Hi guys, I&#39;m running into a problem with updating a completely squeaky clean fresh cloudman install using the current <span style="color:rgb(44,49,67);font-family:Verdana,sans-serif;font-size:13px;line-height:20.796875px;background-color:rgb(255,255,255)">ami-da58aab3</span><div>

Once it is up and running, I have SSHed in and made sure the sample files in run.sh are complete.</div><div>I hit the update button, and 3 or 4 minutes later when the daemon tries to restart, I get status= error.</div><div>

Is anyone else having this issue?? The only threads and posts I have found are from a year ago, and the line is in my run.sh.</div><div>The ultimate goal of all this was just so that I could have a cufflinks version that is not 0.5.</div>

<div><br></div><div>Thanks for any help anyone can provide.</div><div><br></div><div>Brian</div><div><br></div><div><br></div><div>Here are the logs:</div><div><br></div><div>paster.log:</div><div><pre style="font-size:10.399999618530273px;color:rgb(48,48,48);background-color:rgb(255,255,255)">

/mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg/pysam/__init__.py:1: RuntimeWarning: __builtin__.file size changed, may indicate binary incompatibility
  from csamtools import *
python path is: /mnt/galaxyTools/galaxy-central/eggs/numpy-1.6.0-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/boto-2.5.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Fabric-1.4.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/ssh-1.7.14-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Whoosh-0.3.18-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/mercurial-2.2.3-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/pycrypto-2.5-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/python_lzo-1.08_2.03_static-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/bx_python-0.7.1_7b95ff194725-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/amqplib-0.6.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/pexpect-2.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Babel-0.9.4-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/MarkupSafe-0.12-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/Mako-0.4.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/WebHelpers-0.2-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/simplejson-2.1.1-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/WebOb-0.8.5-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Routes-1.12.3-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Cheetah-2.2.2-py2.6-linux-x86_64-ucs4.egg, /mnt/galaxyTools/galaxy-central/eggs/wchartype-0.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/docutils-0.7-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/PasteDeploy-1.5.0-py2.6.egg, /mnt/galaxyTools/galaxy-central/eggs/Paste-1.7.5.1-py2.6.egg, /mnt/galaxyTools/galaxy-central/lib, /usr/lib/python2.6/, /usr/lib/python2.6/plat-linux2, /usr/lib/python2.6/lib-tk, /usr/lib/python2.6/lib-old, /usr/lib/python2.6/lib-dynload
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loading references to tool sheds from tool_sheds_conf.xml
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference to tool shed: Galaxy main tool shed
tool_shed.tool_shed_registry DEBUG 2013-03-15 02:47:27,538 Loaded reference to tool shed: Galaxy test tool shed
galaxy.model.migrate.check DEBUG 2013-03-15 02:47:27,556 psycopg2 egg successfully loaded for postgres dialect
galaxy.model.migrate.check INFO 2013-03-15 02:47:27,633 At database version 114
tool_shed.galaxy_install.migrate.check DEBUG 2013-03-15 02:47:27,643 psycopg2 egg successfully loaded for postgres dialect
Traceback (most recent call last):
  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/webapps/galaxy/buildapp.py&quot;, line 37, in app_factory
    app = UniverseApplication( global_conf = global_conf, **kwargs )
  File &quot;/mnt/galaxyTools/galaxy-central/lib/galaxy/app.py&quot;, line 54, in __init__
    verify_tools( self, db_url, kwargs.get( &#39;global_conf&#39;, {} ).get( &#39;__file__&#39;, None ), self.config.database_engine_options )
  File &quot;/mnt/galaxyTools/galaxy-central/lib/tool_shed/galaxy_install/migrate/check.py&quot;, line 145, in verify_tools
    raise Exception( msg )
Exception: 
&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;&gt;</pre></div><div><div>Console Log:</div><div><ul style="margin:0px;padding:0px;list-style:none;color:rgb(48,48,48);font-family:verdana,&#39;Bitstream Vera Sans&#39;,geneva,arial,helvetica,helve,sans-serif;font-size:12px">

<li>02:46:56 - Removing &#39;Galaxy&#39; service</li><li>02:46:56 - Shutting down Galaxy...</li><li>02:47:25 - Starting Galaxy...</li><li>02:47:25 - Galaxy service state changed from &#39;Shut down&#39; to &#39;Starting&#39;</li>

<li>02:47:26 - Saved file &#39;persistent_data.yaml&#39; to bucket &#39;cm-5b0fce1cf71e5f439fc17473dd4dcd1d&#39;</li><li>02:48:28 - Galaxy daemon not running.</li><li>02:48:28 - Galaxy service state changed from &#39;Starting&#39; to &#39;Error&#39;</li>

<li>02:48:29 - Saved file &#39;persistent_data.yaml&#39; to bucket &#39;cm-5b0fce1cf71e5f439fc17473dd4dcd1d&#39;</li><li>02:49:30 - Galaxy daemon not running.</li></ul></div><div></div></div><div>pgSQL.log:</div><div><pre style="font-size:10.399999618530273px;color:rgb(48,48,48);background-color:rgb(255,255,255)">

LOG:  database system was shut down at 2013-03-15 02:11:48 UTC
LOG:  autovacuum launcher started
LOG:  database system is ready to accept connections
ERROR:  relation &quot;page_revision&quot; does not exist
STATEMENT:  ALTER TABLE page ADD CONSTRAINT page_latest_revision_id_fk FOREIGN KEY(latest_revision_id) REFERENCES page_revision (id)
ERROR:  relation &quot;visualization_revision&quot; does not exist
STATEMENT:  ALTER TABLE visualization ADD CONSTRAINT visualization_latest_revision_id_fk FOREIGN KEY(latest_revision_id) REFERENCES visualization_revision (id)
LOG:  unexpected EOF on client connection</pre></div><div>SGE log:</div><div><pre style="font-size:10.399999618530273px;color:rgb(48,48,48);background-color:rgb(255,255,255)">03/15/2013 01:12:20|  main|ip-10-149-20-174|I|read job database with 0 entries in 0 seconds
03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file &quot;/opt/sge/default/common/./sched_configuration&quot; for reading: No such file or directory
03/15/2013 01:12:20|  main|ip-10-149-20-174|E|error opening file &quot;/opt/sge/default/spool/qmaster/./sharetree&quot; for reading: No such file or directory
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster hard descriptor limit is set to 8192
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster soft descriptor limit is set to 8192
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will use max. 8172 file descriptors for communication
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|qmaster will accept max. 99 dynamic event clients
03/15/2013 01:12:20|  main|ip-10-149-20-174|I|starting up GE 6.2u5 (lx24-amd64)
03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can&#39;t open job sequence number file &quot;jobseqnum&quot;: for reading: No such file or directory -- guessing next number
03/15/2013 01:12:20|  main|ip-10-149-20-174|W|can&#39;t open ar sequence number file &quot;arseqnum&quot;: for reading: No such file or directory -- guessing next number
03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost &quot;ip-10-149-20-174.ec2.internal&quot; already exists
03/15/2013 01:12:21|worker|ip-10-149-20-174|E|adminhost &quot;ip-10-149-20-174.ec2.internal&quot; already exists
03/15/2013 02:46:57|listen|ip-10-149-20-174|E|commlib error: got read error (closing &quot;ip-10-149-20-174.ec2.internal/drmaa/416&quot;)</pre></div><div><br></div><div>-- </div><div><div>Brian Lin<br><a href="mailto:contact@brian-lin.com" target="_blank">contact@brian-lin.com</a><br>


<a href="mailto:brian.lin@tufts.edu" target="_blank">brian.lin@tufts.edu</a></div>
</div>