Question: No left space
0
gravatar for jarod_v6
2.7 years ago by
jarod_v60
Italy
jarod_v60 wrote:

I Have this error

__
  return self.application(environ, start_response)
File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 133 in __call__
  return self.handle_request( environ, start_response )
File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 160 in handle_request
  trans = self.transaction_factory( environ )
File '/opt/galaxy/lib/galaxy/web/framework/webapp.py', line 73 in <lambda>
  self.set_transaction_factory( lambda e: self.transaction_chooser( e, galaxy_app, session_cookie ) )
File '/opt/galaxy/lib/galaxy/web/framework/webapp.py', line 104 in transaction_chooser
  return GalaxyWebTransaction( environ, galaxy_app, self, session_cookie )
File '/opt/galaxy/lib/galaxy/web/framework/webapp.py', line 200 in __init__
  self.error_message = self._authenticate_api( session_cookie )
File '/opt/galaxy/lib/galaxy/web/framework/webapp.py', line 315 in _authenticate_api
  api_key = self.request.params.get('key', None)
File '/opt/galaxy/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py', line 900 in params
File '/opt/galaxy/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py', line 892 in str_params
File '/opt/galaxy/eggs/WebOb-0.8.5-py2.6.egg/webob/__init__.py', line 818 in str_POST
File '/usr/lib64/python2.6/cgi.py', line 508 in __init__
  self.read_multi(environ, keep_blank_values, strict_parsing)
File '/usr/lib64/python2.6/cgi.py', line 637 in read_multi
  environ, keep_blank_values, strict_parsing)
File '/usr/lib64/python2.6/cgi.py', line 510 in __init__
  self.read_single()
File '/usr/lib64/python2.6/cgi.py', line 647 in read_single
  self.read_lines()
File '/opt/galaxy/lib/galaxy/web/framework/base.py', line 310 in read_lines
  self.read_lines_to_outerboundary()
File '/usr/lib64/python2.6/cgi.py', line 720 in read_lines_to_outerboundary
  self.__write(odelim + line)
File '/usr/lib64/python2.6/cgi.py', line 679 in __write
  self.file.write(line)
IOError: [Errno 28] No space left on device


CGI Variables
-------------
  CONTENT_LENGTH: '1528605094'
  CONTENT_TYPE: 'multipart/form-data; boundary=---------------------------762435369309988811730463758'
  HTTP_ACCEPT: 'application/json'
  HTTP_ACCEPT_ENCODING: 'gzip, deflate'
  HTTP_ACCEPT_LANGUAGE: 'en-US,en;q=0.5'
  HTTP_CACHE_CONTROL: 'no-cache'
  HTTP_CONNECTION: 'keep-alive'
  HTTP_COOKIE: 'galaxysession=c6ca0ddb55be603a2ab7f38dd4bc4cd726a39f6126d3922be725e4e13b2b6958646b3d5ce8965746'
  HTTP_HOST: '172.17.179.93:8082'
  HTTP_PRAGMA: 'no-cache'
  HTTP_REFERER: 'http://172.17.179.93:8082/'
  HTTP_USER_AGENT: 'Mozilla/5.0 (X11; Linux x86_64; rv:38.0) Gecko/20100101 Firefox/38.0'
  HTTP_X_REQUESTED_WITH: 'XMLHttpRequest'
  PATH_INFO: '/api/tools'
  REMOTE_ADDR: '172.17.179.93'
  REQUEST_METHOD: 'POST'
  SERVER_NAME: '172.17.179.93'
  SERVER_PORT: '8082'
  SERVER_PROTOCOL: 'HTTP/1.1'


WSGI Variables
--------------
  application: <paste.recursive.RecursiveMiddleware object at 0x8d9a090>
  is_api_request: True
  paste.expected_exceptions: [<class 'paste.httpexceptions.HTTPException'>]
  paste.httpexceptions: <paste.httpexceptions.HTTPExceptionHandler object at 0x8ab6690>
  paste.httpserver.thread_pool: <paste.httpserver.ThreadPool object at 0x91fd550>
  paste.recursive.forward: <paste.recursive.Forwarder from />
  paste.recursive.include: <paste.recursive.Includer from />
  paste.recursive.include_app_iter: <paste.recursive.IncluderAppIter from />
  paste.recursive.script_name: ''
  paste.throw_errors: True
  request_id: '921eeca0f81e11e5b0bd901b0e567172'
  webob._parsed_query_vars: (MultiDict([]), '')
  wsgi process: 'Multithreaded'

i UPLOAD ONLY 3 FASTQ

setup • 1.0k views
ADD COMMENTlink modified 2.6 years ago • written 2.7 years ago by jarod_v60
0
gravatar for Jennifer Hillman Jackson
2.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

The job ran out of space to write files. To troubleshoot, review the available space in the working directory where the job is running. It could be that there is a problematic external disk mount.

Thanks, Jen, Galaxy team

ADD COMMENTlink written 2.7 years ago by Jennifer Hillman Jackson25k
0
gravatar for jarod_v6
2.7 years ago by
jarod_v60
Italy
jarod_v60 wrote:

So it is also a problem of the permission. I have create a link on database

paster1.log
lrwxrwxrwx  1 galaxy galaxy      17 Apr  4 17:32 database -> /mnt/dati-galaxy/
-rw-r--r--  1 galaxy galaxy    5337 Apr  4 18:02 integrated_tool_panel.xml

I have two mai problems: this error:

/usr/lib/python2.6/site-packages/setuptools-18.4-py2.6.egg/pkg_resources/__init__.py:1256: UserWarning: /usr/local/galaxy/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).

And I have problemds to delete the history

ADD COMMENTlink written 2.7 years ago by jarod_v60
0
gravatar for jarod_v6
2.6 years ago by
jarod_v60
Italy
jarod_v60 wrote:

I have now also this error

Traceback (most recent call last):
  File "/opt/galaxy/tools/data_source/upload.py", line 430, in <module>
    __main__()
  File "/opt/galaxy/tools/data_source/upload.py", line 419, in __main__
    add_file( dataset, registry, json_file, output_path )
  File "/opt/galaxy/tools/data_source/upload.py", line 171, in add_file
    shutil.move( uncompressed, dataset.path )
  File "/usr/lib64/python2.6/shutil.py", line 260, in move
    copy2(src, real_dst)
  File "/usr/lib64/python2.6/shutil.py", line 95, in copy2
    copyfile(src, dst)
  File "/usr/lib64/python2.6/shutil.py", line 51, in copyfile
    with open(dst, 'wb') as fdst:
IOError: [Errno 13] Permission denied: u'/opt/galaxy/database/tmp/upload_file_data_QHm9UL'

I mount a external folder from a NAS

rw-rw-r--  1 galaxy galaxy    3207 Apr  4 17:26 paster1.log
lrwxrwxrwx  1 galaxy galaxy      17 Apr  4 17:32 database -> /mnt/dati-galaxy/
-rw-r--r--  1 galaxy galaxy    5337 Apr  7 14:32 integrated_tool_panel.xml
[g

thanks so much for any help!

ADD COMMENTlink written 2.6 years ago by jarod_v60
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