misc/NFS/app/galaxy/galaxy_dist/dev/database/job_working_directory/000/973/dataset_2527_files/meme.html': No such file or directory
Seems to me, the meme was ran but return its help page and didn't return any result. Still investigating why.
Derrick
On Wed, Jun 6, 2012 at 9:47 AM, Derrick Lin <klin938@gmail.com> wrote:
Hi,
I am hitting the same issue. meme itself runs fine on commandline.
I suspected the html or xml generated by meme contains non-ascii, thus galaxy throw this error.
Have you been able to fix that?
MEME is not on the public galaxy server either..
Regards, Derrick
On Thu, May 31, 2012 at 4:37 AM, Anthonius deBoer <thondeboer@me.com>wrote:
Hi,
I am trying to run MEME and I got this error below when running it. Is this an error complaining about the non-ASCII nature of the OUTPUT or of the program (or input?).
Thanks
Thon
Error Traceback: View as: Interactive | Text | XML (full) ⇝ UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128) URL: http://srp106:8080/dataset/errors?id=176856 Module weberror.evalexception.middleware:364 in respond view
app_iter = self.application(environ, detect_start_response) Module paste.debug.prints:98 in __call__ view environ, self.app) Module paste.wsgilib:539 in intercept_output view app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ view return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ view return self.application(environ, start_response) Module galaxy.web.framework.base:160 in __call__ view body = method( trans, **kwargs ) Module galaxy.web.controllers.dataset:160 in errors view return trans.fill_template( "dataset/errors.mako", hda=hda ) Module galaxy.web.framework:733 in fill_template view return self.fill_template_mako( filename, **kwargs ) Module galaxy.web.framework:744 in fill_template_mako view return template.render( **data ) Module mako.template:296 in render view return runtime._render(self, self.callable_, args, data) Module mako.runtime:660 in _render view **_kwargs_for_callable(callable_, data)) Module mako.runtime:692 in _render_context view _exec_template(inherit, lclcontext, args=args, kwargs=kwargs) Module mako.runtime:718 in _exec_template view callable_(context, *args, **kwargs) Module dataset_errors_mako:74 in render_body view __M_writer(filters.html_escape(unicode(job.stdout ))) UnicodeDecodeError: 'ascii' codec can't decode byte 0xe2 in position 25: ordinal not in range(128)
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participants (2)
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Anthonius deBoer -
Derrick Lin