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(&quot;Failed to get job information for dataset hid %d&quot; % 
data.hid) </operation> <operation_context> job = data.creating_job if not job: 
raise Exception(&quot;Failed to get job information for dataset hid %d&quot; % 
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(&quot;Failed to get job information for dataset hid %d&quot; % 
data.hid) </operation> <operation_context> job = data.creating_job if not job: 
raise Exception(&quot;Failed to get job information for dataset hid %d&quot; % 
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>

-- 
Vladimir Yamshchikov <yaxi...@gmail.com>
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