Local install of Galaxy on SciLinux55. Fails to upload 5.2 GB fastq file from local HD, while normally loading smaller fastq and fasta datasets (less than 1 GB). Chunks of 1.2 GB size remain in */database/tmp, which all represent beginning of the file that fails to upload. Several attempts to upload made and several chunks of the same size are present. Can I just copy the file dataset to database directory instead of uploading through web interface?
This shows up when clicking the button "Run this job again"
⇝ Exception: Failed to get job information for dataset hid 5
clear this
clear this
URL: http://127.0.0.1:8080/tool_runner/rerun?id=8
Module weberror.evalexception.middleware:364 in respond view
<< try:
__traceback_supplement__ = errormiddleware.Supplement, self, environ
app_iter = self.application(environ, detect_start_response)
try:
return_iter = list(app_iter)>> app_iter = self.application(environ, detect_start_response)
Module paste.debug.prints:98 in __call__ view
<< try:
status, headers, body = wsgilib.intercept_output(
environ, self.app)
if status is None:
# Some error occurred>> environ, self.app)
Module paste.wsgilib:539 in intercept_output view
<< data.append(headers)
return output.write
app_iter = application(environ, replacement_start_response)
if data[0] is None:
return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response)
Module paste.recursive:80 in __call__ view
<< environ['paste.recursive.script_name'] = my_script_name
try:
return self.application(environ, start_response)
except ForwardRequestException, e:
middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response)
Module paste.httpexceptions:632 in __call__ view
<< []).append(HTTPException)
try:
return self.application(environ, start_response)
except HTTPException, exc:
return exc(environ, start_response)>> return self.application(environ, start_response)
Module galaxy.web.framework.base:160 in __call__ view
<< kwargs.pop( '_', None )
try:
body = method( trans, **kwargs )
except Exception, e:
body = self.handle_controller_exception( e, trans, **kwargs )>> body = method( trans, **kwargs )
Module galaxy.webapps.galaxy.controllers.tool_runner:129 in rerun view
<< job = data.creating_job
if not job:
raise Exception("Failed to get job information for dataset hid %d" % data.hid)
# Get the tool object
tool_id = job.tool_id>> raise Exception("Failed to get job information for dataset hid %d" % data.hid)
Exception: Failed to get job information for dataset hid 5
URL: http://127.0.0.1:8080/tool_runner/rerun?id=8 File '/home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py', line 129 in rerun raise Exception("Failed to get job information for dataset hid %d" % data.hid) Exception: Failed to get job information for dataset hid 5
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.7"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py </filename> <line> 160 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.webapps.galaxy.controllers.tool_runner </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py </filename> <line> 129 </line> <function> rerun </function> <operation> raise Exception("Failed to get job information for dataset hid %d" % data.hid) </operation> <operation_context> job = data.creating_job if not job: raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id </operation_context> </frame> </stack> <exception> <type> Exception </type> <value> Failed to get job information for dataset hid 5 </value> </exception> </traceback>
<?xml version="1.0" ?> <traceback> <sysinfo> <language version="2.7"> Python </language> </sysinfo> <stack> <frame> <module> weberror.evalexception.middleware </module> <filename> /home/yaximik/galaxy-dist/eggs/WebError-0.8a-py2.7.egg/weberror/evalexception/middleware.py </filename> <line> 364 </line> <function> respond </function> <operation> app_iter = self.application(environ, detect_start_response) </operation> <operation_context> try: __traceback_supplement__ = errormiddleware.Supplement, self, environ app_iter = self.application(environ, detect_start_response) try: return_iter = list(app_iter) </operation_context> </frame> <frame> <module> paste.debug.prints </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/debug/prints.py </filename> <line> 98 </line> <function> __call__ </function> <operation> environ, self.app) </operation> <operation_context> try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred </operation_context> </frame> <frame> <module> paste.wsgilib </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/wsgilib.py </filename> <line> 539 </line> <function> intercept_output </function> <operation> app_iter = application(environ, replacement_start_response) </operation> <operation_context> data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter) </operation_context> </frame> <frame> <module> paste.recursive </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/recursive.py </filename> <line> 80 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware( </operation_context> </frame> <frame> <module> paste.httpexceptions </module> <filename> /home/yaximik/galaxy-dist/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py </filename> <line> 632 </line> <function> __call__ </function> <operation> return self.application(environ, start_response) </operation> <operation_context> []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response) </operation_context> </frame> <frame> <module> galaxy.web.framework.base </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/web/framework/base.py </filename> <line> 160 </line> <function> __call__ </function> <operation> body = method( trans, **kwargs ) </operation> <operation_context> kwargs.pop( '_', None ) try: body = method( trans, **kwargs ) except Exception, e: body = self.handle_controller_exception( e, trans, **kwargs ) </operation_context> </frame> <frame> <module> galaxy.webapps.galaxy.controllers.tool_runner </module> <filename> /home/yaximik/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/tool_runner.py </filename> <line> 129 </line> <function> rerun </function> <operation> raise Exception("Failed to get job information for dataset hid %d" % data.hid) </operation> <operation_context> job = data.creating_job if not job: raise Exception("Failed to get job information for dataset hid %d" % data.hid) # Get the tool object tool_id = job.tool_id </operation_context> </frame> </stack> <exception> <type> Exception </type> <value> Failed to get job information for dataset hid 5 </value> </exception> </traceback>